data_658
#
_chem_comp.id 658
_chem_comp.name N-(4-chlorophenyl)-2-(3,5-dimethyl-1H-pyrazol-1-yl)pyrimidin-4-amine
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C15 H14 Cl N5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2016-01-26
_chem_comp.pdbx_modified_date 2018-03-02
_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 299.758
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 658
_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 5HOM
_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
658 N3 N1 N 0 1 Y N N N N N 38.605 55.973 48.995 -2.963 -1.691 0.075 N3 658 1
658 C4 C1 C 0 1 Y N N N N N 40.002 54.321 46.049 -3.723 1.045 -0.018 C4 658 2
658 N2 N2 N 0 1 Y N N N N N 40.458 56.294 47.108 -1.596 1.705 -0.131 N2 658 3
658 C7 C2 C 0 1 Y N N N N N 36.879 54.660 50.018 -1.286 -3.316 0.081 C7 658 4
658 C6 C3 C 0 1 Y N N N N N 37.626 55.811 49.899 -2.623 -2.970 0.119 C6 658 5
658 C9 C4 C 0 1 Y N N N N N 35.396 51.980 49.905 1.961 -1.561 -0.005 C9 658 6
658 C13 C5 C 0 1 Y N N N N N 33.191 52.322 50.810 2.629 0.616 0.745 C13 658 7
658 C8 C6 C 0 1 Y N N N N N 37.212 53.614 49.153 -0.337 -2.294 -0.002 C8 658 8
658 N5 N3 N 0 1 N N N N N N 36.510 52.416 49.150 1.016 -2.592 -0.043 N5 658 9
658 C1 C7 C 0 1 N N N N N N 42.023 57.372 45.559 -1.830 4.199 -0.232 C1 658 10
658 N1 N4 N 0 1 Y N N N N N 39.745 55.107 47.149 -2.442 0.591 -0.048 N1 658 11
658 CL1 CL1 CL 0 0 N N N N N N 31.783 50.397 52.071 4.994 1.765 0.101 CL1 658 12
658 C2 C8 C 0 1 Y N N N N N 41.149 56.230 45.976 -2.337 2.782 -0.149 C2 658 13
658 C3 C9 C 0 1 Y N N N N N 40.905 55.029 45.296 -3.680 2.395 -0.079 C3 658 14
658 N4 N5 N 0 1 Y N N N N N 38.185 53.720 48.235 -0.752 -1.031 -0.042 N4 658 15
658 C5 C10 C 0 1 Y N N N N N 38.816 54.920 48.184 -2.042 -0.744 -0.004 C5 658 16
658 C10 C11 C 0 1 Y N N N N N 35.392 50.688 50.417 3.161 -1.692 -0.691 C10 658 17
658 C11 C12 C 0 1 Y N N N N N 34.282 50.201 51.082 4.089 -0.671 -0.657 C11 658 18
658 C12 C13 C 0 1 Y N N N N N 33.195 51.025 51.272 3.825 0.483 0.060 C12 658 19
658 C14 C14 C 0 1 Y N N N N N 34.280 52.791 50.098 1.697 -0.403 0.714 C14 658 20
658 C15 C15 C 0 1 N N N N N N 39.380 52.998 45.766 -4.966 0.197 0.062 C15 658 21
658 H6 H1 H 0 1 N N N N N N 36.080 54.571 50.740 -0.981 -4.351 0.116 H6 658 22
658 H5 H2 H 0 1 N N N N N N 37.412 56.629 50.571 -3.383 -3.735 0.184 H5 658 23
658 H10 H3 H 0 1 N N N N N N 32.346 52.967 51.002 2.425 1.517 1.304 H10 658 24
658 H7 H4 H 0 1 N N N N N N 36.853 51.741 48.497 1.308 -3.516 -0.097 H7 658 25
