data_CUP
#
_chem_comp.id CUP
_chem_comp.name (N-SALICYLIDEN-L-PHENYLALANATO)-COPPER(II)
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C16 H13 Cu N O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2007-02-13
_chem_comp.pdbx_modified_date 2023-09-23
_chem_comp.pdbx_ambiguous_flag Y
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 330.825
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code CUP
_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 Y
_chem_comp.pdbx_model_coordinates_db_code ?
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
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
CUP O3 O3 O 0 1 N N N N N N -0.406 6.204 -1.791 ? ? ? O3 CUP 1
CUP C8 C8 C 0 1 N N N N N N 0.133 5.598 -0.870 ? ? ? C8 CUP 2
CUP O2 O2 O 0 1 N N N N N N 1.207 4.661 -1.081 ? ? ? O2 CUP 3
CUP C9 C9 C 0 1 N N S N N N -0.226 5.806 0.574 ? ? ? C9 CUP 4
CUP C10 C10 C 0 1 N N N N N N 0.724 6.921 1.042 ? ? ? C10 CUP 5
CUP C11 C11 C 0 1 Y N N N N N 0.517 7.405 2.456 ? ? ? C11 CUP 6
CUP C16 C16 C 0 1 Y N N N N N -0.623 8.149 2.790 ? ? ? C16 CUP 7
CUP C15 C15 C 0 1 Y N N N N N -0.806 8.592 4.109 ? ? ? C15 CUP 8
CUP C14 C14 C 0 1 Y N N N N N 0.164 8.293 5.071 ? ? ? C14 CUP 9
CUP C13 C13 C 0 1 Y N N N N N 1.299 7.542 4.748 ? ? ? C13 CUP 10
CUP C12 C12 C 0 1 Y N N N N N 1.487 7.105 3.421 ? ? ? C12 CUP 11
CUP N1 N1 N 0 1 N N N N N N 0.078 4.627 1.407 ? ? ? N1 CUP 12
CUP CU1 CU1 CU 0 0 N N N N N N 1.520 3.489 0.872 ? ? ? CU1 CUP 13
CUP C1 C1 C 0 1 N N N N N N -0.608 4.422 2.457 ? ? ? C1 CUP 14
CUP C2 C2 C 0 1 Y N N N N N -0.561 3.275 3.398 ? ? ? C2 CUP 15
CUP C7 C7 C 0 1 Y N N N N N 0.340 2.213 3.349 ? ? ? C7 CUP 16
CUP O1 O1 O 0 1 N N N N N N 1.347 2.126 2.439 ? ? ? O1 CUP 17
CUP C6 C6 C 0 1 Y N N N N N 0.251 1.192 4.310 ? ? ? C6 CUP 18
CUP C5 C5 C 0 1 Y N N N N N -0.735 1.215 5.280 ? ? ? C5 CUP 19
CUP C4 C4 C 0 1 Y N N N N N -1.630 2.271 5.325 ? ? ? C4 CUP 20
CUP C3 C3 C 0 1 Y N N N N N -1.545 3.292 4.394 ? ? ? C3 CUP 21
CUP H14 H14 H 0 1 N N N N N N 0.034 8.649 6.082 ? ? ? H14 CUP 22
CUP H13 H13 H 0 1 N N N N N N 2.026 7.299 5.509 ? ? ? H13 CUP 23
CUP H12 H12 H 0 1 N N N N N N 2.370 6.545 3.151 ? ? ? H12 CUP 24
CUP H16 H16 H 0 1 N N N N N N -1.359 8.381 2.034 ? ? ? H16 CUP 25
CUP H15 H15 H 0 1 N N N N N N -1.686 9.157 4.378 ? ? ? H15 CUP 26
CUP H101 H101 H 0 0 N N N N N N 1.754 6.544 0.961 ? ? ? H101 CUP 27
CUP H102 H102 H 0 0 N N N N N N 0.594 7.781 0.368 ? ? ? H102 CUP 28
