data_W7O
#
_chem_comp.id W7O
_chem_comp.name "5-[2-(3-carboxyphenyl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C14 H12 N2 O6"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2013-03-13
_chem_comp.pdbx_modified_date 2014-02-28
_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 304.255
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code W7O
_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 3W7O
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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
W7O OAA OAA O 0 1 N N N N N N 3.991 19.098 10.116 -4.401 -2.139 0.250 OAA W7O 1
W7O CAO CAO C 0 1 N N N N N N 3.411 18.004 10.391 -4.824 -1.018 0.049 CAO W7O 2
W7O OAE OAE O 0 1 N N N N N N 2.141 17.858 10.213 -6.132 -0.827 -0.209 OAE W7O 3
W7O CAR CAR C 0 1 Y N N N N N 4.138 16.867 10.696 -3.903 0.137 0.093 CAR W7O 4
W7O CAJ CAJ C 0 1 Y N N N N N 5.567 16.936 10.732 -2.548 -0.057 0.365 CAJ W7O 5
W7O CAI CAI C 0 1 Y N N N N N 3.419 15.714 10.967 -4.384 1.426 -0.144 CAI W7O 6
W7O CAG CAG C 0 1 Y N N N N N 4.050 14.530 11.275 -3.520 2.500 -0.102 CAG W7O 7
W7O CAH CAH C 0 1 Y N N N N N 5.476 14.563 11.308 -2.178 2.302 0.173 CAH W7O 8
W7O CAQ CAQ C 0 1 Y N N N N N 6.216 15.746 11.018 -1.694 1.026 0.403 CAQ W7O 9
W7O CAK CAK C 0 1 N N N N N N 7.576 15.747 11.125 -0.230 0.819 0.698 CAK W7O 10
W7O CAL CAL C 0 1 N N N N N N 8.146 16.204 12.513 0.526 0.594 -0.613 CAL W7O 11
W7O CAS CAS C 0 1 N N N N N N 7.694 15.372 13.590 1.990 0.387 -0.318 CAS W7O 12
W7O CAV CAV C 0 1 N N N N N N 8.116 14.018 13.670 2.907 1.530 -0.224 CAV W7O 13
W7O OAD OAD O 0 1 N N N N N N 8.936 13.553 12.871 2.499 2.665 -0.382 OAD W7O 14
W7O NAN NAN N 0 1 N N N N N N 7.615 13.245 14.716 4.209 1.299 0.041 NAN W7O 15
W7O CAU CAU C 0 1 N N N N N N 6.640 13.702 15.612 4.656 0.043 0.215 CAU W7O 16
W7O OAC OAC O 0 1 N N N N N N 6.179 12.973 16.499 5.835 -0.138 0.454 OAC W7O 17
W7O NAM NAM N 0 1 N N N N N N 6.291 15.046 15.475 3.836 -1.018 0.134 NAM W7O 18
W7O CAT CAT C 0 1 N N N N N N 6.802 15.861 14.496 2.492 -0.861 -0.128 CAT W7O 19
W7O CAP CAP C 0 1 N N N N N N 6.191 17.236 14.478 1.603 -2.045 -0.207 CAP W7O 20
W7O OAF OAF O 0 1 N N N N N N 4.935 17.195 14.507 2.125 -3.285 -0.148 OAF W7O 21
W7O OAB OAB O 0 1 N N N N N N 6.890 18.247 14.440 0.404 -1.897 -0.326 OAB W7O 22
W7O H1 H1 H 0 1 N N N N N N 1.775 18.664 9.868 -6.696 -1.613 -0.223 H1 W7O 23
W7O H2 H2 H 0 1 N N N N N N 6.104 17.855 10.548 -2.168 -1.052 0.545 H2 W7O 24
W7O H3 H3 H 0 1 N N N N N N 2.340 15.745 10.936 -5.431 1.582 -0.360 H3 W7O 25
