data_H93 # _chem_comp.id H93 _chem_comp.name 2-azanyl-9-[(2R,3R,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1-methyl-purin-6-one _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C11 H15 N5 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-11-30 _chem_comp.pdbx_modified_date 2022-01-28 _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 297.267 _chem_comp.one_letter_code ? _chem_comp.three_letter_code H93 _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 7DLC _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # 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 H93 C01 C1 C 0 1 N N N N N N -11.943 52.621 1.165 5.308 0.394 0.138 C01 H93 1 H93 C03 C2 C 0 1 N N N N N N -11.363 51.957 3.384 3.375 -1.046 -0.224 C03 H93 2 H93 C05 C3 C 0 1 Y N N N N N -10.405 51.341 4.407 1.973 -1.234 -0.217 C05 H93 3 H93 C06 C4 C 0 1 Y N N N N N -9.186 50.882 3.965 1.154 -0.158 0.146 C06 H93 4 H93 C08 C5 C 0 1 N N N N N N -9.689 51.540 1.550 3.012 1.175 0.471 C08 H93 5 H93 C11 C6 C 0 1 Y N N N N N -9.316 50.546 6.129 -0.079 -1.921 -0.333 C11 H93 6 H93 C13 C7 C 0 1 N N R N N N -7.230 49.873 4.977 -1.346 0.152 0.353 C13 H93 7 H93 C14 C8 C 0 1 N N R N N N -7.160 48.235 4.753 -1.821 0.916 -0.910 C14 H93 8 H93 C15 C9 C 0 1 N N S N N N -5.940 48.117 4.475 -3.332 1.101 -0.628 C15 H93 9 H93 C16 C10 C 0 1 N N R N N N -5.621 49.316 3.483 -3.657 0.015 0.415 C16 H93 10 H93 C18 C11 C 0 1 N N N N N N -5.990 49.019 2.193 -4.747 -0.916 -0.119 C18 H93 11 H93 N02 N1 N 0 1 N N N N N N -10.972 52.024 2.024 3.861 0.165 0.127 N02 H93 12 H93 N07 N2 N 0 1 N N N N N N -8.773 50.959 2.526 1.708 1.014 0.476 N07 H93 13 H93 N09 N3 N 0 1 N N N N N N -9.287 51.625 0.150 3.535 2.394 0.824 N09 H93 14 H93 N10 N4 N 0 1 Y N N N N N -8.542 50.397 5.024 -0.133 -0.617 0.064 N10 H93 15 H93 N12 N5 N 0 1 Y N N N N N -10.486 51.133 5.744 1.160 -2.281 -0.498 N12 H93 16 H93 O04 O1 O 0 1 N N N N N N -12.437 52.381 3.676 4.126 -1.955 -0.533 O04 H93 17 H93 O17 O2 O 0 1 N N N N N N -6.548 50.422 4.016 -2.449 -0.731 0.650 O17 H93 18 H93 O19 O3 O 0 1 N N N N N N -5.327 49.856 1.281 -5.113 -1.853 0.896 O19 H93 19 H93 O20 O4 O 0 1 N N N N N N -5.157 48.370 5.724 -3.585 2.401 -0.092 O20 H93 20 H93 O21 O5 O 0 1 N N N N N N -7.443 47.652 6.057 -1.164 2.181 -1.017 O21 H93 21 H93 H1 H1 H 0 1 N N N N N N -12.828 52.905 1.753 5.611 0.759 1.120 H1 H93 22 H93 H2 H2 H 0 1 N N N N N N -11.513 53.517 0.693 5.826 -0.541 -0.077 H2 H93 23 H93 H3 H3 H 0 1 N N N N N N -12.236 51.901 0.387 5.565 1.134 -0.620 H3 H93 24 H93 H4 H4 H 0 1 N N N N N N -9.053 50.252 7.134 -0.937 -2.559 -0.488 H4 H93 25 H93 H5 H5 H 0 1 N N N N N N -6.743 50.063 5.945 -1.174 0.844 1.178 H5 H93 26 H93 H6 H6 H 0 1 N N N N N N -7.879 47.928 3.979 -1.662 0.320 -1.808 H6 H93 27 H93 H7 H7 H 0 1 N N N N N N -5.651 