CUP H9 H9 H 0 1 N N N N N N -1.275 6.119 0.682 ? ? ? H9 CUP 29
CUP H6 H6 H 0 1 N N N N N N 0.961 0.379 4.291 ? ? ? H6 CUP 30
CUP H5 H5 H 0 1 N N N N N N -0.807 0.413 5.999 ? ? ? H5 CUP 31
CUP H4 H4 H 0 1 N N N N N N -2.395 2.298 6.087 ? ? ? H4 CUP 32
CUP H3 H3 H 0 1 N N N N N N -2.247 4.112 4.436 ? ? ? H3 CUP 33
CUP H1 H1 H 0 1 N N N N N N -1.327 5.191 2.699 ? ? ? H1 CUP 34
#
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
CUP O3 C8 DOUB N N 1
CUP C8 C9 SING N N 2
CUP C8 O2 SING N N 3
CUP O2 CU1 SING N N 4
CUP C9 C10 SING N N 5
CUP C9 H9 SING N N 6
CUP C9 N1 SING N N 7
CUP C10 C11 SING N N 8
CUP C10 H101 SING N N 9
CUP C10 H102 SING N N 10
CUP C11 C12 SING Y N 11
CUP C11 C16 DOUB Y N 12
CUP C16 H16 SING N N 13
CUP C16 C15 SING Y N 14
CUP C15 C14 DOUB Y N 15
CUP C15 H15 SING N N 16
CUP C14 H14 SING N N 17
CUP C14 C13 SING Y N 18
CUP C13 H13 SING N N 19
CUP C13 C12 DOUB Y N 20
CUP C12 H12 SING N N 21
CUP N1 C1 DOUB N N 22
CUP N1 CU1 SING N N 23
CUP CU1 O1 SING N N 24
CUP C1 C2 SING N N 25
CUP C1 H1 SING N N 26
CUP C2 C3 DOUB Y N 27
CUP C2 C7 SING Y N 28
CUP C7 O1 SING N N 29
CUP C7 C6 DOUB Y N 30
CUP C6 H6 SING N N 31
CUP C6 C5 SING Y N 32
CUP C5 H5 SING N N 33
CUP C5 C4 DOUB Y N 34
CUP C4 H4 SING N N 35
CUP C4 C3 SING Y N 36
CUP C3 H3 SING N N 37
#
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
CUP InChI InChI 1.06 InChI=1S/C16H15NO3.Cu/c18-15-9-5-4-8-13(15)11-17-14(16(19)20)10-12-6-2-1-3-7-12;/h1-9,11,14,18H,10H2,(H,19,20);/q;+2/p-2/b17-11+;/t14-;/m0./s1
CUP InChIKey InChI 1.06 YEXSLHMEGKWMMU-VNKRLIBXSA-L
CUP SMILES_CANONICAL CACTVS 3.385 O=C1O[Cu]Oc2ccccc2C=N[C@H]1Cc3ccccc3
CUP SMILES CACTVS 3.385 O=C1O[Cu]Oc2ccccc2C=N[CH]1Cc3ccccc3
CUP SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1ccc(cc1)C[C@H]2C(=O)O[Cu]3[N]2=Cc4ccccc4O3
CUP SMILES "OpenEye OEToolkits" 2.0.7 c1ccc(cc1)CC2C(=O)O[Cu]3[N]2=Cc4ccccc4O3
#
_pdbx_chem_comp_identifier.comp_id CUP
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier
(6~{S})-6-(phenylmethyl)-2,4-dioxa-7$l^{4}-aza-3$l^{3}-cupratricyclo[7.4.0.0^{3,7}]trideca-1(13),7,9,11-tetraen-5-one
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
CUP 'Create component' 2007-02-13 RCSB
CUP 'Modify descriptor' 2023-09-23 RCSB
#
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
CUP O3 O 4.807 -0.057 1
CUP C8 C 3.378 -0.513 2
CUP O2 O 2.908 -1.938 3
CUP C9 C 2.169 0.374 4
CUP C10 C 2.177 1.874 5
