data_GDP
#
_chem_comp.id GDP
_chem_comp.name "GUANOSINE-5'-DIPHOSPHATE"
_chem_comp.type 'RNA LINKING'
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C10 H15 N5 O11 P2'
_chem_comp.mon_nstd_parent_comp_id G
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2024-09-27
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 443.201
_chem_comp.one_letter_code G
_chem_comp.three_letter_code GDP
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1EK0
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
_chem_comp.pdbx_pcm Y
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
GDP PB PB P 0 1 N N N N N N 13.635 17.027 28.402 -5.743 -1.471 0.475 PB GDP 1
GDP O1B O1B O 0 1 N N N N N N 14.317 18.299 28.131 -6.829 -0.831 -0.300 O1B GDP 2
GDP O2B O2B O 0 1 N N N N N N 14.465 15.868 28.851 -6.293 -1.885 1.930 O2B GDP 3
GDP O3B O3B O 0 1 N N N N N N 12.657 17.014 29.609 -5.234 -2.787 -0.301 O3B GDP 4
GDP O3A O3A O 0 1 N N N N N N 13.031 16.438 26.904 -4.519 -0.438 0.638 O3A GDP 5
GDP PA PA P 0 1 N N N N N N 12.164 17.382 25.843 -3.821 0.633 -0.340 PA GDP 6
GDP O1A O1A O 0 1 N N N N N N 11.308 16.310 25.239 -3.718 0.063 -1.702 O1A GDP 7
GDP O2A O2A O 0 1 N N N N N N 11.654 18.737 26.082 -4.708 1.976 -0.386 O2A GDP 8
GDP "O5'" "O5'" O 0 1 N N N N N N 13.417 17.470 24.852 -2.348 0.981 0.208 "O5'" GDP 9
GDP "C5'" "C5'" C 0 1 N N N N N N 14.543 18.324 25.037 -1.434 1.823 -0.497 "C5'" GDP 10
GDP "C4'" "C4'" C 0 1 N N R N N N 15.043 18.710 23.648 -0.133 1.943 0.299 "C4'" GDP 11
GDP "O4'" "O4'" O 0 1 N N N N N N 15.183 17.536 22.793 0.533 0.670 0.344 "O4'" GDP 12
GDP "C3'" "C3'" C 0 1 N N S N N N 13.926 19.400 22.829 0.820 2.933 -0.399 "C3'" GDP 13
GDP "O3'" "O3'" O 0 1 N N N N N N 14.002 20.787 23.226 1.125 4.028 0.467 "O3'" GDP 14
GDP "C2'" "C2'" C 0 1 N N R N N N 14.511 19.303 21.406 2.091 2.098 -0.686 "C2'" GDP 15
GDP "O2'" "O2'" O 0 1 N N N N N N 15.627 20.165 21.220 3.271 2.861 -0.428 "O2'" GDP 16
GDP "C1'" "C1'" C 0 1 N N R N N N 15.015 17.874 21.438 1.952 0.935 0.329 "C1'" GDP 17
GDP N9 N9 N 0 1 Y N N N N N 13.968 16.928 20.922 2.691 -0.243 -0.132 N9 GDP 18
GDP C8 C8 C 0 1 Y N N N N N 13.129 16.056 21.555 2.200 -1.252 -0.908 C8 GDP 19
GDP N7 N7 N 0 1 Y N N N N N 12.358 15.405 20.737 3.131 -2.134 -1.125 N7 GDP 20
GDP C5 C5 C 0 1 Y N N N N N 12.701 15.869 19.474 4.272 -1.746 -0.504 C5 GDP 21
GDP C6 C6 C 0 1 N N N N N N 12.214 15.545 18.183 5.571 -2.295 -0.396 C6 GDP 22
GDP O6 O6 O 0 1 N N N N N N 11.326 14.728 17.882 5.850 -3.350 -0.939 O6 GDP 23
GDP N1 N1 N 0 1 N N N N N N 12.870 16.282 17.187 6.495 -1.620 0.324 N1 GDP 24
GDP C2 C2 C 0 1 N N N N N N 13.858 17.205 17.402 6.171 -0.441 0.927 C2 GDP 25
GDP N2 N2 N 0 1 N N N N N N 14.348 17.795 16.316 7.130 0.222 1.651 N2 GDP 26
GDP N3 N3 N 0 1 N N N N N N 14.329 17.524 18.614 4.968 0.079 0.834 N3 GDP 27
GDP C4 C4 C 0 1 Y N N N N N 13.701 16.819 19.565 4.003 -0.529 0.133 C4 GDP 28
GDP HOB2 HOB2 H 0 0 N N N N N N 15.376 16.131 28.902 -7.033 -2.508 1.908 HOB2 GDP 29
GDP HOB3 HOB3 H 0 0 N N N N N N 12.643 17.873 30.015 -4.521 -3.259 0.151 HOB3 GDP 30
