data_GEL
#
_chem_comp.id GEL
_chem_comp.name 1-O-OCTYL-2-HEPTYLPHOSPHONYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C20 H45 N O8 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2011-06-04
_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 489.521
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code GEL
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1MKV
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
GEL C1 C1 C 0 1 N N N N N N 32.728 5.162 68.424 0.254 2.192 0.310 C1 GEL 1
GEL O1 O1 O 0 1 N N N N N N 32.995 3.823 67.924 0.425 1.100 1.217 O1 GEL 2
GEL C11 C11 C 0 1 N N N N N N 34.243 3.781 67.174 1.334 1.541 2.227 C11 GEL 3
GEL C12 C12 C 0 1 N N N N N N 34.431 2.532 66.281 1.562 0.414 3.236 C12 GEL 4
GEL C13 C13 C 0 1 N N N N N N 34.379 1.243 67.101 2.536 0.886 4.317 C13 GEL 5
GEL C14 C14 C 0 1 N N N N N N 35.471 0.249 66.667 2.764 -0.241 5.326 C14 GEL 6
GEL C15 C15 C 0 1 N N N N N N 36.851 0.735 67.096 3.738 0.230 6.408 C15 GEL 7
GEL C16 C16 C 0 1 N N N N N N 37.360 -0.006 68.344 3.966 -0.897 7.416 C16 GEL 8
GEL C17 C17 C 0 1 N N N N N N 38.916 -0.135 68.322 4.939 -0.424 8.498 C17 GEL 9
GEL C18 C18 C 0 1 N N N N N N 39.647 0.383 69.606 5.167 -1.552 9.506 C18 GEL 10
GEL C2 C2 C 0 1 N N R N N N 31.559 5.808 67.638 -0.713 1.783 -0.801 C2 GEL 11
GEL O2 O2 O 0 1 N N N N N N 30.331 5.006 67.299 -0.183 0.658 -1.505 O2 GEL 12
GEL P2 P2 P 0 1 N N S N N N 29.719 4.788 65.788 -0.004 1.112 -3.039 P2 GEL 13
GEL O1P O1P O 0 1 N N N N N N 28.330 5.567 65.868 -1.318 1.506 -3.594 O1P GEL 14
GEL O2P O2P O 0 1 N N N N N N 30.600 5.419 64.719 1.007 2.362 -3.115 O2P GEL 15
GEL C22 C22 C 0 1 N N N N N N 29.407 3.097 65.592 0.672 -0.276 -4.008 C22 GEL 16
GEL C23 C23 C 0 1 N N N N N N 30.141 2.112 66.491 0.842 0.154 -5.466 C23 GEL 17
GEL C24 C24 C 0 1 N N N N N N 29.598 0.766 66.286 1.410 -1.010 -6.279 C24 GEL 18
GEL C25 C25 C 0 1 N N N N N N 30.653 -0.255 66.201 1.580 -0.579 -7.738 C25 GEL 19
GEL C26 C26 C 0 1 N N N N N N 30.570 -1.164 67.383 2.148 -1.744 -8.551 C26 GEL 20
GEL C27 C27 C 0 1 N N N N N N 31.298 -0.556 68.590 2.318 -1.314 -10.009 C27 GEL 21
GEL C28 C28 C 0 1 N N N N N N 30.777 -1.153 69.891 2.885 -2.479 -10.822 C28 GEL 22
GEL C3 C3 C 0 1 N N N N N N 31.488 7.299 67.292 -2.065 1.411 -0.190 C3 GEL 23
GEL O3 O3 O 0 1 N N N N N N 32.658 8.064 67.596 -1.894 0.320 0.716 O3 GEL 24
GEL P3 P3 P 0 1 N N R N N N 33.292 8.710 66.220 -3.348 -0.017 1.318 P3 GEL 25
GEL O3P O3P O 0 1 N N N N N N 32.943 7.999 64.964 -4.265 -0.387 0.217 O3P GEL 26