CUP C11 C 0.881 2.631 6
CUP C16 C 0.888 4.131 7
CUP C15 C -0.407 4.887 8
CUP C14 C -1.709 4.143 9
CUP C13 C -1.717 2.644 10
CUP C12 C -0.422 1.887 11
CUP N1 N 0.951 -0.501 12
CUP CU1 Cu 1.408 -1.930 13
CUP C1 C -0.514 -0.182 14
CUP C2 C -1.524 -1.292 15
CUP C7 C -1.067 -2.721 16
CUP O1 O 0.398 -3.040 17
CUP C6 C -2.076 -3.830 18
CUP C5 C -3.542 -3.511 19
CUP C4 C -3.998 -2.082 20
CUP C3 C -2.989 -0.973 21
#
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
CUP O3 C8 DOUBLE NONE 1
CUP C8 C9 SINGLE NONE 2
CUP C8 O2 SINGLE NONE 3
CUP O2 CU1 SINGLE NONE 4
CUP C9 C10 SINGLE BEGINWEDGE 5
CUP C9 N1 SINGLE ENDUPRIGHT 6
CUP C10 C11 SINGLE NONE 7
CUP C11 C12 SINGLE NONE 8
CUP C11 C16 DOUBLE NONE 9
CUP C16 C15 SINGLE NONE 10
CUP C15 C14 DOUBLE NONE 11
CUP C14 C13 SINGLE NONE 12
CUP C13 C12 DOUBLE NONE 13
CUP N1 C1 DOUBLE NONE 14
CUP N1 CU1 DATIVE NONE 15
CUP CU1 O1 SINGLE NONE 16
CUP C1 C2 SINGLE ENDUPRIGHT 17
CUP C2 C3 DOUBLE NONE 18
CUP C2 C7 SINGLE NONE 19
CUP C7 O1 SINGLE NONE 20
CUP C7 C6 DOUBLE NONE 21
CUP C6 C5 SINGLE NONE 22
CUP C5 C4 DOUBLE NONE 23
CUP C4 C3 SINGLE NONE 24
#
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
CUP MurckoScaffold S1 scaffold 'O=C1O[Cu@SP2]2<-N(=C/c3ccccc3O2)\[C@H]1Cc1ccccc1' 'InChI=1S/C16H15NO3.Cu/c18-15-9-5-4-8-13(15)11-17-14(16(19)20)10-12-6-2-1-3-7-12;/h1-9,11,14,18H,10H2,(H,19,20);/q;+2/p-2/b17-11+;/t14-;/m0./s1' YEXSLHMEGKWMMU-VNKRLIBXSA-L
CUP peptide F1 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
CUP phenyl F2 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-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
CUP O3 S1 1
CUP C8 S1 1
CUP O2 S1 1
CUP C9 S1 1
CUP C10 S1 1
CUP C11 S1 1
CUP C16 S1 1
CUP C15 S1 1
CUP C14 S1 1
CUP C13 S1 1
CUP C12 S1 1
CUP N1 S1 1
CUP CU1 S1 1
CUP C1 S1 1
CUP C2 S1 1
CUP C7 S1 1
CUP O1 S1 1
CUP C6 S1 1
CUP C5 S1 1
CUP C4 S1 1
CUP C3 S1 1
CUP O3 F1 1
CUP C8 F1 1
CUP C9 F1 1
CUP N1 F1 1
CUP C11 F2 1
CUP C12 F2 1
CUP C13 F2 1
CUP C14 F2 1
CUP C15 F2 1
CUP C16 F2 1
CUP C2 F2 2
CUP C3 F2 2
CUP C4 F2 2
CUP C5 F2 2
CUP C6 F2 2
CUP C7 F2 2
#
_pdbe_chem_comp_rdkit_properties.comp_id CUP
_pdbe_chem_comp_rdkit_properties.exactmw 330.019
_pdbe_chem_comp_rdkit_properties.amw 330.830
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 0
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_pdbe_chem_comp_rdkit_properties.NumHBD 0
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 21
