data_8MY # _chem_comp.id 8MY _chem_comp.name 4-({4-amino-6-[3-(hydroxymethyl)-1H-pyrazol-1-yl]pyrimidin-2-yl}amino)benzonitrile _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H13 N7 O" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-02-20 _chem_comp.pdbx_modified_date 2017-06-02 _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 307.310 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 8MY _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 5UT6 _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 8MY C10 C1 C 0 1 Y N N N N N -28.982 16.590 75.720 0.071 1.880 -0.251 C10 8MY 1 8MY C13 C2 C 0 1 Y N N N N N -29.304 14.461 76.800 1.760 0.198 -0.068 C13 8MY 2 8MY C15 C3 C 0 1 Y N N N N N -29.565 12.277 77.619 3.560 -1.463 0.118 C15 8MY 3 8MY C17 C4 C 0 1 Y N N N N N -27.429 11.631 77.557 5.291 -0.064 0.062 C17 8MY 4 8MY C22 C5 C 0 1 Y N N N N N -34.711 16.131 76.990 -3.762 -1.768 -0.612 C22 8MY 5 8MY C02 C6 C 0 1 N N N N N N -36.920 13.815 78.954 -6.861 0.120 0.161 C02 8MY 6 8MY C03 C7 C 0 1 Y N N N N N -35.662 14.445 78.378 -5.479 -0.252 0.109 C03 8MY 7 8MY C04 C8 C 0 1 Y N N N N N -34.418 13.928 78.682 -4.516 0.546 0.733 C04 8MY 8 8MY C05 C9 C 0 1 Y N N N N N -33.290 14.525 78.133 -3.188 0.185 0.681 C05 8MY 9 8MY C06 C10 C 0 1 Y N N N N N -33.465 15.624 77.292 -2.805 -0.972 0.010 C06 8MY 10 8MY C08 C11 C 0 1 Y N N N N N -31.016 15.945 76.531 -0.481 -0.355 -0.090 C08 8MY 11 8MY C12 C12 C 0 1 Y N N N N N -28.475 15.360 76.158 1.421 1.540 -0.184 C12 8MY 12 8MY C16 C13 C 0 1 Y N N N N N -28.702 11.219 77.875 4.911 -1.408 0.152 C16 8MY 13 8MY C18 C14 C 0 1 N N N N N N -26.163 10.783 77.670 6.706 0.454 0.063 C18 8MY 14 8MY C23 C15 C 0 1 Y N N N N N -35.820 15.527 77.539 -5.091 -1.414 -0.564 C23 8MY 15 8MY N01 N1 N 0 1 N N N N N N -37.871 13.368 79.363 -7.958 0.415 0.202 N01 8MY 16 8MY N07 N2 N 0 1 N N N N N N -32.368 16.343 76.690 -1.460 -1.334 -0.040 N07 8MY 17 8MY N09 N3 N 0 1 Y N N N N N -30.248 16.860 75.917 -0.842 0.914 -0.201 N09 8MY 18 8MY N11 N4 N 0 1 N N N N N N -28.105 17.527 75.040 -0.315 3.206 -0.362 N11 8MY 19 8MY N14 N5 N 0 1 Y N N N N N -28.827 13.280 77.195 3.100 -0.190 0.002 N14 8MY 20 8MY N20 N6 N 0 1 Y N N N N N -27.514 12.897 77.132 4.209 0.665 -0.034 N20 8MY 21 8MY N21 N7 N 0 1 Y N N N N N -30.567 14.797 76.953 0.792 -0.713 -0.024 N21 8MY 22 8MY O19 O1 O 0 1 N N N N N N -25.520 10.870 76.420 7.615 -0.643 0.171 O19 8MY 23 8MY H1 H1 H 0 1 N N N N N N -30.638 12.276 77.744 2.957 -2.357 0.168 H1 8MY 24 8MY H2 H2 H 0 1 N N N N N N -34.815 16.984 76.336 -3.461 -2.664 -1.135 H2 8MY 25 8MY H3 H3 H 0 1 N N N N N N -34.324 13.074 79.336 -4.812 1.444 1.255 H3 8MY 26 8MY H4 H4 H 0 1 N N N N N N -32.302 14.148 78.352 -2.443 0.801 1.163 H4 8MY 27 8MY H5 H5 H 0 1 N N N N N N -27.436 15.115 75.994 2.186 2.302 -0.223 