data_HKM
#
_chem_comp.id HKM
_chem_comp.name 2-({2-[(4-methyl-1,3-thiazol-2-yl)amino]pyridin-3-yl}oxy)benzonitrile
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C16 H12 N4 O S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2018-07-09
_chem_comp.pdbx_modified_date 2019-07-05
_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 308.358
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code HKM
_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 6E0E
_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
HKM C18 C1 C 0 1 Y N N N N N 41.553 10.940 62.250 -4.901 0.434 -1.725 C18 HKM 1
HKM C13 C2 C 0 1 Y N N N N N 40.717 15.342 62.825 -0.844 -0.588 -0.254 C13 HKM 2
HKM C12 C3 C 0 1 Y N N N N N 41.235 15.230 64.131 -1.583 -1.748 -0.073 C12 HKM 3
HKM C17 C4 C 0 1 Y N N N N N 41.021 12.240 62.164 -3.520 0.412 -1.727 C17 HKM 4
HKM C16 C5 C 0 1 Y N N N N N 41.846 13.324 61.829 -2.820 0.608 -0.546 C16 HKM 5
HKM C15 C6 C 0 1 N N N N N N 44.135 14.084 61.206 -2.809 1.033 1.874 C15 HKM 6
HKM C11 C7 C 0 1 Y N N N N N 40.666 15.951 65.199 -0.907 -2.925 0.218 C11 HKM 7
HKM C10 C8 C 0 1 Y N N N N N 39.573 16.796 64.939 0.470 -2.908 0.318 C10 HKM 8
HKM C8 C9 C 0 1 Y N N N N N 39.621 16.218 62.622 0.546 -0.646 -0.137 C8 HKM 9
HKM N2 N1 N 0 1 Y N N N N N 37.722 17.469 59.782 3.480 1.472 -0.347 N2 HKM 10
HKM C6 C10 C 0 1 N N N N N N 36.125 18.718 58.253 5.813 2.323 -0.343 C6 HKM 11
HKM C1 C11 C 0 1 Y N N N N N 38.063 17.134 61.054 2.684 0.458 -0.200 C1 HKM 12
HKM C4 C12 C 0 1 Y N N N N N 36.068 18.549 60.789 5.083 -0.024 0.079 C4 HKM 13
HKM C19 C13 C 0 1 Y N N N N N 42.908 10.681 61.987 -5.597 0.657 -0.548 C19 HKM 14
HKM C20 C14 C 0 1 Y N N N N N 43.737 11.753 61.630 -4.917 0.854 0.635 C20 HKM 15
HKM C21 C15 C 0 1 Y N N N N N 43.205 13.053 61.552 -3.521 0.828 0.649 C21 HKM 16
HKM C3 C16 C 0 1 Y N N N N N 36.622 18.258 59.604 4.773 1.242 -0.202 C3 HKM 17
HKM S5 S1 S 0 1 Y N N N N N 36.911 17.859 62.215 3.586 -0.950 0.155 S5 HKM 18
HKM N7 N2 N 0 1 N N N N N N 39.084 16.382 61.379 1.303 0.510 -0.315 N7 HKM 19
HKM N9 N3 N 0 1 Y N N N N N 39.094 16.902 63.675 1.150 -1.790 0.142 N9 HKM 20
HKM O14 O1 O 0 1 N N N N N N 41.299 14.628 61.741 -1.463 0.586 -0.546 O14 HKM 21
HKM N22 N4 N 0 1 N N N N N N 44.882 14.939 60.975 -2.244 1.195 2.846 N22 HKM 22
HKM H1 H1 H 0 1 N N N N N N 40.904 10.122 62.525 -5.442 0.281 -2.647 H1 HKM 23
HKM H2 H2 H 0 1 N N N N N N 42.080 14.583 64.315 -2.660 -1.736 -0.157 H2 HKM 24
HKM H3 H3 H 0 1 N N N N N N 39.971 12.404 62.357 -2.984 0.243 -2.649 H3 HKM 25