658 H3 H5 H 0 1 N N N N N N 41.966 58.172 46.312 -1.748 4.495 -1.278 H3 658 26
658 H1 H6 H 0 1 N N N N N N 43.063 57.025 45.471 -2.526 4.864 0.280 H1 658 27
658 H2 H7 H 0 1 N N N N N N 41.682 57.758 44.587 -0.850 4.263 0.241 H2 658 28
658 H4 H8 H 0 1 N N N N N N 41.344 54.720 44.359 -4.533 3.059 -0.075 H4 658 29
658 H8 H9 H 0 1 N N N N N N 36.262 50.060 50.295 3.368 -2.592 -1.251 H8 658 30
658 H9 H10 H 0 1 N N N N N N 34.268 49.185 51.449 5.023 -0.772 -1.190 H9 658 31
658 H11 H11 H 0 1 N N N N N N 34.265 53.791 49.690 0.765 -0.298 1.248 H11 658 32
658 H14 H12 H 0 1 N N N N N N 40.000 52.200 46.201 -5.227 0.033 1.108 H14 658 33
658 H13 H13 H 0 1 N N N N N N 38.374 52.963 46.210 -5.787 0.707 -0.442 H13 658 34
658 H12 H14 H 0 1 N N N N N N 39.306 52.853 44.678 -4.783 -0.763 -0.421 H12 658 35
#
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
658 C3 C2 SING Y N 1
658 C3 C4 DOUB Y N 2
658 C1 C2 SING N N 3
658 C15 C4 SING N N 4
658 C2 N2 DOUB Y N 5
658 C4 N1 SING Y N 6
658 N2 N1 SING Y N 7
658 N1 C5 SING N N 8
658 C5 N4 DOUB Y N 9
658 C5 N3 SING Y N 10
658 N4 C8 SING Y N 11
658 N3 C6 DOUB Y N 12
658 N5 C8 SING N N 13
658 N5 C9 SING N N 14
658 C8 C7 DOUB Y N 15
658 C6 C7 SING Y N 16
658 C9 C14 DOUB Y N 17
658 C9 C10 SING Y N 18
658 C14 C13 SING Y N 19
658 C10 C11 DOUB Y N 20
658 C13 C12 DOUB Y N 21
658 C11 C12 SING Y N 22
658 C12 CL1 SING N N 23
658 C7 H6 SING N N 24
658 C6 H5 SING N N 25
658 C13 H10 SING N N 26
658 N5 H7 SING N N 27
658 C1 H3 SING N N 28
658 C1 H1 SING N N 29
658 C1 H2 SING N N 30
658 C3 H4 SING N N 31
658 C10 H8 SING N N 32
658 C11 H9 SING N N 33
658 C14 H11 SING N N 34
658 C15 H14 SING N N 35
658 C15 H13 SING N N 36
658 C15 H12 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
658 SMILES ACDLabs 12.01 n2ccc(Nc1ccc(Cl)cc1)nc2n3c(cc(n3)C)C
658 InChI InChI 1.03 InChI=1S/C15H14ClN5/c1-10-9-11(2)21(20-10)15-17-8-7-14(19-15)18-13-5-3-12(16)4-6-13/h3-9H,1-2H3,(H,17,18,19)
658 InChIKey InChI 1.03 MYCRDMLFNQGDBT-UHFFFAOYSA-N
658 SMILES_CANONICAL CACTVS 3.385 Cc1cc(C)n(n1)c2nccc(Nc3ccc(Cl)cc3)n2
658 SMILES CACTVS 3.385 Cc1cc(C)n(n1)c2nccc(Nc3ccc(Cl)cc3)n2
658 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 Cc1cc(n(n1)c2nccc(n2)Nc3ccc(cc3)Cl)C
658 SMILES "OpenEye OEToolkits" 2.0.4 Cc1cc(n(n1)c2nccc(n2)Nc3ccc(cc3)Cl)C
#
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
658 "SYSTEMATIC NAME" ACDLabs 12.01 N-(4-chlorophenyl)-2-(3,5-dimethyl-1H-pyrazol-1-yl)pyrimidin-4-amine
658 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.4 ~{N}-(4-chlorophenyl)-2-(3,5-dimethylpyrazol-1-yl)pyrimidin-4-amine
