data_JD7
#
_chem_comp.id JD7
_chem_comp.name 4-[(5S)-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-5-yl]benzonitrile
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C14 H13 N3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms fadrozole
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2018-08-30
_chem_comp.pdbx_modified_date 2020-06-17
_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 223.273
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code JD7
_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 6M7X
_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
JD7 C01 C1 C 0 1 N N N N N N 52.059 -47.786 -3.943 2.909 2.070 -0.118 C01 JD7 1
JD7 C02 C2 C 0 1 N N N N N N 53.115 -46.682 -4.105 1.388 1.934 -0.222 C02 JD7 2
JD7 C03 C3 C 0 1 N N S N N N 52.649 -45.202 -4.117 0.908 0.786 0.673 C03 JD7 3
JD7 N04 N1 N 0 1 Y N N N N N 51.597 -45.029 -3.143 1.707 -0.405 0.376 N04 JD7 4
JD7 C05 C4 C 0 1 Y N N N N N 51.171 -43.812 -2.622 1.438 -1.687 0.677 C05 JD7 5
JD7 N06 N2 N 0 1 Y N N N N N 50.169 -44.007 -1.743 2.413 -2.434 0.227 N06 JD7 6
JD7 C07 C5 C 0 1 Y N N N N N 49.945 -45.385 -1.722 3.330 -1.654 -0.371 C07 JD7 7
JD7 C08 C6 C 0 1 Y N N N N N 50.819 -46.044 -2.580 2.907 -0.386 -0.287 C08 JD7 8
JD7 C09 C7 C 0 1 N N N N N N 50.975 -47.479 -2.899 3.573 0.865 -0.798 C09 JD7 9
JD7 C10 C8 C 0 1 Y N N N N N 52.196 -44.755 -5.538 -0.546 0.502 0.396 C10 JD7 10
JD7 C11 C9 C 0 1 Y N N N N N 53.078 -44.626 -6.620 -1.476 0.621 1.413 C11 JD7 11
JD7 C12 C10 C 0 1 Y N N N N N 52.671 -44.217 -7.900 -2.809 0.363 1.167 C12 JD7 12
JD7 C13 C11 C 0 1 Y N N N N N 51.349 -43.899 -8.196 -3.218 -0.018 -0.113 C13 JD7 13
JD7 C14 C12 C 0 1 Y N N N N N 50.458 -44.016 -7.131 -2.273 -0.136 -1.135 C14 JD7 14
JD7 C15 C13 C 0 1 Y N N N N N 50.867 -44.425 -5.856 -0.945 0.130 -0.875 C15 JD7 15
JD7 C16 C14 C 0 1 N N N N N N 50.875 -43.481 -9.462 -4.599 -0.288 -0.376 C16 JD7 16
JD7 N17 N3 N 0 1 N N N N N N 50.480 -43.135 -10.510 -5.695 -0.502 -0.585 N17 JD7 17
JD7 H2 H1 H 0 1 N N N N N N 51.567 -47.937 -4.915 3.227 2.988 -0.612 H2 JD7 18
JD7 H1 H2 H 0 1 N N N N N N 52.572 -48.712 -3.644 3.201 2.102 0.932 H1 JD7 19
JD7 H3 H3 H 0 1 N N N N N N 53.633 -46.866 -5.058 0.918 2.865 0.098 H3 JD7 20
JD7 H4 H4 H 0 1 N N N N N N 53.827 -46.791 -3.274 1.112 1.727 -1.256 H4 JD7 21
JD7 H5 H5 H 0 1 N N N N N N 53.509 -44.579 -3.831 1.036 1.061 1.720 H5 JD7 22
JD7 H6 H6 H 0 1 N N N N N N 51.584 -42.849 -2.884 0.563 -2.042 1.202 H6 JD7 23
JD7 H7 H7 H 0 1 N N N N N N 49.193 -45.874 -1.120 4.245 -1.990 -0.837 H7 JD7 24
JD7 H9 H8 H 0 1 N N N N N N 50.014 -47.852 -3.282 3.445 0.935 -1.879 H9 JD7 25
JD7 H8 H9 H 0 1 N N N N N N 51.231 -48.011 -1.971 4.635 0.843 -0.553 H8 JD7 26
JD7 H10 H10 H 0 1 N N N N N N 54.122 -44.852 -6.461 -1.159 0.916 2.402 H10 JD7 27
JD7 H11 H11 H 0 1 N N N N N N 53.411 -44.147 -8.683 -3.534 0.456 1.961 H11 JD7 28
JD7 H12 H12 H 0 1 N N N N N N 49.416 -43.783 -7.295 -2.582 -0.431 -2.126 H12 JD7 29
JD7 H13 H13 H 0 1 N N N N N N 50.123 -44.490 -5.076 -0.213 0.040 -1.664 H13 JD7 30
#
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
JD7 N17 C16 TRIP N N 1
JD7 C16 C13 SING N N 2
JD7 C13 C12 DOUB Y N 3
JD7 C13 C14 SING Y N 4
JD7 C12 C11 SING Y N 5
JD7 C14 C15 DOUB Y N 6
JD7 C11 C10 DOUB Y N 7
JD7 C15 C10 SING Y N 8
JD7 C10 C03 SING N N 9
JD7 C03 C02 SING N N 10