HKM H4 H4 H 0 1 N N N N N N 41.062 15.856 66.199 -1.452 -3.846 0.365 H4 HKM 26
HKM H5 H5 H 0 1 N N N N N N 39.118 17.357 65.741 0.999 -3.822 0.545 H5 HKM 27
HKM H6 H6 H 0 1 N N N N N N 36.781 18.320 57.465 5.988 2.789 0.627 H6 HKM 28
HKM H7 H7 H 0 1 N N N N N N 35.100 18.352 58.095 6.742 1.887 -0.710 H7 HKM 29
HKM H8 H8 H 0 1 N N N N N N 36.132 19.817 58.215 5.461 3.076 -1.049 H8 HKM 30
HKM H9 H9 H 0 1 N N N N N N 35.179 19.155 60.879 6.078 -0.414 0.233 H9 HKM 31
HKM H10 H10 H 0 1 N N N N N N 43.302 9.678 62.058 -6.676 0.677 -0.558 H10 HKM 32
HKM H11 H11 H 0 1 N N N N N N 44.781 11.582 61.415 -5.464 1.028 1.550 H11 HKM 33
HKM H12 H12 H 0 1 N N N N N N 39.517 15.873 60.635 0.864 1.350 -0.520 H12 HKM 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
HKM C6 C3 SING N N 1
HKM C3 N2 SING Y N 2
HKM C3 C4 DOUB Y N 3
HKM N2 C1 DOUB Y N 4
HKM C4 S5 SING Y N 5
HKM N22 C15 TRIP N N 6
HKM C1 N7 SING N N 7
HKM C1 S5 SING Y N 8
HKM C15 C21 SING N N 9
HKM N7 C8 SING N N 10
HKM C21 C20 DOUB Y N 11
HKM C21 C16 SING Y N 12
HKM C20 C19 SING Y N 13
HKM O14 C16 SING N N 14
HKM O14 C13 SING N N 15
HKM C16 C17 DOUB Y N 16
HKM C19 C18 DOUB Y N 17
HKM C17 C18 SING Y N 18
HKM C8 C13 DOUB Y N 19
HKM C8 N9 SING Y N 20
HKM C13 C12 SING Y N 21
HKM N9 C10 DOUB Y N 22
HKM C12 C11 DOUB Y N 23
HKM C10 C11 SING Y N 24
HKM C18 H1 SING N N 25
HKM C12 H2 SING N N 26
HKM C17 H3 SING N N 27
HKM C11 H4 SING N N 28
HKM C10 H5 SING N N 29
HKM C6 H6 SING N N 30
HKM C6 H7 SING N N 31
HKM C6 H8 SING N N 32
HKM C4 H9 SING N N 33
HKM C19 H10 SING N N 34
HKM C20 H11 SING N N 35
HKM N7 H12 SING N N 36
#
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
HKM SMILES ACDLabs 12.01 "c1cc(c(C#N)cc1)Oc2cccnc2Nc3nc(C)cs3"
HKM InChI InChI 1.03 InChI=1S/C16H12N4OS/c1-11-10-22-16(19-11)20-15-14(7-4-8-18-15)21-13-6-3-2-5-12(13)9-17/h2-8,10H,1H3,(H,18,19,20)
HKM InChIKey InChI 1.03 KPJJEXKLZAXHEE-UHFFFAOYSA-N
HKM SMILES_CANONICAL CACTVS 3.385 "Cc1csc(Nc2ncccc2Oc3ccccc3C#N)n1"
HKM SMILES CACTVS 3.385 "Cc1csc(Nc2ncccc2Oc3ccccc3C#N)n1"
HKM SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "Cc1csc(n1)Nc2c(cccn2)Oc3ccccc3C#N"
HKM SMILES "OpenEye OEToolkits" 2.0.6 "Cc1csc(n1)Nc2c(cccn2)Oc3ccccc3C#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
HKM "SYSTEMATIC NAME" ACDLabs 12.01 2-({2-[(4-methyl-1,3-thiazol-2-yl)amino]pyridin-3-yl}oxy)benzonitrile
HKM "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 2-[2-[(4-methyl-1,3-thiazol-2-yl)amino]pyridin-3-yl]oxybenzenecarbonitrile
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
HKM 'Create component' 2018-07-09 RCSB