GEL O4P O4P O 0 1 N N N N N N 34.862 8.488 66.400 -3.925 1.276 2.084 O4P GEL 27
GEL O5P O5P O 0 1 N N N N N N 32.984 10.249 65.967 -3.229 -1.244 2.354 O5P GEL 28
GEL C31 C31 C 0 1 N N N N N N 32.425 10.770 67.116 -4.545 -1.494 2.851 C31 GEL 29
GEL C32 C32 C 0 1 N N N N N N 32.364 12.251 66.855 -4.502 -2.656 3.846 C32 GEL 30
GEL N3 N3 N 0 1 N N N N N N 31.504 12.436 65.699 -3.613 -2.311 4.964 N3 GEL 31
GEL H11 1H1 H 0 1 N N N N N N 32.541 5.165 69.523 -0.150 3.050 0.847 H11 GEL 32
GEL H12 2H1 H 0 1 N N N N N N 33.641 5.800 68.409 1.217 2.457 -0.124 H12 GEL 33
GEL H111 1H11 H 0 0 N N N N N N 34.357 4.708 66.565 0.916 2.408 2.739 H111 GEL 34
GEL H112 2H11 H 0 0 N N N N N N 35.110 3.892 67.865 2.284 1.815 1.767 H112 GEL 35
GEL H121 1H12 H 0 0 N N N N N N 33.693 2.513 65.445 1.981 -0.452 2.723 H121 GEL 36
GEL H122 2H12 H 0 0 N N N N N N 35.369 2.596 65.682 0.613 0.140 3.696 H122 GEL 37
GEL H131 1H13 H 0 0 N N N N N N 34.432 1.454 68.194 2.117 1.752 4.830 H131 GEL 38
GEL H132 2H13 H 0 0 N N N N N N 33.366 0.777 67.063 3.485 1.159 3.857 H132 GEL 39
GEL H141 1H14 H 0 0 N N N N N N 35.262 -0.780 67.040 3.183 -1.107 4.814 H141 GEL 40
GEL H142 2H14 H 0 0 N N N N N N 35.428 0.043 65.572 1.815 -0.515 5.786 H142 GEL 41
GEL H151 1H15 H 0 0 N N N N N N 37.583 0.666 66.257 3.319 1.097 6.920 H151 GEL 42
GEL H152 2H15 H 0 0 N N N N N N 36.861 1.839 67.248 4.687 0.504 5.947 H152 GEL 43
GEL H161 1H16 H 0 0 N N N N N N 37.000 0.475 69.283 4.384 -1.763 6.904 H161 GEL 44
GEL H162 2H16 H 0 0 N N N N N N 36.866 -0.998 68.462 3.016 -1.170 7.876 H162 GEL 45
GEL H171 1H17 H 0 0 N N N N N N 39.210 -1.189 68.112 4.521 0.441 9.010 H171 GEL 46
GEL H172 2H17 H 0 0 N N N N N N 39.329 0.367 67.416 5.889 -0.151 8.038 H172 GEL 47
GEL H181 1H18 H 0 0 N N N N N N 40.758 0.290 69.590 5.861 -1.216 10.277 H181 GEL 48
GEL H182 2H18 H 0 0 N N N N N N 39.352 1.437 69.815 4.218 -1.826 9.966 H182 GEL 49
GEL H183 3H18 H 0 0 N N N N N N 39.233 -0.119 70.511 5.586 -2.418 8.994 H183 GEL 50
GEL H2 H2 H 0 1 N N N N N N 32.529 5.596 67.131 -0.844 2.616 -1.493 H2 GEL 51
GEL HOP2 2HOP H 0 0 N N N N N N 30.246 5.293 63.846 1.849 2.063 -2.745 HOP2 GEL 52
GEL H221 1H22 H 0 0 N N N N N N 28.309 2.919 65.680 1.640 -0.566 -3.600 H221 GEL 53
GEL H222 2H22 H 0 0 N N N N N N 29.585 2.817 64.527 -0.012 -1.122 -3.957 H222 GEL 54
GEL H231 1H23 H 0 0 N N N N N N 31.245 2.148 66.342 -0.125 0.445 -5.875 H231 GEL 55
GEL H232 2H23 H 0 0 N N N N N N 30.114 2.418 67.562 1.527 1.001 -5.518 H232 GEL 56