H5 8MY 28 8MY H6 H6 H 0 1 N N N N N N -28.981 10.247 78.255 5.579 -2.253 0.236 H6 8MY 29 8MY H7 H7 H 0 1 N N N N N N -26.423 9.738 77.893 6.896 0.993 -0.865 H7 8MY 30 8MY H8 H8 H 0 1 N N N N N N -25.510 11.176 78.463 6.846 1.127 0.909 H8 8MY 31 8MY H9 H9 H 0 1 N N N N N N -36.808 15.899 77.313 -5.833 -2.032 -1.047 H9 8MY 32 8MY H10 H10 H 0 1 N N N N N N -32.593 17.250 76.335 -1.210 -2.271 -0.040 H10 8MY 33 8MY H11 H11 H 0 1 N N N N N N -28.624 18.342 74.780 -1.256 3.436 -0.404 H11 8MY 34 8MY H12 H12 H 0 1 N N N N N N -27.358 17.788 75.652 0.357 3.905 -0.398 H12 8MY 35 8MY H13 H13 H 0 1 N N N N N N -24.721 10.356 76.438 8.547 -0.383 0.178 H13 8MY 36 # 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 8MY N11 C10 SING N N 1 8MY C10 N09 DOUB Y N 2 8MY C10 C12 SING Y N 3 8MY N09 C08 SING Y N 4 8MY C12 C13 DOUB Y N 5 8MY O19 C18 SING N N 6 8MY C08 N07 SING N N 7 8MY C08 N21 DOUB Y N 8 8MY N07 C06 SING N N 9 8MY C13 N21 SING Y N 10 8MY C13 N14 SING N N 11 8MY C22 C06 DOUB Y N 12 8MY C22 C23 SING Y N 13 8MY N20 N14 SING Y N 14 8MY N20 C17 DOUB Y N 15 8MY N14 C15 SING Y N 16 8MY C06 C05 SING Y N 17 8MY C23 C03 DOUB Y N 18 8MY C17 C18 SING N N 19 8MY C17 C16 SING Y N 20 8MY C15 C16 DOUB Y N 21 8MY C05 C04 DOUB Y N 22 8MY C03 C04 SING Y N 23 8MY C03 C02 SING N N 24 8MY C02 N01 TRIP N N 25 8MY C15 H1 SING N N 26 8MY C22 H2 SING N N 27 8MY C04 H3 SING N N 28 8MY C05 H4 SING N N 29 8MY C12 H5 SING N N 30 8MY C16 H6 SING N N 31 8MY C18 H7 SING N N 32 8MY C18 H8 SING N N 33 8MY C23 H9 SING N N 34 8MY N07 H10 SING N N 35 8MY N11 H11 SING N N 36 8MY N11 H12 SING N N 37 8MY O19 H13 SING N N 38 # 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 8MY SMILES ACDLabs 12.01 "c3(nc(Nc1ccc(C#N)cc1)nc(n2ccc(CO)n2)c3)N" 8MY InChI InChI 1.03 InChI=1S/C15H13N7O/c16-8-10-1-3-11(4-2-10)18-15-19-13(17)7-14(20-15)22-6-5-12(9-23)21-22/h1-7,23H,9H2,(H3,17,18,19,20) 8MY InChIKey InChI 1.03 NMBKNACBCUDEER-UHFFFAOYSA-N 8MY SMILES_CANONICAL CACTVS 3.385 "Nc1cc(nc(Nc2ccc(cc2)C#N)n1)n3ccc(CO)n3" 8MY SMILES CACTVS 3.385 "Nc1cc(nc(Nc2ccc(cc2)C#N)n1)n3ccc(CO)n3" 8MY SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1cc(ccc1C#N)Nc2nc(cc(n2)n3ccc(n3)CO)N" 8MY SMILES "OpenEye OEToolkits" 2.0.6 "c1cc(ccc1C#N)Nc2nc(cc(n2)n3ccc(n3)CO)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 8MY "SYSTEMATIC NAME" ACDLabs 12.01 4-({4-amino-6-[3-(hydroxymethyl)-1H-pyrazol-1-yl]pyrimidin-2-yl}amino)benzonitrile 8MY "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 4-[[4-azanyl-6-[3-(hydroxymethyl)pyrazol-1-yl]pyrimidin-2-yl]amino]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 8MY 'Create component' 2017-02-20 RCSB 8MY 'Initial release' 2017-06-07 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 8MY C10 C 11.270 1.419 1 8MY C13 C 9.971 -0.831 2 8MY C15 C 8.516 -3.072 