data_VJG
#
_chem_comp.id VJG
_chem_comp.name "{(1S,2R)-2-[4-(1H-tetrazol-5-yl)benzene-1-carbonyl]cyclopentyl}acetic acid"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C15 H16 N4 O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-08-17
_chem_comp.pdbx_modified_date 2021-09-03
_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 300.313
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VJG
_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 7JT6
_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
VJG C12 C1 C 0 1 Y N N N N N 1.393 -32.267 22.161 0.457 0.038 0.591 C12 VJG 1
VJG C13 C2 C 0 1 Y N N N N N 1.803 -32.611 23.435 1.311 -0.629 1.477 C13 VJG 2
VJG C14 C3 C 0 1 Y N N N N N 2.446 -31.691 24.236 2.655 -0.695 1.213 C14 VJG 3
VJG C15 C4 C 0 1 Y N N N N N 1.625 -30.991 21.675 0.976 0.635 -0.564 C15 VJG 4
VJG C16 C5 C 0 1 Y N N N N N 2.269 -30.065 22.478 2.320 0.566 -0.825 C16 VJG 5
VJG C17 C6 C 0 1 Y N N N N N 2.683 -30.418 23.755 3.171 -0.099 0.060 C17 VJG 6
VJG C18 C7 C 0 1 Y N N N N N 3.393 -29.408 24.645 4.621 -0.171 -0.223 C18 VJG 7
VJG C02 C8 C 0 1 N N N N N N 0.681 -33.326 21.329 -0.986 0.105 0.869 C02 VJG 8
VJG C03 C9 C 0 1 N N R N N N -0.041 -34.466 22.085 -1.905 0.823 -0.085 C03 VJG 9
VJG C04 C10 C 0 1 N N N N N N 0.954 -35.751 22.229 -1.966 2.327 0.252 C04 VJG 10
VJG C05 C11 C 0 1 N N N N N N 0.116 -36.990 21.692 -3.420 2.771 0.018 C05 VJG 11
VJG C06 C12 C 0 1 N N N N N N -1.202 -36.553 21.662 -4.193 1.521 -0.452 C06 VJG 12
VJG C07 C13 C 0 1 N N S N N N -1.135 -34.901 21.396 -3.363 0.333 0.096 C07 VJG 13
VJG C08 C14 C 0 1 N N N N N N -2.404 -34.265 21.941 -3.617 -0.931 -0.728 C08 VJG 14
VJG C09 C15 C 0 1 N N N N N N -2.605 -32.818 21.502 -5.044 -1.378 -0.535 C09 VJG 15
VJG N19 N1 N 0 1 Y N N N N N 3.151 -28.091 24.680 5.567 -0.776 0.535 N19 VJG 16
VJG N20 N2 N 0 1 Y N N N N N 3.983 -27.555 25.605 6.696 -0.609 -0.065 N20 VJG 17
VJG N21 N3 N 0 1 Y N N N N N 4.727 -28.531 26.131 6.503 0.062 -1.146 N21 VJG 18
VJG N22 N4 N 0 1 Y N N N N N 4.358 -29.690 25.536 5.250 0.336 -1.267 N22 VJG 19
VJG O01 O1 O 0 1 N N N N N N 0.681 -33.275 20.148 -1.436 -0.417 1.867 O01 VJG 20
VJG O10 O2 O 0 1 N N N N N N -2.778 -32.542 20.287 -5.781 -0.749 0.187 O10 VJG 21
VJG O11 O3 O 0 1 N N N N N N -2.611 -31.897 22.361 -5.494 -2.474 -1.165 O11 VJG 22
VJG H1 H1 H 0 1 N N N N N N 1.618 -33.608 23.806 0.912 -1.089 2.368 H1 VJG 23
VJG H2 H2 H 0 1 N N N N N N 2.762 -31.964 25.232 3.314 -1.209 1.896 H2 VJG 24
VJG H3 H3 H 0 1 N N N N N N 1.307 -30.721 20.679 0.318 1.149 -1.249 H3 VJG 25
VJG H4 H4 H 0 1 N N N N N N 2.450 -29.066 22.110 2.721 1.026 -1.716 H4 VJG 26
VJG H5 H5 H 0 1 N N N N N N -0.303 -34.120 23.096 -1.576 0.675 -1.114 H5 VJG 27