W7O H4 H4 H 0 1 N N N N N N 3.496 13.626 11.480 -3.890 3.498 -0.286 H4 W7O 26
W7O H5 H5 H 0 1 N N N N N N 6.013 13.661 11.561 -1.505 3.146 0.204 H5 W7O 27
W7O H6 H6 H 0 1 N N N N N N 7.931 14.724 10.933 0.168 1.701 1.200 H6 W7O 28
W7O H7 H7 H 0 1 N N N N N N 7.976 16.424 10.356 -0.109 -0.051 1.342 H7 W7O 29
W7O H8 H8 H 0 1 N N N N N N 9.245 16.165 12.474 0.129 -0.288 -1.115 H8 W7O 30
W7O H9 H9 H 0 1 N N N N N N 7.822 17.238 12.705 0.405 1.464 -1.257 H9 W7O 31
W7O H10 H10 H 0 1 N N N N N N 7.969 12.317 14.833 4.827 2.044 0.106 H10 W7O 32
W7O H11 H11 H 0 1 N N N N N N 5.636 15.435 16.123 4.195 -1.909 0.266 H11 W7O 33
W7O H12 H12 H 0 1 N N N N N N 4.588 18.079 14.495 1.506 -4.025 -0.204 H12 W7O 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
W7O OAA CAO DOUB N N 1
W7O OAE CAO SING N N 2
W7O CAO CAR SING N N 3
W7O CAR CAJ DOUB Y N 4
W7O CAR CAI SING Y N 5
W7O CAJ CAQ SING Y N 6
W7O CAI CAG DOUB Y N 7
W7O CAQ CAK SING N N 8
W7O CAQ CAH DOUB Y N 9
W7O CAK CAL SING N N 10
W7O CAG CAH SING Y N 11
W7O CAL CAS SING N N 12
W7O OAD CAV DOUB N N 13
W7O CAS CAV SING N N 14
W7O CAS CAT DOUB N N 15
W7O CAV NAN SING N N 16
W7O OAB CAP DOUB N N 17
W7O CAP CAT SING N N 18
W7O CAP OAF SING N N 19
W7O CAT NAM SING N N 20
W7O NAN CAU SING N N 21
W7O NAM CAU SING N N 22
W7O CAU OAC DOUB N N 23
W7O OAE H1 SING N N 24
W7O CAJ H2 SING N N 25
W7O CAI H3 SING N N 26
W7O CAG H4 SING N N 27
W7O CAH H5 SING N N 28
W7O CAK H6 SING N N 29
W7O CAK H7 SING N N 30
W7O CAL H8 SING N N 31
W7O CAL H9 SING N N 32
W7O NAN H10 SING N N 33
W7O NAM H11 SING N N 34
W7O OAF H12 SING N N 35
#
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
W7O SMILES ACDLabs 12.01 O=C1NC(C(=O)O)=C(C(=O)N1)CCc2cccc(C(=O)O)c2
W7O InChI InChI 1.03 InChI=1S/C14H12N2O6/c17-11-9(10(13(20)21)15-14(22)16-11)5-4-7-2-1-3-8(6-7)12(18)19/h1-3,6H,4-5H2,(H,18,19)(H,20,21)(H2,15,16,17,22)
W7O InChIKey InChI 1.03 NEPNOJKMVGCINS-UHFFFAOYSA-N
W7O SMILES_CANONICAL CACTVS 3.370 OC(=O)C1=C(CCc2cccc(c2)C(O)=O)C(=O)NC(=O)N1
W7O SMILES CACTVS 3.370 OC(=O)C1=C(CCc2cccc(c2)C(O)=O)C(=O)NC(=O)N1
W7O SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 c1cc(cc(c1)C(=O)O)CCC2=C(NC(=O)NC2=O)C(=O)O
W7O SMILES "OpenEye OEToolkits" 1.7.6 c1cc(cc(c1)C(=O)O)CCC2=C(NC(=O)NC2=O)C(=O)O
#
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
W7O "SYSTEMATIC NAME" ACDLabs 12.01 "5-[2-(3-carboxyphenyl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid"
W7O "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "5-[2-(3-carboxyphenyl)ethyl]-2,4-bis(oxidanylidene)-1H-pyrimidine-6-carboxylic 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