GEL H241 1H24 H 0 0 N N N N N N 28.851 0.508 67.073 2.378 -1.300 -5.871 H241 GEL 57
GEL H242 2H24 H 0 0 N N N N N N 28.932 0.732 65.392 0.725 -1.857 -6.228 H242 GEL 58
GEL H251 1H25 H 0 0 N N N N N N 30.618 -0.814 65.237 0.612 -0.289 -8.146 H251 GEL 59
GEL H252 2H25 H 0 0 N N N N N N 31.666 0.196 66.088 2.265 0.266 -7.789 H252 GEL 60
GEL H261 1H26 H 0 0 N N N N N N 29.514 -1.427 67.627 3.116 -2.035 -8.142 H261 GEL 61
GEL H262 2H26 H 0 0 N N N N N N 30.947 -2.185 67.145 1.463 -2.591 -8.499 H262 GEL 62
GEL H271 1H27 H 0 0 N N N N N N 32.404 -0.661 68.501 1.350 -1.023 -10.417 H271 GEL 63
GEL H272 2H27 H 0 0 N N N N N N 31.235 0.557 68.592 3.002 -0.467 -10.060 H272 GEL 64
GEL H281 1H28 H 0 0 N N N N N N 31.305 -0.711 70.767 3.007 -2.172 -11.861 H281 GEL 65
GEL H282 2H28 H 0 0 N N N N N N 29.670 -1.047 69.979 3.853 -2.769 -10.414 H282 GEL 66
GEL H283 3H28 H 0 0 N N N N N N 30.839 -2.266 69.888 2.201 -3.325 -10.771 H283 GEL 67
GEL H31 1H3 H 0 1 N N N N N N 31.218 7.427 66.217 -2.470 2.269 0.346 H31 GEL 68
GEL H32 2H3 H 0 1 N N N N N N 30.596 7.759 67.777 -2.755 1.120 -0.982 H32 GEL 69
GEL HOP4 4HOP H 0 0 N N N N N N 35.227 8.860 65.606 -3.300 1.484 2.792 HOP4 GEL 70
GEL H311 1H31 H 0 0 N N N N N N 31.447 10.314 67.396 -4.920 -0.601 3.352 H311 GEL 71
GEL H312 2H31 H 0 0 N N N N N N 32.961 10.492 68.053 -5.204 -1.750 2.022 H312 GEL 72
GEL H321 1H32 H 0 0 N N N N N N 32.040 12.841 67.743 -5.505 -2.846 4.226 H321 GEL 73
GEL H322 2H32 H 0 0 N N N N N N 33.369 12.718 66.735 -4.127 -3.549 3.346 H322 GEL 74
GEL HN31 1HN3 H 0 0 N N N N N N 31.462 13.439 65.522 -3.615 -3.101 5.591 HN31 GEL 75
GEL HN32 2HN3 H 0 0 N N N N N N 30.584 12.008 65.808 -2.681 -2.245 4.583 HN32 GEL 76
#
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
GEL C1 O1 SING N N 1
GEL C1 C2 SING N N 2
GEL C1 H11 SING N N 3
GEL C1 H12 SING N N 4
GEL O1 C11 SING N N 5
GEL C11 C12 SING N N 6
GEL C11 H111 SING N N 7
GEL C11 H112 SING N N 8
GEL C12 C13 SING N N 9
GEL C12 H121 SING N N 10
GEL C12 H122 SING N N 11
GEL C13 C14 SING N N 12
GEL C13 H131 SING N N 13
GEL C13 H132 SING N N 14
GEL C14 C15 SING N N 15
GEL C14 H141 SING N N 16
GEL C14 H142 SING N N 17
GEL C15 C16 SING N N 18
GEL C15 H151 SING N N 19
GEL C15 H152 SING N N 20
GEL C16 C17 SING N N 21
GEL C16 H161 SING N N 22
GEL C16 H162 SING N N 23
GEL C17 C18 SING N N 24
GEL C17 H171 SING N N 25
GEL C17 H172 SING N N 26
GEL C18 H181 SING N N 27
GEL C18 H182 SING N N 28
GEL C18 H183 SING N N 29
GEL C2 O2 SING N N 30
GEL C2 C3 SING N N 31