VJG H6 H6 H 0 1 N N N N N N 1.237 -35.904 23.281 -1.689 2.488 1.294 H6 VJG 28
VJG H7 H7 H 0 1 N N N N N N 1.860 -35.607 21.623 -1.295 2.884 -0.403 H7 VJG 29
VJG H8 H8 H 0 1 N N N N N N 0.222 -37.850 22.370 -3.849 3.147 0.947 H8 VJG 30
VJG H9 H9 H 0 1 N N N N N N 0.451 -37.274 20.684 -3.456 3.544 -0.749 H9 VJG 31
VJG H10 H10 H 0 1 N N N N N N -1.697 -36.766 22.621 -5.197 1.512 -0.030 H10 VJG 32
VJG H11 H11 H 0 1 N N N N N N -1.751 -37.049 20.848 -4.237 1.488 -1.541 H11 VJG 33
VJG H12 H12 H 0 1 N N N N N N -1.054 -34.726 20.313 -3.588 0.159 1.148 H12 VJG 34
VJG H13 H13 H 0 1 N N N N N N -3.265 -34.856 21.594 -3.442 -0.719 -1.782 H13 VJG 35
VJG H14 H14 H 0 1 N N N N N N -2.361 -34.291 23.040 -2.942 -1.720 -0.399 H14 VJG 36
VJG H15 H15 H 0 1 N N N N N N 2.481 -27.596 24.127 5.422 -1.246 1.371 H15 VJG 37
VJG H16 H16 H 0 1 N N N N N N -2.757 -31.063 21.931 -6.416 -2.721 -1.010 H16 VJG 38
#
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
VJG O01 C02 DOUB N N 1
VJG O10 C09 DOUB N N 2
VJG C02 C03 SING N N 3
VJG C02 C12 SING N N 4
VJG C07 C06 SING N N 5
VJG C07 C08 SING N N 6
VJG C07 C03 SING N N 7
VJG C09 C08 SING N N 8
VJG C09 O11 SING N N 9
VJG C06 C05 SING N N 10
VJG C15 C12 DOUB Y N 11
VJG C15 C16 SING Y N 12
VJG C05 C04 SING N N 13
VJG C03 C04 SING N N 14
VJG C12 C13 SING Y N 15
VJG C16 C17 DOUB Y N 16
VJG C13 C14 DOUB Y N 17
VJG C17 C14 SING Y N 18
VJG C17 C18 SING N N 19
VJG C18 N19 SING Y N 20
VJG C18 N22 DOUB Y N 21
VJG N19 N20 SING Y N 22
VJG N22 N21 SING Y N 23
VJG N20 N21 DOUB Y N 24
VJG C13 H1 SING N N 25
VJG C14 H2 SING N N 26
VJG C15 H3 SING N N 27
VJG C16 H4 SING N N 28
VJG C03 H5 SING N N 29
VJG C04 H6 SING N N 30
VJG C04 H7 SING N N 31
VJG C05 H8 SING N N 32
VJG C05 H9 SING N N 33
VJG C06 H10 SING N N 34
VJG C06 H11 SING N N 35
VJG C07 H12 SING N N 36
VJG C08 H13 SING N N 37
VJG C08 H14 SING N N 38
VJG N19 H15 SING N N 39
VJG O11 H16 SING N N 40
#
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
VJG SMILES ACDLabs 12.01 c1(ccc(cc1)c2nnnn2)C(C3CCCC3CC(O)=O)=O
VJG InChI InChI 1.03 InChI=1S/C15H16N4O3/c20-13(21)8-11-2-1-3-12(11)14(22)9-4-6-10(7-5-9)15-16-18-19-17-15/h4-7,11-12H,1-3,8H2,(H,20,21)(H,16,17,18,19)/t11-,12+/m0/s1
VJG InChIKey InChI 1.03 IOEUDWHXQXYIDQ-NWDGAFQWSA-N
VJG SMILES_CANONICAL CACTVS 3.385 OC(=O)C[C@@H]1CCC[C@H]1C(=O)c2ccc(cc2)c3[nH]nnn3
VJG SMILES CACTVS 3.385 OC(=O)C[CH]1CCC[CH]1C(=O)c2ccc(cc2)c3[nH]nnn3
VJG SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1cc(ccc1c2[nH]nnn2)C(=O)[C@@H]3CCC[C@H]3CC(=O)O
VJG SMILES "OpenEye OEToolkits" 2.0.7 c1cc(ccc1c2[nH]nnn2)C(=O)C3CCCC3CC(=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
VJG "SYSTEMATIC NAME" ACDLabs 12.01 "{(1S,2R)-2-[4-(1H-tetrazol-5-yl)benzene-1-carbonyl]cyclopentyl}acetic acid"