GDP HOA2 HOA2 H 0 0 N N N N N N 10.749 18.789 25.799 -4.818 2.404 0.474 HOA2 GDP 31
GDP "H5'" "H5'1" H 0 1 N N N N N N 14.247 19.224 25.596 -1.222 1.390 -1.475 "H5'" GDP 32
GDP "H5''" "H5'2" H 0 0 N N N N N N 15.333 17.793 25.589 -1.874 2.811 -0.625 "H5''" GDP 33
GDP "H4'" "H4'" H 0 1 N N N N N N 15.955 19.324 23.692 -0.349 2.285 1.312 "H4'" GDP 34
GDP "H3'" "H3'" H 0 1 N N N N N N 12.939 18.927 22.938 0.380 3.294 -1.329 "H3'" GDP 35
GDP "HO3'" "HO3'" H 0 0 N Y N N N N 13.340 21.286 22.762 1.722 4.683 0.078 "HO3'" GDP 36
GDP "H2'" "H2'" H 0 1 N N N N N N 13.729 19.439 20.644 2.088 1.724 -1.710 "H2'" GDP 37
GDP "HO2'" "HO2'" H 0 0 N N N N N N 15.954 20.073 20.333 3.357 3.652 -0.979 "HO2'" GDP 38
GDP "H1'" "H1'" H 0 1 N N N N N N 15.948 17.778 20.863 2.295 1.244 1.316 "H1'" GDP 39
GDP H8 H8 H 0 1 N N N N N N 13.109 15.921 22.626 1.190 -1.310 -1.285 H8 GDP 40
GDP HN1 HN1 H 0 1 N N N N N N 12.593 16.120 16.240 7.392 -1.977 0.412 HN1 GDP 41
GDP HN21 HN21 H 0 0 N N N N N N 15.071 18.480 16.402 8.023 -0.150 1.728 HN21 GDP 42
GDP HN22 HN22 H 0 0 N N N N N N 13.993 17.554 15.413 6.915 1.062 2.086 HN22 GDP 43
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
GDP PB O1B DOUB N N 1
GDP PB O2B SING N N 2
GDP PB O3B SING N N 3
GDP PB O3A SING N N 4
GDP O2B HOB2 SING N N 5
GDP O3B HOB3 SING N N 6
GDP O3A PA SING N N 7
GDP PA O1A DOUB N N 8
GDP PA O2A SING N N 9
GDP PA "O5'" SING N N 10
GDP O2A HOA2 SING N N 11
GDP "O5'" "C5'" SING N N 12
GDP "C5'" "C4'" SING N N 13
GDP "C5'" "H5'" SING N N 14
GDP "C5'" "H5''" SING N N 15
GDP "C4'" "O4'" SING N N 16
GDP "C4'" "C3'" SING N N 17
GDP "C4'" "H4'" SING N N 18
GDP "O4'" "C1'" SING N N 19
GDP "C3'" "O3'" SING N N 20
GDP "C3'" "C2'" SING N N 21
GDP "C3'" "H3'" SING N N 22
GDP "O3'" "HO3'" SING N N 23
GDP "C2'" "O2'" SING N N 24
GDP "C2'" "C1'" SING N N 25
GDP "C2'" "H2'" SING N N 26
GDP "O2'" "HO2'" SING N N 27
GDP "C1'" N9 SING N N 28
GDP "C1'" "H1'" SING N N 29
GDP N9 C8 SING Y N 30
GDP N9 C4 SING Y N 31
GDP C8 N7 DOUB Y N 32
GDP C8 H8 SING N N 33
GDP N7 C5 SING Y N 34
GDP C5 C6 SING N N 35
GDP C5 C4 DOUB Y N 36
GDP C6 O6 DOUB N N 37
GDP C6 N1 SING N N 38
GDP N1 C2 SING N N 39
GDP N1 HN1 SING N N 40
GDP C2 N2 SING N N 41
GDP C2 N3 DOUB N N 42
GDP N2 HN21 SING N N 43
GDP N2 HN22 SING N N 44
GDP N3 C4 SING N N 45
#
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
GDP SMILES ACDLabs 12.01 'O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O'
GDP InChI InChI 1.03 'InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1'
GDP InChIKey InChI 1.03 QGWNDRXFNXRZMB-UUOKFMHZSA-N
GDP SMILES_CANONICAL CACTVS 3.385 'NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O'
GDP SMILES CACTVS 3.385 'NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O'
GDP SMILES_CANONICAL 'OpenEye OEToolkits' 1.7.6 'c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N'
GDP SMILES 'OpenEye OEToolkits' 1.7.6 'c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N'
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
GDP 'SYSTEMATIC NAME' ACDLabs 12.01
;guanosine 5'-(trihydrogen diphosphate)
;