_pdbe_chem_comp_rdkit_properties.NumAtoms 34
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.125
_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 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 145.188
_pdbe_chem_comp_rdkit_properties.tpsa 41.430
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.993
_pdbe_chem_comp_rdkit_properties.CrippenMR 73.548
_pdbe_chem_comp_rdkit_properties.chi0v 10.915
_pdbe_chem_comp_rdkit_properties.chi1v 6.631
_pdbe_chem_comp_rdkit_properties.chi2v 3.659
_pdbe_chem_comp_rdkit_properties.chi3v 3.659
_pdbe_chem_comp_rdkit_properties.chi4v 2.713
_pdbe_chem_comp_rdkit_properties.chi0n 22.973
_pdbe_chem_comp_rdkit_properties.chi1n 11.941
_pdbe_chem_comp_rdkit_properties.chi2n 2.303
_pdbe_chem_comp_rdkit_properties.chi3n 2.303
_pdbe_chem_comp_rdkit_properties.chi4n 1.451
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.101
_pdbe_chem_comp_rdkit_properties.kappa1 4.972
_pdbe_chem_comp_rdkit_properties.kappa2 5.024
_pdbe_chem_comp_rdkit_properties.kappa3 2.245
_pdbe_chem_comp_rdkit_properties.Phi 1.189
#
#
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
CUP O3 -0.005 -0.073 -3.490 ETKDGv3 1
CUP C8 -0.671 0.126 -2.440 ETKDGv3 2
CUP O2 0.065 -0.093 -3.598 ETKDGv3 3
CUP C9 -0.092 0.916 -1.304 ETKDGv3 4
CUP C10 1.131 0.215 -0.679 ETKDGv3 5
CUP C11 1.808 1.101 0.335 ETKDGv3 6
CUP C16 1.531 0.992 1.647 ETKDGv3 7
CUP C15 2.180 1.891 2.624 ETKDGv3 8
CUP C14 3.040 2.828 2.205 ETKDGv3 9
CUP C13 3.341 2.964 0.766 ETKDGv3 10
CUP C12 2.757 2.148 -0.121 ETKDGv3 11
CUP N1 -1.115 1.222 -0.292 ETKDGv3 12
CUP CU1 -1.822 0.964 0.422 ETKDGv3 13
CUP C1 -1.888 0.403 0.367 ETKDGv3 14
CUP C2 -1.973 -1.044 0.101 ETKDGv3 15
CUP C7 -2.861 -1.557 -0.974 ETKDGv3 16
CUP O1 -3.592 -0.674 -1.762 ETKDGv3 17
CUP C6 -2.968 -2.876 -1.184 ETKDGv3 18
CUP C5 -2.225 -3.825 -0.330 ETKDGv3 19
CUP C4 -1.459 -3.369 0.668 ETKDGv3 20
CUP C3 -1.343 -1.915 0.907 ETKDGv3 21
CUP H14 3.515 3.488 2.920 ETKDGv3 22
CUP H13 4.032 3.726 0.430 ETKDGv3 23
CUP H12 2.978 2.257 -1.176 ETKDGv3 24
CUP H16 0.829 0.251 2.006 ETKDGv3 25
CUP H15 1.956 1.792 3.678 ETKDGv3 26
CUP H101 1.867 -0.025 -1.477 ETKDGv3 27
CUP H102 0.841 -0.753 -0.222 ETKDGv3 28
CUP H9 0.250 1.886 -1.727 ETKDGv3 29
CUP H6 -3.609 -3.255 -1.970 ETKDGv3 30
CUP H5 -2.312 -4.889 -0.505 ETKDGv3 31
CUP H4 -0.923 -4.063 1.303 ETKDGv3 32
CUP H3 -0.736 -1.566 1.733 ETKDGv3 33
CUP H1 -2.528 0.808 1.139 ETKDGv3 34
#