data_58G
#
_chem_comp.id 58G
_chem_comp.name 6-{[(1R,3S)-3-phenylcyclopentyl]amino}pyridine-3-carboxamide
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C17 H19 N3 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2015-08-20
_chem_comp.pdbx_modified_date 2016-08-24
_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 281.352
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 58G
_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 5D9F
_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
58G C17 C1 C 0 1 Y N N N N N -18.244 45.316 -12.721 6.685 0.930 -0.106 C17 58G 1
58G C16 C2 C 0 1 Y N N N N N -17.314 44.652 -11.965 5.578 1.613 0.362 C16 58G 2
58G C18 C3 C 0 1 Y N N N N N -19.112 44.619 -13.526 6.551 -0.364 -0.573 C18 58G 3
58G C5 C4 C 0 1 Y N N N N N -19.887 42.328 -7.089 -3.684 -1.044 -0.184 C5 58G 4
58G C15 C5 C 0 1 Y N N N N N -17.252 43.282 -12.019 4.339 1.001 0.368 C15 58G 5
58G C19 C6 C 0 1 Y N N N N N -19.046 43.249 -13.572 5.311 -0.975 -0.573 C19 58G 6
58G C6 C7 C 0 1 Y N N N N N -18.828 41.973 -7.883 -2.327 -0.862 -0.207 C6 58G 7
58G C21 C8 C 0 1 Y N N N N N -21.181 40.805 -8.344 -3.921 1.347 0.025 C21 58G 8
58G C4 C9 C 0 1 Y N N N N N -21.090 41.726 -7.332 -4.509 0.085 -0.068 C4 58G 9
58G C14 C10 C 0 1 Y N N N N N -18.115 42.581 -12.818 4.207 -0.296 -0.093 C14 58G 10
58G C7 C11 C 0 1 Y N N N N N -18.988 41.043 -8.883 -1.809 0.428 -0.110 C7 58G 11
58G C2 C12 C 0 1 N N N N N N -22.255 42.077 -6.514 -5.977 -0.060 -0.045 C2 58G 12
58G C11 C13 C 0 1 N N N N N N -16.642 40.707 -12.531 2.275 -1.026 1.342 C11 58G 13
58G C10 C14 C 0 1 N N N N N N -16.730 39.700 -11.419 0.751 -1.131 1.130 C10 58G 14
58G C13 C15 C 0 1 N N N N N N -18.935 40.578 -11.771 1.815 -0.092 -0.842 C13 58G 15
58G C12 C16 C 0 1 N N S N N N -18.045 41.107 -12.862 2.855 -0.961 -0.093 C12 58G 16
58G C9 C17 C 0 1 N N R N N N -18.063 39.894 -10.752 0.458 -0.537 -0.259 C9 58G 17
58G N20 N1 N 0 1 Y N N N N N -20.158 40.451 -9.123 -2.610 1.478 0.004 N20 58G 18
58G N1 N2 N 0 1 N N N N N N -22.090 43.225 -5.797 -6.760 1.032 0.066 N1 58G 19
58G N8 N3 N 0 1 N N N N N N -17.837 40.764 -9.626 -0.437 0.616 -0.133 N8 58G 20
58G O3 O1 O 0 1 N N N N N N -23.252 41.384 -6.515 -6.480 -1.163 -0.127 O3 58G 21
58G H1 H1 H 0 1 N N N N N N -18.295 46.394 -12.684 7.653 1.408 -0.110 H1 58G 22
58G H2 H2 H 0 1 N N N N N N -16.635 45.203 -11.331 5.682 2.626 0.723 H2 58G 23
58G H3 H3 H 0 1 N N N N N N -19.843 45.147 -14.120 7.416 -0.899 -0.938 H3 58G 24
58G H4 H4 H 0 1 N N N N N N -19.775 43.057 -6.300 -4.109 -2.034 -0.258 H4 58G 25
58G H5 H5 H 0 1 N N N N N N -16.518 42.754 -11.428 3.475 1.535 0.734 H5 58G 26
58G H6 H6 H 0 1 N N N N N N -19.727 42.697 -14.202 5.207 -1.986 -0.938 H6 58G 27
58G H7 H7 H 0 1 N N N N N N -17.861 42.427 -7.722 -1.665 -1.710 -0.300 H7 58G 28