GDP 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.7.6 '[(2R,3S,4R,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate'
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
GDP 'Create component' 1999-07-08 EBI
GDP 'Modify descriptor' 2011-06-04 RCSB
GDP 'Other modification' 2014-05-12 RCSB
GDP 'Modify PCM' 2024-09-27 PDBE
#
loop_
_pdbx_chem_comp_pcm.pcm_id
_pdbx_chem_comp_pcm.comp_id
_pdbx_chem_comp_pcm.modified_residue_id
_pdbx_chem_comp_pcm.type
_pdbx_chem_comp_pcm.category
_pdbx_chem_comp_pcm.position
_pdbx_chem_comp_pcm.polypeptide_position
_pdbx_chem_comp_pcm.comp_id_linking_atom
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession
1 GDP LEU None 'Covalent chemical modification' 'Amino-acid side chain' 'Any position' N3 CD2 ? ?
2 GDP LEU None 'Covalent chemical modification' 'Amino-acid side chain' 'Any position' O6 CD1 ? ?
3 GDP PHE None 'Covalent chemical modification' 'Amino-acid side chain' 'Any position' "C2'" CE1 ? ?
#
_pdbe_chem_comp_drugbank_details.comp_id GDP
_pdbe_chem_comp_drugbank_details.drugbank_id DB04315
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name "Guanosine-5'-Diphosphate"
_pdbe_chem_comp_drugbank_details.description
'A guanine nucleotide containing two phosphate groups esterified to the sugar moiety. [PubChem]'
_pdbe_chem_comp_drugbank_details.cas_number 146-91-8
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_drugbank_classification.comp_id GDP
_pdbe_chem_comp_drugbank_classification.drugbank_id DB04315
_pdbe_chem_comp_drugbank_classification.parent 'Purine ribonucleoside diphosphates'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Purine nucleotides'
_pdbe_chem_comp_drugbank_classification.superclass 'Nucleosides, nucleotides, and analogues'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as purine ribonucleoside diphosphates. These are purine ribobucleotides with diphosphate group linked to the ribose moiety.'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
GDP DB04315 'Protein-glutamine gamma-glutamyltransferase 2' Humans P21980 yes 1
GDP DB04315 'Elongation factor 1-alpha' 'Plasmodium falciparum (isolate K1 / Thailand)' Q00080 yes 2
GDP DB04315 'Adenylosuccinate synthetase' 'Plasmodium falciparum' Q9U8D3 yes 3
GDP DB04315 'Ras-related protein Rab-9A' Humans P51151 yes 4
GDP DB04315 'GTPase HRas' Humans P01112 unknown 5
GDP DB04315 'Transforming protein RhoA' Humans P61586 unknown 6
GDP DB04315 'Ras-related protein Rab-11A' Humans P62491 unknown 7
GDP DB04315 'Adenylosuccinate synthetase' 'Escherichia coli (strain K12)' P0A7D4 unknown 8
GDP DB04315 'Cell division protein FtsZ' 'Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)' P9WN95 unknown 9
GDP DB04315 'Protein-glutamine gamma-glutamyltransferase E' Humans Q08188 unknown 10
GDP DB04315 'Ras-related protein Rab-8B' Humans Q92930 unknown 11
GDP DB04315 'ADP-ribosylation factor 6' Humans P62330 unknown 12
GDP DB04315 'Adenylosuccinate synthetase isozyme 1' Humans Q8N142 unknown 13
GDP DB04315 'Elongation factor G' 'Thermus thermophilus' P13551 unknown 14
GDP DB04315 'Elongation factor Tu, mitochondrial' Humans P49411 unknown 15