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
658 'Create component' 2016-01-26 RCSB
658 'Initial release' 2018-03-07 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
658 N3 N 12.093 2.337 1
658 C4 C 14.763 0.697 2
658 N2 N 13.549 -1.405 3
658 C7 C 9.495 2.337 4
658 C6 C 10.794 3.087 5
658 C9 C 6.897 0.837 6
658 C13 C 5.598 3.087 7
658 C8 C 9.495 0.837 8
658 N5 N 8.196 0.087 9
658 C1 C 15.626 -3.087 10
658 N1 N 13.392 0.087 11
658 CL1 Cl 3.000 3.087 12
658 C2 C 15.016 -1.717 13
658 C3 C 15.766 -0.418 14
658 N4 N 10.794 0.087 15
658 C5 C 12.093 0.837 16
658 C10 C 5.598 0.087 17
658 C11 C 4.299 0.837 18
658 C12 C 4.299 2.337 19
658 C14 C 6.897 2.337 20
658 C15 C 15.075 2.164 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
658 C3 C2 SINGLE NONE 1
658 C3 C4 DOUBLE NONE 2
658 C1 C2 SINGLE NONE 3
658 C15 C4 SINGLE NONE 4
658 C2 N2 DOUBLE NONE 5
658 C4 N1 SINGLE NONE 6
658 N2 N1 SINGLE NONE 7
658 N1 C5 SINGLE NONE 8
658 C5 N4 SINGLE NONE 9
658 C5 N3 DOUBLE NONE 10
658 N4 C8 DOUBLE NONE 11
658 N3 C6 SINGLE NONE 12
658 N5 C8 SINGLE NONE 13
658 N5 C9 SINGLE NONE 14
658 C8 C7 SINGLE NONE 15
658 C6 C7 DOUBLE NONE 16
658 C9 C14 SINGLE NONE 17
658 C9 C10 DOUBLE NONE 18
658 C14 C13 DOUBLE NONE 19
658 C10 C11 SINGLE NONE 20
658 C13 C12 SINGLE NONE 21
658 C11 C12 DOUBLE NONE 22
658 C12 CL1 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
658 MurckoScaffold S1 scaffold c1ccc(Nc2ccnc(-n3cccn3)n2)cc1 InChI=1S/C13H11N5/c1-2-5-11(6-3-1)16-12-7-9-14-13(17-12)18-10-4-8-15-18/h1-10H,(H,14,16,17) LTUAUIQMCGAGGZ-UHFFFAOYSA-N
658 phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
658 pyrazole F2 fragment 'c1cn[nH]c1' InChI=1S/C3H4N2/c1-2-4-5-3-1/h1-3H,(H,4,5) WTKZEGDFNFYCGP-UHFFFAOYSA-N
658 pyrimidine F3 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
658 N3 S1 1
658 C4 S1 1
658 N2 S1 1
658 C7 S1 1
658 C6 S1 1
658 C9 S1 1
658 C13 S1 1
658 C8 S1 1
658 N5 S1 1
658 N1 S1 1
658 C2 S1 1
658 C3 S1 1
658 N4 S1 1
658 C5 S1 1
658 C10 S1 1
658 C11 S1 1
658 C12 S1 1
658 C14 S1 1
658 C9 F1 1
658 C14 F1 1
658 C13 F1 1
658 C12 F1 1
658 C11 F1 1
658 C10 F1 1
658 C4 F2 1
658 C3 F2 1
658 C2 F2 1
658 N2 F2 1
658 N1 F2 1
658 C7 F3 1
658 C8 F3 1
658 N4 F3 1
658 C5 F3 1
658 N3 F3 1
658 C6 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 658
_pdbe_chem_comp_rdkit_properties.exactmw 299.094
_pdbe_chem_comp_rdkit_properties.amw 299.765
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 21
_pdbe_chem_comp_rdkit_properties.NumAtoms 35
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.133
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 3