W7O 'Create component' 2013-03-13 PDBJ
W7O 'Initial release' 2014-03-05 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 '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
W7O OAA O 3.000 5.393 1
W7O CAO C 4.299 4.643 2
W7O OAE O 5.598 5.393 3
W7O CAR C 4.299 3.143 4
W7O CAJ C 5.598 2.393 5
W7O CAI C 3.000 2.393 6
W7O CAG C 3.000 0.892 7
W7O CAH C 4.299 0.142 8
W7O CAQ C 5.598 0.892 9
W7O CAK C 6.897 0.142 10
W7O CAL C 6.897 -1.357 11
W7O CAS C 8.196 -2.107 12
W7O CAV C 9.495 -1.357 13
W7O OAD O 9.495 0.142 14
W7O NAN N 10.794 -2.107 15
W7O CAU C 10.794 -3.607 16
W7O OAC O 12.093 -4.357 17
W7O NAM N 9.495 -4.357 18
W7O CAT C 8.196 -3.607 19
W7O CAP C 6.897 -4.357 20
W7O OAF O 5.598 -3.607 21
W7O OAB O 6.897 -5.857 22
#
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
W7O OAA CAO DOUBLE NONE 1
W7O OAE CAO SINGLE NONE 2
W7O CAO CAR SINGLE NONE 3
W7O CAR CAJ DOUBLE NONE 4
W7O CAR CAI SINGLE NONE 5
W7O CAJ CAQ SINGLE NONE 6
W7O CAI CAG DOUBLE NONE 7
W7O CAQ CAK SINGLE NONE 8
W7O CAQ CAH DOUBLE NONE 9
W7O CAK CAL SINGLE NONE 10
W7O CAG CAH SINGLE NONE 11
W7O CAL CAS SINGLE NONE 12
W7O OAD CAV DOUBLE NONE 13
W7O CAS CAV SINGLE NONE 14
W7O CAS CAT DOUBLE NONE 15
W7O CAV NAN SINGLE NONE 16
W7O OAB CAP DOUBLE NONE 17
W7O CAP CAT SINGLE NONE 18
W7O CAP OAF SINGLE NONE 19
W7O CAT NAM SINGLE NONE 20
W7O NAN CAU SINGLE NONE 21
W7O NAM CAU SINGLE NONE 22
W7O CAU OAC DOUBLE NONE 23
#
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
W7O MurckoScaffold S1 scaffold 'O=c1[nH]cc(CCc2ccccc2)c(=O)[nH]1' InChI=1S/C12H12N2O2/c15-11-10(8-13-12(16)14-11)7-6-9-4-2-1-3-5-9/h1-5,8H,6-7H2,(H2,13,14,15,16) JIXBEKSHVUECRD-UHFFFAOYSA-N
W7O phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
W7O pyrimidine F2 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-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
W7O CAR S1 1
W7O CAJ S1 1
W7O CAI S1 1
W7O CAG S1 1
W7O CAH S1 1
W7O CAQ S1 1
W7O CAK S1 1
W7O CAL S1 1
W7O CAS S1 1
W7O CAV S1 1
W7O OAD S1 1
W7O NAN S1 1
W7O CAU S1 1
W7O OAC S1 1
W7O NAM S1 1
W7O CAT S1 1
W7O CAR F1 1
W7O CAJ F1 1
W7O CAQ F1 1
W7O CAH F1 1
W7O CAG F1 1
W7O CAI F1 1
W7O CAS F2 1
W7O CAV F2 1
W7O NAN F2 1
W7O CAU F2 1
W7O NAM F2 1
W7O CAT F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id W7O
_pdbe_chem_comp_rdkit_properties.exactmw 304.070
_pdbe_chem_comp_rdkit_properties.amw 304.258
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 8
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 22
_pdbe_chem_comp_rdkit_properties.NumAtoms 34