GDP DB04315 'GTPase Der' 'Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)' Q9X1F8 unknown 16
GDP DB04315 'GDP-mannose mannosyl hydrolase' 'Escherichia coli (strain K12)' P32056 unknown 17
GDP DB04315 'Probable GTP-binding protein EngB' 'Bacillus subtilis (strain 168)' P38424 unknown 18
GDP DB04315 'Eukaryotic translation initiation factor 2 subunit 3' Humans P41091 unknown 19
GDP DB04315 'Guanine nucleotide-binding protein G(i) subunit alpha-1' Humans P63096 unknown 20
GDP DB04315 'Signal recognition particle protein' 'Thermus aquaticus' O07347 unknown 21
GDP DB04315 'Guanine nucleotide-binding protein G(t) subunit alpha-1' Humans P11488 unknown 22
GDP DB04315 'Elongation factor Tu-B' 'Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)' P60339 unknown 23
GDP DB04315 'Nucleoside diphosphate kinase A' Humans P15531 unknown 24
GDP DB04315 'GTP-binding protein Rheb' Humans Q15382 unknown 25
GDP DB04315 'Cell division control protein 42 homolog' Humans P60953 unknown 26
GDP DB04315 'Elongation factor Tu' 'Shigella flexneri' Q83JC4 unknown 27
GDP DB04315 'ADP-ribosylation factor 1' Humans P84077 unknown 28
GDP DB04315 'Elongation factor 2' Humans P13639 unknown 29
GDP DB04315 'Bifunctional (p)ppGpp synthase/hydrolase RelA' 'Streptococcus dysgalactiae subsp. equisimilis' Q54089 unknown 30
GDP DB04315 'Ras-related protein Rap-2a' Humans P10114 unknown 31
GDP DB04315 'Elongation factor-like GTPase 1' Humans Q7Z2Z2 unknown 32
GDP DB04315 'ADP-ribosylation factor-like protein 1' Humans P40616 unknown 33
GDP DB04315 'GTP-binding nuclear protein Ran' Humans P62826 unknown 34
GDP DB04315 'Ras-related protein Rab-7a' Humans P51149 unknown 35
GDP DB04315 'Interferon-inducible GTPase 5' Humans Q6NXR0 unknown 36
GDP DB04315 'Eukaryotic peptide chain release factor GTP-binding subunit ERF3A' Humans P15170 unknown 37
GDP DB04315 'Ras-related protein Rab-5A' Humans P20339 unknown 38
GDP DB04315 'Elongation factor 1-alpha 1' Humans P68104 unknown 39
GDP DB04315 'ADP-ribosylation factor 4' Humans P18085 unknown 40
GDP DB04315 'GDP-mannose 4,6 dehydratase' Humans O60547 unknown 41
GDP DB04315 'Ras-related protein Ral-A' Humans P11233 unknown 42
GDP DB04315 'Elongation factor Tu' 'Thermus aquaticus' Q01698 unknown 43
GDP DB04315 'ADP-ribosylation factor-like protein 5B' Humans Q96KC2 unknown 44
GDP DB04315 'GTPase (Rab6)' 'Plasmodium falciparum' Q26000 unknown 45
GDP DB04315 'ADP-ribosylation factor-like protein 3' Humans P36405 unknown 46
GDP DB04315 'Nucleoside diphosphate kinase B' Humans P22392 unknown 47
GDP DB04315 'GDP-mannose 4,6-dehydratase' 'Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)' Q51366 unknown 48
GDP DB04315 'Ras-related C3 botulinum toxin substrate 1' Humans P63000 unknown 49
GDP DB04315 'Putative ribosome biogenesis GTPase RsgA' 'Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)' Q9X242 unknown 50
GDP DB04315 'Small COPII coat GTPase SAR1B' Humans Q9Y6B6 unknown 51
GDP DB04315 'ADP-ribosylation factor-like protein 5A' Humans Q9Y689 unknown 52
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.09.6 'Core functionality.'