58G H8 H8 H 0 1 N N N N N N -22.139 40.338 -8.521 -4.545 2.224 0.115 H8 58G 29
58G H9 H9 H 0 1 N N N N N N -16.158 40.258 -13.411 2.522 -0.119 1.895 H9 58G 30
58G H10 H10 H 0 1 N N N N N N -16.065 41.584 -12.203 2.649 -1.905 1.867 H10 58G 31
58G H11 H11 H 0 1 N N N N N N -16.657 38.681 -11.826 0.440 -2.176 1.162 H11 58G 32
58G H12 H12 H 0 1 N N N N N N -15.918 39.865 -10.695 0.227 -0.562 1.898 H12 58G 33
58G H13 H13 H 0 1 N N N N N N -19.481 41.408 -11.299 1.987 0.966 -0.643 H13 58G 34
58G H14 H14 H 0 1 N N N N N N -19.654 39.859 -12.191 1.852 -0.288 -1.914 H14 58G 35
58G H15 H15 H 0 1 N N N N N N -18.349 40.718 -13.845 2.916 -1.958 -0.530 H15 58G 36
58G H16 H16 H 0 1 N N N N N N -18.496 38.930 -10.447 0.006 -1.293 -0.901 H16 58G 37
58G H17 H17 H 0 1 N N N N N N -22.828 43.559 -5.210 -6.359 1.912 0.132 H17 58G 38
58G H18 H18 H 0 1 N N N N N N -21.231 43.733 -5.858 -7.725 0.936 0.081 H18 58G 39
58G H19 H19 H 0 1 N N N N N N -17.170 40.329 -9.021 -0.069 1.511 -0.066 H19 58G 40
#
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
58G C19 C18 DOUB Y N 1
58G C19 C14 SING Y N 2
58G C18 C17 SING Y N 3
58G C12 C14 SING N N 4
58G C12 C11 SING N N 5
58G C12 C13 SING N N 6
58G C14 C15 DOUB Y N 7
58G C17 C16 DOUB Y N 8
58G C11 C10 SING N N 9
58G C15 C16 SING Y N 10
58G C13 C9 SING N N 11
58G C10 C9 SING N N 12
58G C9 N8 SING N N 13
58G N8 C7 SING N N 14
58G N20 C7 DOUB Y N 15
58G N20 C21 SING Y N 16
58G C7 C6 SING Y N 17
58G C21 C4 DOUB Y N 18
58G C6 C5 DOUB Y N 19
58G C4 C5 SING Y N 20
58G C4 C2 SING N N 21
58G O3 C2 DOUB N N 22
58G C2 N1 SING N N 23
58G C17 H1 SING N N 24
58G C16 H2 SING N N 25
58G C18 H3 SING N N 26
58G C5 H4 SING N N 27
58G C15 H5 SING N N 28
58G C19 H6 SING N N 29
58G C6 H7 SING N N 30
58G C21 H8 SING N N 31
58G C11 H9 SING N N 32
58G C11 H10 SING N N 33
58G C10 H11 SING N N 34
58G C10 H12 SING N N 35
58G C13 H13 SING N N 36
58G C13 H14 SING N N 37
58G C12 H15 SING N N 38
58G C9 H16 SING N N 39
58G N1 H17 SING N N 40
58G N1 H18 SING N N 41
58G N8 H19 SING N N 42
#
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
58G SMILES ACDLabs 12.01 c1ccc(cc1)C2CCC(C2)Nc3ccc(cn3)C(N)=O
58G InChI InChI 1.03 InChI=1S/C17H19N3O/c18-17(21)14-7-9-16(19-11-14)20-15-8-6-13(10-15)12-4-2-1-3-5-12/h1-5,7,9,11,13,15H,6,8,10H2,(H2,18,21)(H,19,20)/t13-,15+/m0/s1
58G InChIKey InChI 1.03 JBSAILAEEJVXKB-DZGCQCFKSA-N
58G SMILES_CANONICAL CACTVS 3.385 NC(=O)c1ccc(N[C@@H]2CC[C@@H](C2)c3ccccc3)nc1
58G SMILES CACTVS 3.385 NC(=O)c1ccc(N[CH]2CC[CH](C2)c3ccccc3)nc1
58G SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 c1ccc(cc1)[C@H]2CC[C@H](C2)Nc3ccc(cn3)C(=O)N
58G SMILES "OpenEye OEToolkits" 1.9.2 c1ccc(cc1)C2CCC(C2)Nc3ccc(cn3)C(=O)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