3 8MY C17 C 6.298 -2.085 4 8MY C22 C 16.467 -1.581 5 8MY C02 C 19.065 1.419 6 8MY C03 C 17.766 0.669 7 8MY C04 C 16.467 1.419 8 8MY C05 C 15.168 0.669 9 8MY C06 C 15.168 -0.831 10 8MY C08 C 12.569 -0.831 11 8MY C12 C 9.971 0.669 12 8MY C16 C 7.048 -3.384 13 8MY C18 C 4.807 -1.929 14 8MY C23 C 17.766 -0.831 15 8MY N01 N 20.364 2.169 16 8MY N07 N 13.868 -1.581 17 8MY N09 N 12.569 0.669 18 8MY N11 N 11.270 2.919 19 8MY N14 N 8.672 -1.581 20 8MY N20 N 7.302 -0.971 21 8MY N21 N 11.270 -1.581 22 8MY O19 O 3.925 -3.142 23 # 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 8MY N11 C10 SINGLE NONE 1 8MY C10 N09 DOUBLE NONE 2 8MY C10 C12 SINGLE NONE 3 8MY N09 C08 SINGLE NONE 4 8MY C12 C13 DOUBLE NONE 5 8MY O19 C18 SINGLE NONE 6 8MY C08 N07 SINGLE NONE 7 8MY C08 N21 DOUBLE NONE 8 8MY N07 C06 SINGLE NONE 9 8MY C13 N21 SINGLE NONE 10 8MY C13 N14 SINGLE NONE 11 8MY C22 C06 DOUBLE NONE 12 8MY C22 C23 SINGLE NONE 13 8MY N20 N14 SINGLE NONE 14 8MY N20 C17 DOUBLE NONE 15 8MY N14 C15 SINGLE NONE 16 8MY C06 C05 SINGLE NONE 17 8MY C23 C03 DOUBLE NONE 18 8MY C17 C18 SINGLE NONE 19 8MY C17 C16 SINGLE NONE 20 8MY C15 C16 DOUBLE NONE 21 8MY C05 C04 DOUBLE NONE 22 8MY C03 C04 SINGLE NONE 23 8MY C03 C02 SINGLE NONE 24 8MY C02 N01 TRIPLE NONE 25 # 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 8MY MurckoScaffold S1 scaffold c1ccc(Nc2nccc(-n3cccn3)n2)cc1 InChI=1S/C13H11N5/c1-2-5-11(6-3-1)16-13-14-9-7-12(17-13)18-10-4-8-15-18/h1-10H,(H,14,16,17) TWSHDGRWBHFGSI-UHFFFAOYSA-N 8MY phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N 8MY pyrazole F2 fragment 'c1cn[nH]c1' InChI=1S/C3H4N2/c1-2-4-5-3-1/h1-3H,(H,4,5) WTKZEGDFNFYCGP-UHFFFAOYSA-N 8MY pyrimidine F3 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N 8MY Z54628578 F4 fragment CNc1ncccn1 InChI=1S/C5H7N3/c1-6-5-7-3-2-4-8-5/h2-4H,1H3,(H,6,7,8) BQNXHDSGGRTFNX-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 8MY C10 S1 1 8MY C13 S1 1 8MY C15 S1 1 8MY C17 S1 1 8MY C22 S1 1 8MY C03 S1 1 8MY C04 S1 1 8MY C05 S1 1 8MY C06 S1 1 8MY C08 S1 1 8MY C12 S1 1 8MY C16 S1 1 8MY C23 S1 1 8MY N07 S1 1 8MY N09 S1 1 8MY N14 S1 1 8MY N20 S1 1 8MY N21 S1 1 8MY C22 F1 1 8MY C06 F1 1 8MY C05 F1 1 8MY C04 F1 1 8MY C03 F1 1 8MY C23 F1 1 8MY C15 F2 1 8MY C16 F2 1 8MY C17 F2 1 8MY N20 F2 1 8MY N14 F2 1 8MY C12 F3 1 8MY C10 F3 1 8MY N09 F3 1 8MY C08 F3 1 8MY N21 F3 1 8MY C13 F3 1 8MY C06 F4 1 8MY N07 F4 1 8MY C08 F4 1 8MY N09 F4 1 8MY C10 F4 1 8MY C12 F4 1 8MY C13 F4 1 8MY N21 F4 1 # _pdbe_chem_comp_rdkit_properties.comp_id 8MY _pdbe_chem_comp_rdkit_properties.exactmw 307.118 _pdbe_chem_comp_rdkit_properties.amw 307.317 _pdbe_chem_comp_rdkit_properties.lipinskiHBA 8 _pdbe_chem_comp_rdkit_properties.lipinskiHBD 4 _pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6 _pdbe_chem_comp_rdkit_properties.NumHBD 3 _pdbe_chem_comp_rdkit_properties.NumHBA 8 _pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 23 _pdbe_chem_comp_rdkit_properties.NumAtoms 36 _pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8 _pdbe_chem_comp_rdkit_properties.NumAmideBonds 0 _pdbe_chem_comp_rdkit_properties.FractionCSP3 0.067 _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 149.924 _pdbe_chem_comp_rdkit_properties.tpsa 125.670 _pdbe_chem_comp_rdkit_properties.CrippenClogP -0.089 _pdbe_chem_comp_rdkit_properties.CrippenMR 80.264 _pdbe_chem_comp_rdkit_properties.chi0v 11.039 _pdbe_chem_comp_rdkit_properties.chi1v 5.864 _pdbe_chem_comp_rdkit_properties.chi2v 2.348 _pdbe_chem_comp_rdkit_properties.chi3v 2.348 _pdbe_chem_comp_rdkit_properties.chi4v 1.441 _pdbe_chem_comp_rdkit_properties.chi0n 24.039 _pdbe_chem_comp_rdkit_properties.chi1n 12.114 _pdbe_chem_comp_rdkit_properties.chi2n 2.348 _pdbe_chem_comp_rdkit_properties.chi3n 2.348 _pdbe_chem_comp_rdkit_properties.chi4n 1.441 _pdbe_chem_comp_rdkit_properties.hallKierAlpha -3.440 _pdbe_chem_comp_rdkit_properties.kappa1 5.641 _pdbe_chem_comp_rdkit_properties.kappa2 6.128 _pdbe_chem_comp_rdkit_properties.kappa3 3.252 _pdbe_chem_comp_rdkit_properties.Phi 1.503 # 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 8MY UniChem ChEMBL CHEMBL4072814 8MY UniChem PDBe 8MY 8MY UniChem PubChem 127053606 8MY UniChem BindingDb 50243385 # 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 8MY C10 0.115 -0.408 -1.952 ETKDGv3 1 8MY C13 -1.612 -0.154 -0.270 ETKDGv3 2 8MY C15 -3.436 0.119 1.494 ETKDGv3 3 8MY C17 -5.137 0.112 0.063 ETKDGv3 4 8MY C22 3.594 0.674 0.138 ETKDGv3 5 8MY C02 7.327 0.199 0.443 ETKDGv3 6 8MY C03 5.908 0.091 0.664 ETKDGv3 7 8MY C04 5.396 -0.786 1.739 ETKDGv3 8 8MY C05 4.077 -0.892 1.947 ETKDGv3 9 8MY C06 3.120 -0.144 1.097 ETKDGv3 10 8MY C08 0.695 -0.237 0.358 ETKDGv3 11 8MY C12 -1.305 -0.282 -1.569 ETKDGv3 12 8MY C16 -4.755 0.217 1.474 ETKDGv3 13 8MY C18 -6.526 0.239 -0.475 ETKDGv3 14 8MY C23 5.049 0.787 -0.096 ETKDGv3 15 8MY N01 8.467 0.285 0.266 ETKDGv3 16 8MY N07 1.713 -0.250 1.369 ETKDGv3 17 8MY N09 1.035 -0.388 -1.032 ETKDGv3 18 8MY N11 0.483 -0.555 -3.323 ETKDGv3 19 8MY N14 -2.976 -0.033 0.157 ETKDGv3 20 8MY N20 -4.091 -0.016 -0.687 ETKDGv3 21 8MY N21 -0.556 -0.141 0.707 ETKDGv3 22 8MY O19 -6.847 1.590 -0.662 ETKDGv3 23 8MY H1 -2.808 0.157 2.374 ETKDGv3 24 8MY H2 2.925 1.282 -0.457 ETKDGv3 25 8MY H3 6.085 -1.342 2.362 ETKDGv3 26 8MY H4 3.709 -1.535 2.736 ETKDGv3 27 8MY H5 -2.074 -0.298 -2.331 ETKDGv3 28 8MY H6 -5.404 0.350 2.330 ETKDGv3 29 8MY H7 -7.240 -0.203 0.250 ETKDGv3 30 8MY H8 -6.622 -0.322 -1.432 ETKDGv3 31 8MY H9 5.408 1.441 -0.882 ETKDGv3 32 8MY H10 1.419 -0.444 2.353 ETKDGv3 33 8MY H11 1.487 -0.643 -3.595 ETKDGv3 34 8MY H12 -0.246 -0.574 -4.071 ETKDGv3 35 8MY H13 -6.379 1.882 -1.487 ETKDGv3 36 #