pdbeccdutils 0.8.6 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
GDP PB P 17.401 3.442 1
GDP O1B O 18.771 2.830 2
GDP O2B O 18.014 4.812 3
GDP O3B O 16.789 2.073 4
GDP O3A O 16.032 4.055 5
GDP PA P 14.817 3.175 6
GDP O1A O 15.697 1.960 7
GDP O2A O 13.938 4.391 8
GDP "O5'" O 13.602 2.296 9
GDP "C5'" C 12.233 2.908 10
GDP "C4'" C 11.018 2.029 11
GDP "O4'" O 11.015 0.529 12
GDP "C3'" C 9.592 2.495 13
GDP "O3'" O 9.131 3.922 14
GDP "C2'" C 8.708 1.283 15
GDP "O2'" O 7.208 1.285 16
GDP "C1'" C 9.588 0.068 17
GDP N9 N 9.122 -1.358 18
GDP C8 C 9.997 -2.565 19
GDP N7 N 9.122 -3.772 20
GDP C5 C 7.702 -3.315 21
GDP C6 C 6.404 -4.065 22
GDP O6 O 6.404 -5.565 23
GDP N1 N 5.104 -3.315 24
GDP C2 C 5.104 -1.815 25
GDP N2 N 3.805 -1.065 26
GDP N3 N 6.404 -1.065 27
GDP C4 C 7.702 -1.815 28
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
GDP PB O1B DOUBLE NONE 1
GDP PB O2B SINGLE NONE 2
GDP PB O3B SINGLE NONE 3
GDP PB O3A SINGLE NONE 4
GDP O3A PA SINGLE NONE 5
GDP PA O1A DOUBLE NONE 6
GDP PA O2A SINGLE BEGINWEDGE 7
GDP PA "O5'" SINGLE NONE 8
GDP "O5'" "C5'" SINGLE NONE 9
GDP "C4'" "C5'" SINGLE BEGINWEDGE 10
GDP "C4'" "O4'" SINGLE NONE 11
GDP "C4'" "C3'" SINGLE NONE 12
GDP "O4'" "C1'" SINGLE NONE 13
GDP "C3'" "O3'" SINGLE BEGINDASH 14
GDP "C3'" "C2'" SINGLE NONE 15
GDP "C2'" "O2'" SINGLE BEGINDASH 16
GDP "C2'" "C1'" SINGLE NONE 17
GDP "C1'" N9 SINGLE BEGINWEDGE 18
GDP N9 C8 SINGLE NONE 19
GDP N9 C4 SINGLE NONE 20
GDP C8 N7 DOUBLE NONE 21
GDP N7 C5 SINGLE NONE 22
GDP C5 C6 SINGLE NONE 23
GDP C5 C4 DOUBLE NONE 24
GDP C6 O6 DOUBLE NONE 25
GDP C6 N1 SINGLE NONE 26
GDP N1 C2 SINGLE NONE 27
GDP C2 N2 SINGLE NONE 28
GDP C2 N3 DOUBLE NONE 29
GDP N3 C4 SINGLE NONE 30
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
GDP MurckoScaffold S1 scaffold 'O=c1[nH]cnc2c1ncn2[C@H]1CCCO1' InChI=1S/C9H10N4O2/c14-9-7-8(10-4-11-9)13(5-12-7)6-2-1-3-15-6/h4-6H,1-3H2,(H,10,11,14)/t6-/m1/s1 JBXHFRZBULGPSC-ZCFIWIBFSA-N
GDP imidazole F1 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
GDP phosphate F2 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
GDP purine F3 fragment 'c1ncc2[nH]cnc2n1' InChI=1S/C5H4N4/c1-4-5(8-2-6-1)9-3-7-4/h1-3H,(H,6,7,8,9) KDCGOANMDULRCW-UHFFFAOYSA-N
GDP pyrimidine F4 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
GDP ribose F5 fragment OCC1OCC(O)C1O InChI=1S/C5H10O4/c6-1-4-5(8)3(7)2-9-4/h3-8H,1-2H2 KZVAAIRBJJYZOW-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