HKM 'Initial release' 2019-07-10 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
HKM C18 C 3.000 0.902 1
HKM C13 C 8.196 0.902 2
HKM C12 C 8.196 2.402 3
HKM C17 C 4.299 0.152 4
HKM C16 C 5.598 0.902 5
HKM C15 C 6.897 3.152 6
HKM C11 C 9.495 3.152 7
HKM C10 C 10.794 2.402 8
HKM C8 C 9.495 0.152 9
HKM N2 N 12.165 -1.488 10
HKM C6 C 14.660 -2.446 11
HKM C1 C 10.794 -2.098 12
HKM C4 C 12.418 -3.902 13
HKM C19 C 3.000 2.402 14
HKM C20 C 4.299 3.152 15
HKM C21 C 5.598 2.402 16
HKM C3 C 13.168 -2.603 17
HKM S5 S 10.951 -3.590 18
HKM N7 N 9.495 -1.348 19
HKM N9 N 10.794 0.902 20
HKM O14 O 6.897 0.152 21
HKM N22 N 8.196 3.902 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
HKM C6 C3 SINGLE NONE 1
HKM C3 N2 SINGLE NONE 2
HKM C3 C4 DOUBLE NONE 3
HKM N2 C1 DOUBLE NONE 4
HKM C4 S5 SINGLE NONE 5
HKM N22 C15 TRIPLE NONE 6
HKM C1 N7 SINGLE NONE 7
HKM C1 S5 SINGLE NONE 8
HKM C15 C21 SINGLE NONE 9
HKM N7 C8 SINGLE NONE 10
HKM C21 C20 DOUBLE NONE 11
HKM C21 C16 SINGLE NONE 12
HKM C20 C19 SINGLE NONE 13
HKM O14 C16 SINGLE NONE 14
HKM O14 C13 SINGLE NONE 15
HKM C16 C17 DOUBLE NONE 16
HKM C19 C18 DOUBLE NONE 17
HKM C17 C18 SINGLE NONE 18
HKM C8 C13 SINGLE NONE 19
HKM C8 N9 DOUBLE NONE 20
HKM C13 C12 DOUBLE NONE 21
HKM N9 C10 SINGLE NONE 22
HKM C12 C11 SINGLE NONE 23
HKM C10 C11 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
HKM MurckoScaffold S1 scaffold c1ccc(Oc2cccnc2Nc2nccs2)cc1 InChI=1S/C14H11N3OS/c1-2-5-11(6-3-1)18-12-7-4-8-15-13(12)17-14-16-9-10-19-14/h1-10H,(H,15,16,17) ZESYBYXAZCYFET-UHFFFAOYSA-N
HKM phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
HKM pyridine F2 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-UHFFFAOYSA-N
HKM thiazole F3 fragment c1cscn1 InChI=1S/C3H3NS/c1-2-5-3-4-1/h1-3H FZWLAAWBMGSTSO-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
HKM C18 S1 1
HKM C13 S1 1
HKM C12 S1 1
HKM C17 S1 1
HKM C16 S1 1
HKM C11 S1 1
HKM C10 S1 1
HKM C8 S1 1
HKM N2 S1 1
HKM C1 S1 1
HKM C4 S1 1
HKM C19 S1 1
HKM C20 S1 1
HKM C21 S1 1
HKM C3 S1 1
HKM S5 S1 1
HKM N7 S1 1
HKM N9 S1 1
HKM O14 S1 1
HKM C18 F1 1
HKM C19 F1 1
HKM C20 F1 1
HKM C21 F1 1
HKM C16 F1 1
HKM C17 F1 1
HKM C10 F2 1
HKM C11 F2 1
HKM C12 F2 1
HKM C13 F2 1
HKM C8 F2 1
HKM N9 F2 1
HKM C4 F3 1
HKM C3 F3 1
HKM N2 F3 1
HKM C1 F3 1
HKM S5 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id HKM
_pdbe_chem_comp_rdkit_properties.exactmw 308.073
_pdbe_chem_comp_rdkit_properties.amw 308.366
_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 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 22
_pdbe_chem_comp_rdkit_properties.NumAtoms 34