VJG "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-[(1~{S},2~{R})-2-[4-(1~{H}-1,2,3,4-tetrazol-5-yl)phenyl]carbonylcyclopentyl]ethanoic 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
VJG 'Create component' 2020-08-17 RCSB
VJG 'Initial release' 2021-09-08 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 '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
VJG C12 C 4.299 1.754 1
VJG C13 C 5.598 1.004 2
VJG C14 C 5.598 -0.496 3
VJG C15 C 3.000 1.004 4
VJG C16 C 3.000 -0.496 5
VJG C17 C 4.299 -1.246 6
VJG C18 C 4.299 -2.747 7
VJG C02 C 4.299 3.253 8
VJG C03 C 5.598 4.003 9
VJG C04 C 5.755 5.495 10
VJG C05 C 7.222 5.807 11
VJG C06 C 7.972 4.508 12
VJG C07 C 6.968 3.393 13
VJG C08 C 7.280 1.926 14
VJG C09 C 8.707 1.463 15
VJG N19 N 5.513 -3.628 16
VJG N20 N 5.049 -5.055 17
VJG N21 N 3.549 -5.055 18
VJG N22 N 3.086 -3.628 19
VJG O01 O 3.000 4.003 20
VJG O10 O 9.019 -0.004 21
VJG O11 O 9.822 2.466 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
VJG O01 C02 DOUBLE NONE 1
VJG O10 C09 DOUBLE NONE 2
VJG C03 C02 SINGLE BEGINDASH 3
VJG C02 C12 SINGLE NONE 4
VJG C07 C06 SINGLE NONE 5
VJG C07 C08 SINGLE BEGINWEDGE 6
VJG C07 C03 SINGLE NONE 7
VJG C09 C08 SINGLE NONE 8
VJG C09 O11 SINGLE NONE 9
VJG C06 C05 SINGLE NONE 10
VJG C15 C12 SINGLE NONE 11
VJG C15 C16 DOUBLE NONE 12
VJG C05 C04 SINGLE NONE 13
VJG C03 C04 SINGLE NONE 14
VJG C12 C13 DOUBLE NONE 15
VJG C16 C17 SINGLE NONE 16
VJG C13 C14 SINGLE NONE 17
VJG C17 C14 DOUBLE NONE 18
VJG C17 C18 SINGLE NONE 19
VJG C18 N19 SINGLE NONE 20
VJG C18 N22 DOUBLE NONE 21
VJG N19 N20 SINGLE NONE 22
VJG N22 N21 SINGLE NONE 23
VJG N20 N21 DOUBLE 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
VJG MurckoScaffold S1 scaffold 'O=C(c1ccc(-c2nnn[nH]2)cc1)C1CCCC1' InChI=1S/C13H14N4O/c18-12(9-3-1-2-4-9)10-5-7-11(8-6-10)13-14-16-17-15-13/h5-9H,1-4H2,(H,14,15,16,17) DDFFQODXYZPSQL-UHFFFAOYSA-N
VJG cyclopentane F1 fragment C1CCCC1 InChI=1S/C5H10/c1-2-4-5-3-1/h1-5H2 RGSFGYAAUTVSQA-UHFFFAOYSA-N
VJG 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
VJG C12 S1 1
VJG C13 S1 1
VJG C14 S1 1
VJG C15 S1 1
VJG C16 S1 1
VJG C17 S1 1
VJG C18 S1 1
VJG C02 S1 1
VJG C03 S1 1
VJG C04 S1 1
VJG C05 S1 1
VJG C06 S1 1
VJG C07 S1 1
VJG N19 S1 1
VJG N20 S1 1
VJG N21 S1 1
VJG N22 S1 1
VJG O01 S1 1
VJG C03 F1 1
VJG C07 F1 1
VJG C06 F1 1
VJG C05 F1 1
VJG C04 F1 1
VJG C12 F2 1
VJG C15 F2 1
VJG C16 F2 1
VJG C17 F2 1
VJG C14 F2 1
VJG C13 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id VJG
_pdbe_chem_comp_rdkit_properties.exactmw 300.122
_pdbe_chem_comp_rdkit_properties.amw 300.318
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 22
_pdbe_chem_comp_rdkit_properties.NumAtoms 38