GEL C2 H2 SING N N 32
GEL O2 P2 SING N N 33
GEL P2 O1P DOUB N N 34
GEL P2 O2P SING N N 35
GEL P2 C22 SING N N 36
GEL O2P HOP2 SING N N 37
GEL C22 C23 SING N N 38
GEL C22 H221 SING N N 39
GEL C22 H222 SING N N 40
GEL C23 C24 SING N N 41
GEL C23 H231 SING N N 42
GEL C23 H232 SING N N 43
GEL C24 C25 SING N N 44
GEL C24 H241 SING N N 45
GEL C24 H242 SING N N 46
GEL C25 C26 SING N N 47
GEL C25 H251 SING N N 48
GEL C25 H252 SING N N 49
GEL C26 C27 SING N N 50
GEL C26 H261 SING N N 51
GEL C26 H262 SING N N 52
GEL C27 C28 SING N N 53
GEL C27 H271 SING N N 54
GEL C27 H272 SING N N 55
GEL C28 H281 SING N N 56
GEL C28 H282 SING N N 57
GEL C28 H283 SING N N 58
GEL C3 O3 SING N N 59
GEL C3 H31 SING N N 60
GEL C3 H32 SING N N 61
GEL O3 P3 SING N N 62
GEL P3 O3P DOUB N N 63
GEL P3 O4P SING N N 64
GEL P3 O5P SING N N 65
GEL O4P HOP4 SING N N 66
GEL O5P C31 SING N N 67
GEL C31 C32 SING N N 68
GEL C31 H311 SING N N 69
GEL C31 H312 SING N N 70
GEL C32 N3 SING N N 71
GEL C32 H321 SING N N 72
GEL C32 H322 SING N N 73
GEL N3 HN31 SING N N 74
GEL N3 HN32 SING N N 75
#
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
GEL SMILES ACDLabs 10.04 O=P(OCC(OP(=O)(O)CCCCCCC)COCCCCCCCC)(OCCN)O
GEL SMILES_CANONICAL CACTVS 3.341 CCCCCCCCOC[C@H](CO[P@@](O)(=O)OCCN)O[P@](O)(=O)CCCCCCC
GEL SMILES CACTVS 3.341 CCCCCCCCOC[CH](CO[P](O)(=O)OCCN)O[P](O)(=O)CCCCCCC
GEL SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CCCCCCCCOCC(CO[P@](=O)(O)OCCN)O[P@](=O)(CCCCCCC)O
GEL SMILES "OpenEye OEToolkits" 1.5.0 CCCCCCCCOCC(COP(=O)(O)OCCN)OP(=O)(CCCCCCC)O
GEL InChI InChI 1.03 InChI=1S/C20H45NO8P2/c1-3-5-7-9-10-12-15-26-18-20(19-28-31(24,25)27-16-14-21)29-30(22,23)17-13-11-8-6-4-2/h20H,3-19,21H2,1-2H3,(H,22,23)(H,24,25)/t20-/m1/s1
GEL InChIKey InChI 1.03 RCCNUBYROFOKAU-HXUWFJFHSA-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
GEL "SYSTEMATIC NAME" ACDLabs 10.04 "(1R)-2-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octyloxy)methyl]ethyl hydrogen (S)-heptylphosphonate"
GEL "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[1-(2-aminoethoxy-hydroxy-phosphoryl)oxy-3-octoxy-propan-2-yl]oxy-heptyl-phosphinic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
GEL 'Create component' 1999-07-08 EBI
GEL 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id GEL
_pdbe_chem_comp_drugbank_details.drugbank_id DB03565
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 1-O-Octyl-2-Heptylphosphonyl-Sn-Glycero-3-Phosphoethanolamine
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number ?