JD7 C03 N04 SING N N 11
JD7 C02 C01 SING N N 12
JD7 C01 C09 SING N N 13
JD7 N04 C05 SING Y N 14
JD7 N04 C08 SING Y N 15
JD7 C09 C08 SING N N 16
JD7 C05 N06 DOUB Y N 17
JD7 C08 C07 DOUB Y N 18
JD7 N06 C07 SING Y N 19
JD7 C01 H2 SING N N 20
JD7 C01 H1 SING N N 21
JD7 C02 H3 SING N N 22
JD7 C02 H4 SING N N 23
JD7 C03 H5 SING N N 24
JD7 C05 H6 SING N N 25
JD7 C07 H7 SING N N 26
JD7 C09 H9 SING N N 27
JD7 C09 H8 SING N N 28
JD7 C11 H10 SING N N 29
JD7 C12 H11 SING N N 30
JD7 C14 H12 SING N N 31
JD7 C15 H13 SING N N 32
#
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
JD7 SMILES ACDLabs 12.01 "C1Cc3n(C(C1)c2ccc(cc2)C#N)cnc3"
JD7 InChI InChI 1.03 InChI=1S/C14H13N3/c15-8-11-4-6-12(7-5-11)14-3-1-2-13-9-16-10-17(13)14/h4-7,9-10,14H,1-3H2/t14-/m0/s1
JD7 InChIKey InChI 1.03 CLPFFLWZZBQMAO-AWEZNQCLSA-N
JD7 SMILES_CANONICAL CACTVS 3.385 "N#Cc1ccc(cc1)[C@@H]2CCCc3cncn23"
JD7 SMILES CACTVS 3.385 "N#Cc1ccc(cc1)[CH]2CCCc3cncn23"
JD7 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1cc(ccc1C#N)[C@@H]2CCCc3n2cnc3"
JD7 SMILES "OpenEye OEToolkits" 2.0.6 "c1cc(ccc1C#N)C2CCCc3n2cnc3"
#
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
JD7 "SYSTEMATIC NAME" ACDLabs 12.01 4-[(5S)-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-5-yl]benzonitrile
JD7 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 4-[(5~{S})-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-5-yl]benzenecarbonitrile
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
JD7 'Create component' 2018-08-30 RCSB
JD7 'Initial release' 2018-11-21 RCSB
JD7 'Modify synonyms' 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id JD7
_pdbx_chem_comp_synonyms.name fadrozole
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id JD7
_pdbe_chem_comp_synonyms.name fadrozole
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
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
JD7 C01 C 3.000 4.500 1
JD7 C02 C 3.000 3.000 2
JD7 C03 C 4.299 2.250 3
JD7 N04 N 5.598 3.000 4
JD7 C05 C 7.018 2.543 5
JD7 N06 N 7.893 3.750 6
JD7 C07 C 7.018 4.957 7
JD7 C08 C 5.598 4.500 8
JD7 C09 C 4.299 5.250 9
JD7 C10 C 4.299 0.750 10
JD7 C11 C 3.000 0.000 11
JD7 C12 C 3.000 -1.500 12
JD7 C13 C 4.299 -2.250 13
JD7 C14 C 5.598 -1.500 14
JD7 C15 C 5.598 0.000 15
JD7 C16 C 4.299 -3.750 16
JD7 N17 N 4.299 -5.250 17
#
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
JD7 N17 C16 TRIPLE NONE 1
JD7 C16 C13 SINGLE NONE 2
JD7 C13 C12 SINGLE NONE 3
JD7 C13 C14 DOUBLE NONE 4
JD7 C12 C11 DOUBLE NONE 5
JD7 C14 C15 SINGLE NONE 6
JD7 C11 C10 SINGLE NONE 7
JD7 C15 C10 DOUBLE NONE 8
JD7 C03 C10 SINGLE BEGINDASH 9
JD7 C03 C02 SINGLE NONE 10
JD7 C03 N04 SINGLE NONE 11
JD7 C02 C01 SINGLE NONE 12
JD7 C01 C09 SINGLE NONE 13
JD7 N04 C05 SINGLE NONE 14
JD7 N04 C08 SINGLE NONE 15
JD7 C09 C08 SINGLE NONE 16
JD7 C05 N06 DOUBLE NONE 17
JD7 C08 C07 DOUBLE NONE 18
JD7 N06 C07 SINGLE NONE 19
#
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
JD7 MurckoScaffold S1 scaffold 'c1ccc([C@@H]2CCCc3cncn32)cc1' InChI=1S/C13H14N2/c1-2-5-11(6-3-1)13-8-4-7-12-9-14-10-15(12)13/h1-3,5-6,9-10,13H,4,7-8H2/t13-/m0/s1 XDPBQHBDPQIORF-ZDUSSCGKSA-N
JD7 imidazole F1 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
JD7 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
JD7 C01 S1 1
JD7 C02 S1 1
JD7 C03 S1 1
JD7 N04 S1 1
JD7 C05 S1 1
JD7 N06 S1 1
JD7 C07 S1 1