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.400
_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 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 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 148.917
_pdbe_chem_comp_rdkit_properties.tpsa 108.830
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.506
_pdbe_chem_comp_rdkit_properties.CrippenMR 75.440
_pdbe_chem_comp_rdkit_properties.chi0v 10.514
_pdbe_chem_comp_rdkit_properties.chi1v 5.660
_pdbe_chem_comp_rdkit_properties.chi2v 2.474
_pdbe_chem_comp_rdkit_properties.chi3v 2.474
_pdbe_chem_comp_rdkit_properties.chi4v 1.555
_pdbe_chem_comp_rdkit_properties.chi0n 26.514
_pdbe_chem_comp_rdkit_properties.chi1n 13.515
_pdbe_chem_comp_rdkit_properties.chi2n 2.474
_pdbe_chem_comp_rdkit_properties.chi3n 2.474
_pdbe_chem_comp_rdkit_properties.chi4n 1.555
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.570
_pdbe_chem_comp_rdkit_properties.kappa1 4.711
_pdbe_chem_comp_rdkit_properties.kappa2 6.047
_pdbe_chem_comp_rdkit_properties.kappa3 2.878
_pdbe_chem_comp_rdkit_properties.Phi 1.295
#
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
VJG UniChem PubChem 156595824
VJG UniChem BRENDA 275522
#
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
VJG C12 1.140 -0.296 0.500 ETKDGv3 1
VJG C13 2.282 -0.585 1.151 ETKDGv3 2
VJG C14 3.575 -0.039 0.689 ETKDGv3 3
VJG C15 1.208 0.567 -0.709 ETKDGv3 4
VJG C16 2.380 1.060 -1.128 ETKDGv3 5
VJG C17 3.634 0.752 -0.397 ETKDGv3 6
VJG C18 4.920 1.310 -0.875 ETKDGv3 7
VJG C02 -0.155 -0.850 0.975 ETKDGv3 8
VJG C03 -1.482 -0.233 0.572 ETKDGv3 9
VJG C04 -2.524 -0.349 1.691 ETKDGv3 10
VJG C05 -3.374 -1.578 1.384 ETKDGv3 11
VJG C06 -3.031 -2.031 -0.035 ETKDGv3 12
VJG C07 -2.086 -0.981 -0.631 ETKDGv3 13
VJG C08 -2.789 -0.044 -1.645 ETKDGv3 14
VJG C09 -3.906 0.768 -1.057 ETKDGv3 15
VJG N19 6.192 1.100 -0.279 ETKDGv3 16
VJG N20 7.060 1.828 -1.092 ETKDGv3 17
VJG N21 6.397 2.383 -2.024 ETKDGv3 18
VJG N22 5.033 2.072 -1.913 ETKDGv3 19
VJG O01 -0.152 -1.890 1.692 ETKDGv3 20
VJG O10 -5.068 0.285 -0.979 ETKDGv3 21
VJG O11 -3.656 2.052 -0.584 ETKDGv3 22
VJG H1 2.276 -1.211 2.035 ETKDGv3 23
VJG H2 4.463 -0.292 1.251 ETKDGv3 24
VJG H3 0.318 0.791 -1.279 ETKDGv3 25
VJG H4 2.404 1.681 -2.015 ETKDGv3 26
VJG H5 -1.325 0.845 0.350 ETKDGv3 27
VJG H6 -3.173 0.554 1.689 ETKDGv3 28
VJG H7 -2.061 -0.418 2.700 ETKDGv3 29
VJG H8 -4.455 -1.328 1.461 ETKDGv3 30
VJG H9 -3.148 -2.391 2.109 ETKDGv3 31
VJG H10 -2.506 -3.010 0.013 ETKDGv3 32
VJG H11 -3.950 -2.172 -0.645 ETKDGv3 33
VJG H12 -1.285 -1.506 -1.201 ETKDGv3 34
VJG H13 -2.038 0.649 -2.080 ETKDGv3 35
VJG H14 -3.187 -0.651 -2.487 ETKDGv3 36
VJG H15 6.463 0.545 0.561 ETKDGv3 37
VJG H16 -4.396 2.609 -0.175 ETKDGv3 38
#