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_drugbank_classification.comp_id GEL
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03565
_pdbe_chem_comp_drugbank_classification.parent Glycerophosphoethanolamines
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class Glycerophospholipids
_pdbe_chem_comp_drugbank_classification.superclass 'Lipids and lipid-like molecules'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as glycerophosphoethanolamines. These are glycerolipids characterized by an ethanolamine ester of glycerophosphoric acid. As is the case with diacylglycerols, glycerophosphoethanolamines can have many different combinations of fatty acids of varying lengths and saturation attached to the C-1 and C-2 atoms.'
#
_pdbe_chem_comp_drugbank_targets.comp_id GEL
_pdbe_chem_comp_drugbank_targets.drugbank_id DB03565
_pdbe_chem_comp_drugbank_targets.name 'Phospholipase A2'
_pdbe_chem_comp_drugbank_targets.organism Humans
_pdbe_chem_comp_drugbank_targets.uniprot_id P04054
_pdbe_chem_comp_drugbank_targets.pharmacologically_active unknown
_pdbe_chem_comp_drugbank_targets.ordinal 1
#
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
GEL C1 C 14.691 3.073 1
GEL O1 O 15.990 2.323 2
GEL C11 C 15.990 0.823 3
GEL C12 C 17.290 0.073 4
GEL C13 C 17.290 -1.427 5
GEL C14 C 18.588 -2.177 6
GEL C15 C 18.588 -3.677 7
GEL C16 C 19.887 -4.427 8
GEL C17 C 19.887 -5.927 9
GEL C18 C 21.187 -6.677 10
GEL C2 C 14.691 4.573 11
GEL O2 O 13.392 5.323 12
GEL P2 P 12.093 4.573 13
GEL O1P O 11.343 5.872 14
GEL O2P O 12.843 3.274 15
GEL C22 C 10.794 3.823 16
GEL C23 C 9.495 4.573 17
GEL C24 C 8.196 3.823 18
GEL C25 C 6.897 4.573 19
GEL C26 C 5.598 3.823 20
GEL C27 C 4.299 4.573 21
GEL C28 C 3.000 3.823 22
GEL C3 C 15.990 5.323 23
GEL O3 O 17.290 4.573 24
GEL P3 P 18.588 5.323 25
GEL O3P O 19.338 4.024 26
GEL O4P O 17.838 6.622 27
GEL O5P O 19.887 6.073 28
GEL C31 C 21.187 5.323 29
GEL C32 C 22.486 6.073 30
GEL N3 N 23.785 5.323 31
#
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
GEL C1 O1 SINGLE NONE 1
GEL C2 C1 SINGLE BEGINWEDGE 2
GEL O1 C11 SINGLE NONE 3
GEL C11 C12 SINGLE NONE 4
GEL C12 C13 SINGLE NONE 5
GEL C13 C14 SINGLE NONE 6
GEL C14 C15 SINGLE NONE 7
GEL C15 C16 SINGLE NONE 8
GEL C16 C17 SINGLE NONE 9
GEL C17 C18 SINGLE NONE 10
GEL C2 O2 SINGLE NONE 11
GEL C2 C3 SINGLE NONE 12
GEL O2 P2 SINGLE NONE 13
GEL P2 O1P DOUBLE NONE 14
GEL P2 O2P SINGLE BEGINDASH 15
GEL P2 C22 SINGLE NONE 16
GEL C22 C23 SINGLE NONE 17
GEL C23 C24 SINGLE NONE 18
GEL C24 C25 SINGLE NONE 19
GEL C25 C26 SINGLE NONE 20
GEL C26 C27 SINGLE NONE 21
GEL C27 C28 SINGLE NONE 22
GEL C3 O3 SINGLE NONE 23
GEL O3 P3 SINGLE NONE 24
GEL P3 O3P DOUBLE NONE 25
GEL P3 O4P SINGLE BEGINWEDGE 26
GEL P3 O5P SINGLE NONE 27