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.143
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 139.771
_pdbe_chem_comp_rdkit_properties.tpsa 140.320
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.826
_pdbe_chem_comp_rdkit_properties.CrippenMR 74.604
_pdbe_chem_comp_rdkit_properties.chi0v 10.344
_pdbe_chem_comp_rdkit_properties.chi1v 5.369
_pdbe_chem_comp_rdkit_properties.chi2v 2.190
_pdbe_chem_comp_rdkit_properties.chi3v 2.190
_pdbe_chem_comp_rdkit_properties.chi4v 1.314
_pdbe_chem_comp_rdkit_properties.chi0n 22.344
_pdbe_chem_comp_rdkit_properties.chi1n 11.080
_pdbe_chem_comp_rdkit_properties.chi2n 2.190
_pdbe_chem_comp_rdkit_properties.chi3n 2.190
_pdbe_chem_comp_rdkit_properties.chi4n 1.314
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -3.160
_pdbe_chem_comp_rdkit_properties.kappa1 5.915
_pdbe_chem_comp_rdkit_properties.kappa2 6.083
_pdbe_chem_comp_rdkit_properties.kappa3 3.289
_pdbe_chem_comp_rdkit_properties.Phi 1.635
#
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
W7O UniChem ChEMBL CHEMBL3990355
W7O UniChem PDBe W7O
W7O UniChem ZINC ZINC000098209566
W7O UniChem PubChem 73010374
W7O UniChem BindingDb 50211923
#
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
W7O OAA 3.480 -3.270 -0.486 ETKDGv3 1
W7O CAO 4.158 -2.207 -0.471 ETKDGv3 2
W7O OAE 5.501 -2.250 -0.837 ETKDGv3 3
W7O CAR 3.541 -0.924 -0.071 ETKDGv3 4
W7O CAJ 2.243 -0.855 0.286 ETKDGv3 5
W7O CAI 4.357 0.317 -0.063 ETKDGv3 6
W7O CAG 3.809 1.486 0.287 ETKDGv3 7
W7O CAH 2.386 1.554 0.670 ETKDGv3 8
W7O CAQ 1.636 0.439 0.686 ETKDGv3 9
W7O CAK 0.174 0.501 1.037 ETKDGv3 10
W7O CAL -0.671 0.755 -0.217 ETKDGv3 11
W7O CAS -2.151 0.752 0.116 ETKDGv3 12
W7O CAV -2.748 2.021 0.616 ETKDGv3 13
W7O OAD -2.025 3.036 0.808 ETKDGv3 14
W7O NAN -4.148 2.104 0.886 ETKDGv3 15
W7O CAU -4.962 0.956 0.679 ETKDGv3 16
W7O OAC -6.201 1.008 0.901 ETKDGv3 17
W7O NAM -4.361 -0.255 0.221 ETKDGv3 18
W7O CAT -2.945 -0.347 -0.034 ETKDGv3 19
W7O CAP -2.432 -1.668 -0.473 ETKDGv3 20
W7O OAF -3.250 -2.500 -1.232 ETKDGv3 21
W7O OAB -1.293 -2.078 -0.124 ETKDGv3 22
W7O H1 5.937 -3.122 -1.114 ETKDGv3 23
W7O H2 1.623 -1.743 0.284 ETKDGv3 24
W7O H3 5.403 0.287 -0.343 ETKDGv3 25
W7O H4 4.408 2.388 0.287 ETKDGv3 26
W7O H5 1.957 2.513 0.934 ETKDGv3 27
W7O H6 -0.005 1.310 1.780 ETKDGv3 28
W7O H7 -0.130 -0.452 1.520 ETKDGv3 29
W7O H8 -0.391 1.742 -0.646 ETKDGv3 30
W7O H9 -0.430 0.019 -1.013 ETKDGv3 31
W7O H10 -4.569 2.996 1.230 ETKDGv3 32
W7O H11 -4.969 -1.096 0.097 ETKDGv3 33
W7O H12 -2.932 -3.416 -1.525 ETKDGv3 34
#