58G "SYSTEMATIC NAME" ACDLabs 12.01 6-{[(1R,3S)-3-phenylcyclopentyl]amino}pyridine-3-carboxamide
58G "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 6-[[(1R,3S)-3-phenylcyclopentyl]amino]pyridine-3-carboxamide
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
58G 'Create component' 2015-08-20 RCSB
58G 'Initial release' 2016-08-31 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
58G C17 C 3.882 3.797 1
58G C16 C 3.000 2.584 2
58G C18 C 5.373 3.640 3
58G C5 C 12.532 -2.117 4
58G C15 C 3.610 1.214 5
58G C19 C 5.984 2.270 6
58G C6 C 11.233 -2.867 7
58G C21 C 11.233 0.133 8
58G C4 C 12.532 -0.617 9
58G C14 C 5.102 1.057 10
58G C7 C 9.934 -2.117 11
58G C2 C 13.831 0.133 12
58G C11 C 4.962 -1.613 13
58G C10 C 5.966 -2.728 14
58G C13 C 7.179 -0.625 15
58G C12 C 5.712 -0.314 16
58G C9 C 7.336 -2.117 17
58G N20 N 9.934 -0.617 18
58G N1 N 13.831 1.633 19
58G N8 N 8.635 -2.867 20
58G O3 O 15.130 -0.617 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
58G C19 C18 SINGLE NONE 1
58G C19 C14 DOUBLE NONE 2
58G C18 C17 DOUBLE NONE 3
58G C12 C14 SINGLE BEGINDASH 4
58G C12 C11 SINGLE NONE 5
58G C12 C13 SINGLE NONE 6
58G C14 C15 SINGLE NONE 7
58G C17 C16 SINGLE NONE 8
58G C11 C10 SINGLE NONE 9
58G C15 C16 DOUBLE NONE 10
58G C13 C9 SINGLE NONE 11
58G C10 C9 SINGLE NONE 12
58G C9 N8 SINGLE BEGINDASH 13
58G N8 C7 SINGLE NONE 14
58G N20 C7 DOUBLE NONE 15
58G N20 C21 SINGLE NONE 16
58G C7 C6 SINGLE NONE 17
58G C21 C4 DOUBLE NONE 18
58G C6 C5 DOUBLE NONE 19
58G C4 C5 SINGLE NONE 20
58G C4 C2 SINGLE NONE 21
58G O3 C2 DOUBLE NONE 22
58G C2 N1 SINGLE 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
58G MurckoScaffold S1 scaffold 'c1ccc([C@H]2CC[C@@H](Nc3ccccn3)C2)cc1' InChI=1S/C16H18N2/c1-2-6-13(7-3-1)14-9-10-15(12-14)18-16-8-4-5-11-17-16/h1-8,11,14-15H,9-10,12H2,(H,17,18)/t14-,15+/m0/s1 XPFOSHQMIOCQHR-LSDHHAIUSA-N
58G amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
58G cyclopentane F2 fragment C1CCCC1 InChI=1S/C5H10/c1-2-4-5-3-1/h1-5H2 RGSFGYAAUTVSQA-UHFFFAOYSA-N
58G phenyl F3 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
58G pyridine F4 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-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
58G C17 S1 1
58G C16 S1 1
58G C18 S1 1
58G C5 S1 1
58G C15 S1 1
58G C19 S1 1
58G C6 S1 1
58G C21 S1 1
58G C4 S1 1
58G C14 S1 1
58G C7 S1 1
58G C11 S1 1
58G C10 S1 1
58G C13 S1 1
58G C12 S1 1
58G C9 S1 1
58G N20 S1 1
58G N8 S1 1
58G N1 F1 1
58G C2 F1 1
58G O3 F1 1
58G C4 F1 1
58G C11 F2 1
58G C12 F2 1
58G C13 F2 1
58G C9 F2 1
58G C10 F2 1
58G C17 F3 1
58G C18 F3 1
58G C19 F3 1
58G C14 F3 1
58G C15 F3 1
58G C16 F3 1
58G C21 F4 1
58G C4 F4 1
58G C5 F4 1
58G C6 F4 1
58G C7 F4 1
58G N20 F4 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 58G
_pdbe_chem_comp_rdkit_properties.exactmw 281.153