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_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 146.903
_pdbe_chem_comp_rdkit_properties.tpsa 55.630
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.615
_pdbe_chem_comp_rdkit_properties.CrippenMR 80.522
_pdbe_chem_comp_rdkit_properties.chi0v 10.870
_pdbe_chem_comp_rdkit_properties.chi1v 5.779
_pdbe_chem_comp_rdkit_properties.chi2v 2.356
_pdbe_chem_comp_rdkit_properties.chi3v 2.356
_pdbe_chem_comp_rdkit_properties.chi4v 1.455
_pdbe_chem_comp_rdkit_properties.chi0n 24.114
_pdbe_chem_comp_rdkit_properties.chi1n 12.349
_pdbe_chem_comp_rdkit_properties.chi2n 2.167
_pdbe_chem_comp_rdkit_properties.chi3n 2.167
_pdbe_chem_comp_rdkit_properties.chi4n 1.361
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.400
_pdbe_chem_comp_rdkit_properties.kappa1 4.813
_pdbe_chem_comp_rdkit_properties.kappa2 5.535
_pdbe_chem_comp_rdkit_properties.kappa3 3.030
_pdbe_chem_comp_rdkit_properties.Phi 1.269
#
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
658 UniChem PDBe 658
658 UniChem SureChEMBL SCHEMBL4210667
658 UniChem 'PubChem TPHARMA' 17169909
658 UniChem PubChem 11857184
#
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
658 N3 -1.623 -1.394 -1.986 ETKDGv3 1
658 C4 -3.428 0.485 -0.496 ETKDGv3 2
658 N2 -1.611 1.038 0.760 ETKDGv3 3
658 C7 0.525 -2.400 -2.353 ETKDGv3 4
658 C6 -0.761 -2.298 -2.696 ETKDGv3 5
658 C9 3.051 -0.785 0.089 ETKDGv3 6
658 C13 4.720 -0.507 1.862 ETKDGv3 7
658 C8 1.031 -1.567 -1.244 ETKDGv3 8
658 N5 2.403 -1.680 -0.831 ETKDGv3 9
658 C1 -2.583 2.657 2.327 ETKDGv3 10
658 N1 -2.037 0.233 -0.300 ETKDGv3 11
658 CL1 5.255 2.000 2.988 ETKDGv3 12
658 C2 -2.628 1.729 1.160 ETKDGv3 13
658 C3 -3.825 1.392 0.386 ETKDGv3 14
658 N4 0.209 -0.772 -0.618 ETKDGv3 15
658 C5 -1.172 -0.669 -1.003 ETKDGv3 16
658 C10 2.798 0.538 0.086 ETKDGv3 17
658 C11 3.503 1.435 1.027 ETKDGv3 18
658 C12 4.415 0.939 1.873 ETKDGv3 19
658 C14 4.078 -1.322 1.015 ETKDGv3 20
658 C15 -4.306 -0.173 -1.515 ETKDGv3 21
658 H6 1.182 -3.079 -2.882 ETKDGv3 22
658 H5 -1.159 -2.895 -3.506 ETKDGv3 23
658 H10 5.464 -0.908 2.538 ETKDGv3 24
658 H7 2.936 -2.523 -1.143 ETKDGv3 25
658 H3 -1.576 3.118 2.409 ETKDGv3 26
658 H1 -2.804 2.093 3.256 ETKDGv3 27
658 H2 -3.337 3.462 2.199 ETKDGv3 28
658 H4 -4.825 1.790 0.505 ETKDGv3 29
658 H8 2.101 0.972 -0.618 ETKDGv3 30
658 H9 3.279 2.494 1.022 ETKDGv3 31
658 H11 4.307 -2.380 1.011 ETKDGv3 32
658 H14 -5.346 0.210 -1.446 ETKDGv3 33
658 H13 -4.320 -1.269 -1.342 ETKDGv3 34
658 H12 -3.918 0.038 -2.533 ETKDGv3 35
#