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.062
_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 148.329
_pdbe_chem_comp_rdkit_properties.tpsa 70.830
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.459
_pdbe_chem_comp_rdkit_properties.CrippenMR 82.202
_pdbe_chem_comp_rdkit_properties.chi0v 11.422
_pdbe_chem_comp_rdkit_properties.chi1v 6.448
_pdbe_chem_comp_rdkit_properties.chi2v 2.874
_pdbe_chem_comp_rdkit_properties.chi3v 2.874
_pdbe_chem_comp_rdkit_properties.chi4v 1.854
_pdbe_chem_comp_rdkit_properties.chi0n 22.605
_pdbe_chem_comp_rdkit_properties.chi1n 11.579
_pdbe_chem_comp_rdkit_properties.chi2n 2.214
_pdbe_chem_comp_rdkit_properties.chi3n 2.214
_pdbe_chem_comp_rdkit_properties.chi4n 1.351
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.910
_pdbe_chem_comp_rdkit_properties.kappa1 5.705
_pdbe_chem_comp_rdkit_properties.kappa2 6.244
_pdbe_chem_comp_rdkit_properties.kappa3 3.050
_pdbe_chem_comp_rdkit_properties.Phi 1.619
#
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
HKM UniChem ChEMBL CHEMBL4648916
HKM UniChem PDBe HKM
HKM UniChem SureChEMBL SCHEMBL1328169
HKM UniChem 'PubChem TPHARMA' 26740932
HKM UniChem PubChem 16752714
HKM UniChem BindingDb 50540201
#
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
HKM C18 -4.226 -0.435 -2.444 ETKDGv3 1
HKM C13 -1.001 -0.688 0.630 ETKDGv3 2
HKM C12 -1.895 -1.529 1.183 ETKDGv3 3
HKM C17 -3.031 -0.562 -1.585 ETKDGv3 4
HKM C16 -2.548 0.512 -0.929 ETKDGv3 5
HKM C15 -2.691 2.993 -0.432 ETKDGv3 6
HKM C11 -1.433 -2.675 1.985 ETKDGv3 7
HKM C10 -0.123 -2.861 2.167 ETKDGv3 8
HKM C8 0.447 -0.919 0.875 ETKDGv3 9
HKM N2 3.671 0.692 -0.035 ETKDGv3 10
HKM C6 6.137 1.374 -0.107 ETKDGv3 11
HKM C1 2.815 -0.010 0.637 ETKDGv3 12
HKM C4 5.141 -0.126 1.602 ETKDGv3 13
HKM C19 -4.825 0.751 -2.589 ETKDGv3 14
HKM C20 -4.292 1.939 -1.893 ETKDGv3 15
HKM C21 -3.209 1.830 -1.108 ETKDGv3 16
HKM C3 5.003 0.617 0.502 ETKDGv3 17
HKM S5 3.564 -0.821 2.041 ETKDGv3 18
HKM N7 1.422 -0.039 0.289 ETKDGv3 19
HKM N9 0.821 -1.947 1.586 ETKDGv3 20
HKM O14 -1.402 0.430 -0.120 ETKDGv3 21
HKM N22 -2.275 3.926 0.111 ETKDGv3 22
HKM H1 -4.612 -1.306 -2.959 ETKDGv3 23
HKM H2 -2.958 -1.365 1.069 ETKDGv3 24
HKM H3 -2.542 -1.524 -1.512 ETKDGv3 25
HKM H4 -2.150 -3.357 2.424 ETKDGv3 26
HKM H5 0.232 -3.698 2.753 ETKDGv3 27
HKM H6 6.399 2.237 0.540 ETKDGv3 28
HKM H7 7.023 0.713 -0.215 ETKDGv3 29
HKM H8 5.849 1.749 -1.111 ETKDGv3 30
HKM H9 6.068 -0.272 2.142 ETKDGv3 31
HKM H10 -5.700 0.845 -3.220 ETKDGv3 32
HKM H11 -4.785 2.895 -2.028 ETKDGv3 33
HKM H12 1.105 0.629 -0.449 ETKDGv3 34
#