GEL O5P C31 SINGLE NONE 28
GEL C31 C32 SINGLE NONE 29
GEL C32 N3 SINGLE NONE 30
#
_pdbe_chem_comp_substructure.comp_id GEL
_pdbe_chem_comp_substructure.substructure_name phosphate
_pdbe_chem_comp_substructure.id F1
_pdbe_chem_comp_substructure.substructure_type fragment
_pdbe_chem_comp_substructure.substructure_smiles O=P(O)(O)O
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)
_pdbe_chem_comp_substructure.substructure_inchikeys NBIIXXVUZAFLBC-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
GEL O3 F1 1
GEL P3 F1 1
GEL O3P F1 1
GEL O4P F1 1
GEL O5P F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id GEL
_pdbe_chem_comp_rdkit_properties.exactmw 489.262
_pdbe_chem_comp_rdkit_properties.amw 489.527
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 9
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 28
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 9
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 31
_pdbe_chem_comp_rdkit_properties.NumAtoms 76
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 11
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 1
_pdbe_chem_comp_rdkit_properties.NumRings 0
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 3
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 251.581
_pdbe_chem_comp_rdkit_properties.tpsa 137.540
_pdbe_chem_comp_rdkit_properties.CrippenClogP 4.997
_pdbe_chem_comp_rdkit_properties.CrippenMR 123.303
_pdbe_chem_comp_rdkit_properties.chi0v 16.396
_pdbe_chem_comp_rdkit_properties.chi1v 9.749
_pdbe_chem_comp_rdkit_properties.chi2v 3.104
_pdbe_chem_comp_rdkit_properties.chi3v 3.104
_pdbe_chem_comp_rdkit_properties.chi4v 1.769
_pdbe_chem_comp_rdkit_properties.chi0n 59.608
_pdbe_chem_comp_rdkit_properties.chi1n 28.957
_pdbe_chem_comp_rdkit_properties.chi2n 1.666
_pdbe_chem_comp_rdkit_properties.chi3n 1.666
_pdbe_chem_comp_rdkit_properties.chi4n 0.831
_pdbe_chem_comp_rdkit_properties.hallKierAlpha 0.180
_pdbe_chem_comp_rdkit_properties.kappa1 5.025
_pdbe_chem_comp_rdkit_properties.kappa2 19.631
_pdbe_chem_comp_rdkit_properties.kappa3 20.514
_pdbe_chem_comp_rdkit_properties.Phi 3.182
#
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
GEL UniChem ChEMBL CHEMBL1159973
GEL UniChem DrugBank DB03565
GEL UniChem PubChem 129148
GEL UniChem BindingDb 50366475
GEL UniChem 'EPA CompTox Dashboard' DTXSID00152856
GEL UniChem 'Probes And Drugs' PD059605
GEL UniChem Nikkaji J578.073J
GEL UniChem ACTor 120411-63-4
#
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
GEL C1 0.258 1.932 0.986 ETKDGv3 1
GEL O1 0.444 0.624 0.486 ETKDGv3 2
GEL C11 1.822 0.353 0.299 ETKDGv3 3
GEL C12 2.245 0.632 -1.151 ETKDGv3 4
GEL C13 1.467 -0.203 -2.184 ETKDGv3 5
GEL C14 1.943 -1.662 -2.238 ETKDGv3 6