GDP "C4'" S1 1
GDP "O4'" S1 1
GDP "C3'" S1 1
GDP "C2'" S1 1
GDP "C1'" S1 1
GDP N9 S1 1
GDP C8 S1 1
GDP N7 S1 1
GDP C5 S1 1
GDP C6 S1 1
GDP O6 S1 1
GDP N1 S1 1
GDP C2 S1 1
GDP N3 S1 1
GDP C4 S1 1
GDP C5 F1 1
GDP C4 F1 1
GDP N9 F1 1
GDP C8 F1 1
GDP N7 F1 1
GDP O2B F2 1
GDP PB F2 1
GDP O1B F2 1
GDP O3B F2 1
GDP O3A F2 1
GDP O3A F2 2
GDP PA F2 2
GDP O1A F2 2
GDP O2A F2 2
GDP "O5'" F2 2
GDP N7 F3 1
GDP C8 F3 1
GDP N9 F3 1
GDP C4 F3 1
GDP C5 F3 1
GDP C6 F3 1
GDP N1 F3 1
GDP C2 F3 1
GDP N3 F3 1
GDP C5 F4 1
GDP C6 F4 1
GDP N1 F4 1
GDP C2 F4 1
GDP N3 F4 1
GDP C4 F4 1
GDP "C2'" F5 1
GDP "C3'" F5 1
GDP "C4'" F5 1
GDP "O4'" F5 1
GDP "C1'" F5 1
GDP "C5'" F5 1
GDP "O5'" F5 1
GDP "O3'" F5 1
GDP "O2'" F5 1
#
_pdbe_chem_comp_rdkit_properties.comp_id GDP
_pdbe_chem_comp_rdkit_properties.exactmw 443.024
_pdbe_chem_comp_rdkit_properties.amw 443.202
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 16
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 8
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 12
_pdbe_chem_comp_rdkit_properties.NumHBD 7
_pdbe_chem_comp_rdkit_properties.NumHBA 15
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 28
_pdbe_chem_comp_rdkit_properties.NumAtoms 43
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 18
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.500
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 5
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 175.605
_pdbe_chem_comp_rdkit_properties.tpsa 252.570
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.362
_pdbe_chem_comp_rdkit_properties.CrippenMR 84.469
_pdbe_chem_comp_rdkit_properties.chi0v 14.410
_pdbe_chem_comp_rdkit_properties.chi1v 9.343
_pdbe_chem_comp_rdkit_properties.chi2v 4.669
_pdbe_chem_comp_rdkit_properties.chi3v 4.669
_pdbe_chem_comp_rdkit_properties.chi4v 3.103
_pdbe_chem_comp_rdkit_properties.chi0n 27.621
_pdbe_chem_comp_rdkit_properties.chi1n 13.304
_pdbe_chem_comp_rdkit_properties.chi2n 2.754
_pdbe_chem_comp_rdkit_properties.chi3n 2.754
_pdbe_chem_comp_rdkit_properties.chi4n 1.795
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.710
_pdbe_chem_comp_rdkit_properties.kappa1 8.972
_pdbe_chem_comp_rdkit_properties.kappa2 7.274
_pdbe_chem_comp_rdkit_properties.kappa3 4.310
_pdbe_chem_comp_rdkit_properties.Phi 2.331
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
GDP UniChem ChEMBL CHEMBL384759
GDP UniChem DrugBank DB04315
GDP UniChem 'Guide to Pharmacology' 2410