_pdbe_chem_comp_rdkit_properties.amw 281.359
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 21
_pdbe_chem_comp_rdkit_properties.NumAtoms 40
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.294
_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 150.812
_pdbe_chem_comp_rdkit_properties.tpsa 68.010
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.439
_pdbe_chem_comp_rdkit_properties.CrippenMR 81.844
_pdbe_chem_comp_rdkit_properties.chi0v 10.250
_pdbe_chem_comp_rdkit_properties.chi1v 5.572
_pdbe_chem_comp_rdkit_properties.chi2v 2.304
_pdbe_chem_comp_rdkit_properties.chi3v 2.304
_pdbe_chem_comp_rdkit_properties.chi4v 1.402
_pdbe_chem_comp_rdkit_properties.chi0n 29.250
_pdbe_chem_comp_rdkit_properties.chi1n 14.914
_pdbe_chem_comp_rdkit_properties.chi2n 2.304
_pdbe_chem_comp_rdkit_properties.chi3n 2.304
_pdbe_chem_comp_rdkit_properties.chi4n 1.402
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.360
_pdbe_chem_comp_rdkit_properties.kappa1 3.691
_pdbe_chem_comp_rdkit_properties.kappa2 5.955
_pdbe_chem_comp_rdkit_properties.kappa3 3.214
_pdbe_chem_comp_rdkit_properties.Phi 1.047
#
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
58G UniChem PDBe 58G
58G UniChem PubChem 121499142
#
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
58G C17 -4.718 2.474 -1.760 ETKDGv3 1
58G C16 -4.493 2.900 -0.365 ETKDGv3 2
58G C18 -4.166 1.341 -2.210 ETKDGv3 3
58G C5 4.316 -1.188 -1.034 ETKDGv3 4
58G C15 -3.739 2.155 0.453 ETKDGv3 5
58G C19 -3.331 0.516 -1.313 ETKDGv3 6
58G C6 3.082 -1.694 -1.119 ETKDGv3 7
58G C21 3.691 0.134 0.907 ETKDGv3 8
58G C4 4.653 -0.210 0.030 ETKDGv3 9
58G C14 -3.124 0.893 -0.034 ETKDGv3 10
58G C7 2.056 -1.275 -0.143 ETKDGv3 11
58G C2 6.029 0.334 0.120 ETKDGv3 12
58G C11 -2.736 -1.389 1.033 ETKDGv3 13
58G C10 -1.596 -2.257 0.522 ETKDGv3 14
58G C13 -0.794 0.019 0.458 ETKDGv3 15
58G C12 -2.262 0.069 0.905 ETKDGv3 16
58G C9 -0.339 -1.415 0.703 ETKDGv3 17
58G N20 2.371 -0.424 0.793 ETKDGv3 18
58G N1 6.312 1.560 0.801 ETKDGv3 19
58G N8 0.727 -1.811 -0.225 ETKDGv3 20
58G O3 6.977 -0.287 -0.431 ETKDGv3 21
58G H1 -5.329 3.079 -2.417 ETKDGv3 22
58G H2 -4.940 3.819 -0.006 ETKDGv3 23
58G H3 -4.328 1.027 -3.233 ETKDGv3 24
58G H4 5.065 -1.494 -1.754 ETKDGv3 25
58G H5 -3.581 2.481 1.473 ETKDGv3 26
58G H6 -2.890 -0.393 -1.701 ETKDGv3 27
58G H7 2.839 -2.404 -1.899 ETKDGv3 28
58G H8 3.891 0.810 1.726 ETKDGv3 29
58G H9 -2.925 -1.627 2.103 ETKDGv3 30
58G H10 -3.672 -1.597 0.468 ETKDGv3 31
58G H11 -1.527 -3.212 1.086 ETKDGv3 32
58G H12 -1.767 -2.479 -0.555 ETKDGv3 33
58G H13 -0.689 0.265 -0.623 ETKDGv3 34
58G H14 -0.177 0.737 1.041 ETKDGv3 35
58G H15 -2.293 0.524 1.922 ETKDGv3 36
58G H16 0.016 -1.523 1.753 ETKDGv3 37
58G H17 5.553 2.194 1.133 ETKDGv3 38
58G H18 7.299 1.886 0.897 ETKDGv3 39
58G H19 0.535 -2.539 -0.951 ETKDGv3 40
#