GEL C15 1.172 -2.450 -3.307 ETKDGv3 7
GEL C16 1.609 -3.922 -3.384 ETKDGv3 8
GEL C17 2.964 -4.098 -4.084 ETKDGv3 9
GEL C18 3.317 -5.575 -4.233 ETKDGv3 10
GEL C2 -1.237 2.274 0.975 ETKDGv3 11
GEL O2 -1.904 1.396 1.861 ETKDGv3 12
GEL P2 -3.462 1.011 1.267 ETKDGv3 13
GEL O1P -4.382 0.765 2.441 ETKDGv3 14
GEL O2P -4.097 2.282 0.342 ETKDGv3 15
GEL C22 -3.391 -0.488 0.224 ETKDGv3 16
GEL C23 -3.208 -1.775 1.047 ETKDGv3 17
GEL C24 -1.764 -2.021 1.523 ETKDGv3 18
GEL C25 -0.793 -2.471 0.415 ETKDGv3 19
GEL C26 -1.099 -3.845 -0.210 ETKDGv3 20
GEL C27 -0.997 -5.021 0.782 ETKDGv3 21
GEL C28 -2.367 -5.521 1.238 ETKDGv3 22
GEL C3 -1.447 3.726 1.440 ETKDGv3 23
GEL O3 -0.913 4.609 0.481 ETKDGv3 24
GEL P3 -0.955 6.192 1.117 ETKDGv3 25
GEL O3P -2.378 6.566 1.469 ETKDGv3 26
GEL O4P -0.383 7.270 -0.056 ETKDGv3 27
GEL O5P 0.014 6.297 2.518 ETKDGv3 28
GEL C31 1.334 5.955 2.167 ETKDGv3 29
GEL C32 2.220 6.004 3.409 ETKDGv3 30
GEL N3 2.316 7.370 3.917 ETKDGv3 31
GEL H11 0.639 1.996 2.031 ETKDGv3 32
GEL H12 0.800 2.676 0.357 ETKDGv3 33
GEL H111 2.003 -0.714 0.538 ETKDGv3 34
GEL H112 2.482 0.927 0.994 ETKDGv3 35
GEL H121 2.082 1.708 -1.372 ETKDGv3 36
GEL H122 3.335 0.443 -1.258 ETKDGv3 37
GEL H131 1.627 0.256 -3.185 ETKDGv3 38
GEL H132 0.377 -0.159 -1.972 ETKDGv3 39
GEL H141 3.028 -1.676 -2.470 ETKDGv3 40
GEL H142 1.787 -2.148 -1.252 ETKDGv3 41
GEL H151 1.297 -1.968 -4.302 ETKDGv3 42
GEL H152 0.089 -2.422 -3.056 ETKDGv3 43
GEL H161 0.836 -4.481 -3.955 ETKDGv3 44
GEL H162 1.655 -4.360 -2.362 ETKDGv3 45
GEL H171 2.930 -3.635 -5.094 ETKDGv3 46
GEL H172 3.767 -3.604 -3.497 ETKDGv3 47
GEL H181 4.302 -5.674 -4.736 ETKDGv3 48
GEL H182 2.552 -6.095 -4.848 ETKDGv3 49
GEL H183 3.377 -6.060 -3.236 ETKDGv3 50
GEL H2 -1.577 2.172 -0.084 ETKDGv3 51
GEL HOP2 -5.002 1.977 0.077 ETKDGv3 52
GEL H221 -4.357 -0.560 -0.319 ETKDGv3 53
GEL H222 -2.594 -0.371 -0.537 ETKDGv3 54
GEL H231 -3.561 -2.637 0.446 ETKDGv3 55
GEL H232 -3.875 -1.742 1.935 ETKDGv3 56
GEL H241 -1.773 -2.779 2.333 ETKDGv3 57
GEL H242 -1.365 -1.095 1.987 ETKDGv3 58
GEL H251 -0.770 -1.713 -0.393 ETKDGv3 59
GEL H252 0.232 -2.502 0.845 ETKDGv3 60
GEL H261 -0.343 -4.010 -1.006 ETKDGv3 61
GEL H262 -2.077 -3.835 -0.734 ETKDGv3 62
GEL H271 -0.478 -5.869 0.282 ETKDGv3 63
GEL H272 -0.385 -4.746 1.669 ETKDGv3 64
GEL H281 -2.931 -4.723 1.761 ETKDGv3 65
GEL H282 -2.236 -6.373 1.938 ETKDGv3 66
GEL H283 -2.958 -5.871 0.365 ETKDGv3 67
GEL H31 -0.959 3.850 2.435 ETKDGv3 68
GEL H32 -2.536 3.916 1.558 ETKDGv3 69
GEL HOP4 -0.362 8.150 0.399 ETKDGv3 70
GEL H311 1.744 6.664 1.413 ETKDGv3 71
GEL H312 1.380 4.918 1.762 ETKDGv3 72
GEL H321 1.810 5.330 4.194 ETKDGv3 73
GEL H322 3.237 5.644 3.137 ETKDGv3 74
GEL HN31 1.400 7.623 4.355 ETKDGv3 75
GEL HN32 3.022 7.372 4.689 ETKDGv3 76
#