GDP UniChem 'KEGG LIGAND' C00035
GDP UniChem ChEBI 17552
GDP UniChem ZINC ZINC000008215481
GDP UniChem SureChEMBL SCHEMBL37405
GDP UniChem HMDB HMDB0001201
GDP UniChem 'PubChem TPHARMA' 14783776
GDP UniChem PubChem 135398619
GDP UniChem NMRShiftDB 60020598
GDP UniChem BindingDb 92459
GDP UniChem 'EPA CompTox Dashboard' DTXSID90163254
GDP UniChem MetaboLights MTBLC17552
GDP UniChem BRENDA 103551
GDP UniChem BRENDA 106238
GDP UniChem BRENDA 128427
GDP UniChem BRENDA 30057
GDP UniChem BRENDA 44201
GDP UniChem BRENDA 53
GDP UniChem ChemicalBook CB2185552
GDP UniChem MedChemExpress HY-113066
GDP UniChem 'Probes And Drugs' PD051971
GDP UniChem Nikkaji J40.056D
GDP UniChem 'PubChem TPHARMA' 16003989
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
GDP PB 6.141 0.967 1.335 ETKDGv3 1
GDP O1B 6.872 0.394 2.527 ETKDGv3 2
GDP O2B 5.933 2.631 1.576 ETKDGv3 3
GDP O3B 7.079 0.700 -0.050 ETKDGv3 4
GDP O3A 4.626 0.199 1.209 ETKDGv3 5
GDP PA 3.901 0.701 -0.250 ETKDGv3 6
GDP O1A 3.888 2.210 -0.345 ETKDGv3 7
GDP O2A 4.740 0.070 -1.581 ETKDGv3 8
GDP "O5'" 2.285 0.159 -0.288 ETKDGv3 9
GDP "C5'" 2.279 -1.246 -0.192 ETKDGv3 10
GDP "C4'" 0.836 -1.761 -0.169 ETKDGv3 11
GDP "O4'" 0.117 -1.153 0.877 ETKDGv3 12
GDP "C3'" 0.096 -1.488 -1.470 ETKDGv3 13
GDP "O3'" 0.341 -2.500 -2.412 ETKDGv3 14
GDP "C2'" -1.344 -1.455 -1.018 ETKDGv3 15
GDP "O2'" -1.931 -2.727 -1.135 ETKDGv3 16
GDP "C1'" -1.230 -1.057 0.462 ETKDGv3 17
GDP N9 -1.708 0.309 0.668 ETKDGv3 18
GDP C8 -1.049 1.517 0.260 ETKDGv3 19
GDP N7 -1.856 2.525 0.096 ETKDGv3 20
GDP C5 -3.142 1.992 0.389 ETKDGv3 21
GDP C6 -4.447 2.615 0.213 ETKDGv3 22
GDP O6 -4.565 3.827 -0.107 ETKDGv3 23
GDP N1 -5.598 1.781 0.410 ETKDGv3 24
GDP C2 -5.416 0.382 0.732 ETKDGv3 25
GDP N2 -6.552 -0.464 0.902 ETKDGv3 26
GDP N3 -4.213 -0.116 0.859 ETKDGv3 27
GDP C4 -3.061 0.724 0.696 ETKDGv3 28
GDP HOB2 5.311 2.699 2.344 ETKDGv3 29
GDP HOB3 6.989 1.529 -0.584 ETKDGv3 30
GDP HOA2 5.066 -0.816 -1.283 ETKDGv3 31
GDP "H5'" 2.772 -1.579 0.750 ETKDGv3 32
GDP "H5''" 2.801 -1.706 -1.061 ETKDGv3 33
GDP "H4'" 0.862 -2.860 0.018 ETKDGv3 34
GDP "H3'" 0.379 -0.491 -1.883 ETKDGv3 35
GDP "HO3'" -0.049 -2.185 -3.268 ETKDGv3 36
GDP "H2'" -1.917 -0.712 -1.622 ETKDGv3 37
GDP "HO2'" -2.907 -2.598 -1.011 ETKDGv3 38
GDP "H1'" -1.838 -1.741 1.095 ETKDGv3 39
GDP H8 0.014 1.587 0.077 ETKDGv3 40
GDP HN1 -6.559 2.178 0.304 ETKDGv3 41
GDP HN21 -6.431 -1.476 1.130 ETKDGv3 42
GDP HN22 -7.518 -0.080 0.800 ETKDGv3 43
#