JD7 C08 S1 1
JD7 C09 S1 1
JD7 C10 S1 1
JD7 C11 S1 1
JD7 C12 S1 1
JD7 C13 S1 1
JD7 C14 S1 1
JD7 C15 S1 1
JD7 C07 F1 1
JD7 C08 F1 1
JD7 N04 F1 1
JD7 C05 F1 1
JD7 N06 F1 1
JD7 C10 F2 1
JD7 C11 F2 1
JD7 C12 F2 1
JD7 C13 F2 1
JD7 C14 F2 1
JD7 C15 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id JD7
_pdbe_chem_comp_rdkit_properties.exactmw 223.111
_pdbe_chem_comp_rdkit_properties.amw 223.279
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 0
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 1
_pdbe_chem_comp_rdkit_properties.NumHBD 0
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 17
_pdbe_chem_comp_rdkit_properties.NumAtoms 30
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.286
_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 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_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 118.603
_pdbe_chem_comp_rdkit_properties.tpsa 41.610
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.516
_pdbe_chem_comp_rdkit_properties.CrippenMR 63.663
_pdbe_chem_comp_rdkit_properties.chi0v 8.342
_pdbe_chem_comp_rdkit_properties.chi1v 4.592
_pdbe_chem_comp_rdkit_properties.chi2v 2.094
_pdbe_chem_comp_rdkit_properties.chi3v 2.094
_pdbe_chem_comp_rdkit_properties.chi4v 1.340
_pdbe_chem_comp_rdkit_properties.chi0n 21.342
_pdbe_chem_comp_rdkit_properties.chi1n 11.092
_pdbe_chem_comp_rdkit_properties.chi2n 2.094
_pdbe_chem_comp_rdkit_properties.chi3n 2.094
_pdbe_chem_comp_rdkit_properties.chi4n 1.340
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.080
_pdbe_chem_comp_rdkit_properties.kappa1 3.229
_pdbe_chem_comp_rdkit_properties.kappa2 4.061
_pdbe_chem_comp_rdkit_properties.kappa3 1.719
_pdbe_chem_comp_rdkit_properties.Phi 0.771
#
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
JD7 UniChem ChEMBL CHEMBL31215
JD7 UniChem PDBe JD7
JD7 UniChem ZINC ZINC000000006398
JD7 UniChem fdasrs K9H9854X63
JD7 UniChem 'PubChem TPHARMA' 96068276
JD7 UniChem Nikkaji J551.415K
JD7 UniChem BindingDb 9920
JD7 UniChem BRENDA 41105
JD7 UniChem 'Probes And Drugs' PD119612
JD7 UniChem PubChem 13688212
JD7 UniChem SureChEMBL SCHEMBL13449014
#
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
JD7 C01 0.175 -1.022 -2.204 ETKDGv3 1
JD7 C02 0.429 -1.872 -0.939 ETKDGv3 2
JD7 C03 -0.220 -1.265 0.329 ETKDGv3 3
JD7 N04 -1.582 -0.832 0.025 ETKDGv3 4
JD7 C05 -2.580 -0.308 0.892 ETKDGv3 5
JD7 N06 -3.562 0.239 0.244 ETKDGv3 6
JD7 C07 -3.230 0.109 -1.142 ETKDGv3 7
JD7 C08 -2.059 -0.492 -1.259 ETKDGv3 8
JD7 C09 -1.325 -0.856 -2.508 ETKDGv3 9
JD7 C10 0.613 -0.123 0.883 ETKDGv3 10
JD7 C11 0.420 1.278 0.414 ETKDGv3 11
JD7 C12 1.190 2.264 0.888 ETKDGv3 12
JD7 C13 2.246 1.972 1.880 ETKDGv3 13
JD7 C14 2.436 0.713 2.299 ETKDGv3 14
JD7 C15 1.591 -0.379 1.773 ETKDGv3 15
JD7 C16 3.068 3.040 2.387 ETKDGv3 16
JD7 N17 3.728 3.898 2.794 ETKDGv3 17
JD7 H2 0.666 -1.511 -3.074 ETKDGv3 18
JD7 H1 0.644 -0.022 -2.082 ETKDGv3 19
JD7 H3 0.006 -2.887 -1.107 ETKDGv3 20
JD7 H4 1.524 -1.994 -0.788 ETKDGv3 21
JD7 H5 -0.286 -2.068 1.097 ETKDGv3 22
JD7 H6 -2.528 -0.346 1.972 ETKDGv3 23
JD7 H7 -3.845 0.464 -1.959 ETKDGv3 24
JD7 H9 -1.734 -1.813 -2.897 ETKDGv3 25
JD7 H8 -1.465 -0.068 -3.279 ETKDGv3 26
JD7 H10 -0.342 1.514 -0.316 ETKDGv3 27
JD7 H11 1.039 3.279 0.540 ETKDGv3 28
JD7 H12 3.208 0.480 3.023 ETKDGv3 29
JD7 H13 1.774 -1.390 2.116 ETKDGv3 30
#