47.162 4.012 -3.911 0.945 -1.538 H7 H93 28 H93 H8 H8 H 0 1 N N N N N N -4.566 49.613 3.577 -3.989 0.484 1.342 H8 H93 29 H93 H9 H9 H 0 1 N N N N N N -7.076 49.158 2.087 -5.620 -0.328 -0.402 H9 H93 30 H93 H10 H10 H 0 1 N N N N N N -5.732 47.972 1.976 -4.372 -1.452 -0.991 H10 H93 31 H93 H11 H11 H 0 1 N N N N N N -8.390 51.287 -0.134 4.488 2.554 0.745 H11 H93 32 H93 H12 H12 H 0 1 N N N N N N -9.909 52.022 -0.525 2.951 3.095 1.152 H12 H93 33 H93 H13 H13 H 0 1 N N N N N N -5.594 49.636 0.396 -5.801 -2.477 0.626 H13 H93 34 H93 H14 H14 H 0 1 N N N N N N -5.320 47.672 6.347 -4.517 2.571 0.103 H14 H93 35 H93 H15 H15 H 0 1 N N N N N N -8.367 47.748 6.254 -1.428 2.697 -1.791 H15 H93 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 H93 N09 C08 SING N N 1 H93 C01 N02 SING N N 2 H93 O19 C18 SING N N 3 H93 C08 N02 SING N N 4 H93 C08 N07 DOUB N N 5 H93 N02 C03 SING N N 6 H93 C18 C16 SING N N 7 H93 N07 C06 SING N N 8 H93 C03 O04 DOUB N N 9 H93 C03 C05 SING N N 10 H93 C16 O17 SING N N 11 H93 C16 C15 SING N N 12 H93 C06 C05 DOUB Y N 13 H93 C06 N10 SING Y N 14 H93 O17 C13 SING N N 15 H93 C05 N12 SING Y N 16 H93 C15 C14 SING N N 17 H93 C15 O20 SING N N 18 H93 C14 C13 SING N N 19 H93 C14 O21 SING N N 20 H93 C13 N10 SING N N 21 H93 N10 C11 SING Y N 22 H93 N12 C11 DOUB Y N 23 H93 C01 H1 SING N N 24 H93 C01 H2 SING N N 25 H93 C01 H3 SING N N 26 H93 C11 H4 SING N N 27 H93 C13 H5 SING N N 28 H93 C14 H6 SING N N 29 H93 C15 H7 SING N N 30 H93 C16 H8 SING N N 31 H93 C18 H9 SING N N 32 H93 C18 H10 SING N N 33 H93 N09 H11 SING N N 34 H93 N09 H12 SING N N 35 H93 O19 H13 SING N N 36 H93 O20 H14 SING N N 37 H93 O21 H15 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 H93 InChI InChI 1.03 InChI=1S/C11H15N5O5/c1-15-9(20)5-8(14-11(15)12)16(3-13-5)10-7(19)6(18)4(2-17)21-10/h3-4,6-7,10,17-19H,2H2,1H3,(H2,12,14)/t4-,6-,7-,10-/m1/s1 H93 InChIKey InChI 1.03 UTAIYTHAJQNQDW-KQYNXXCUSA-N H93 SMILES_CANONICAL CACTVS 3.385 CN1C(=Nc2n(cnc2C1=O)[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)N H93 SMILES CACTVS 3.385 CN1C(=Nc2n(cnc2C1=O)[CH]3O[CH](CO)[CH](O)[CH]3O)N H93 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CN1C(=O)c2c(n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N=C1N H93 SMILES "OpenEye OEToolkits" 2.0.7 CN1C(=O)c2c(n(cn2)C3C(C(C(O3)CO)O)O)N=C1N # _pdbx_chem_comp_identifier.comp_id H93 _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier 2-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1-methyl-purin-6-one # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site H93 'Create component' 2020-11-30 PDBJ H93 'Initial release' 2022-02-02 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 H93 C01 C 3.805 -3.589 1 H93 C03 C 6.404 -3.589 2 H93 C05 C 7.702 -2.839 3 H93 C06 C 7.702 -1.339 4 H93 C08 C 5.104 -1.339 5 H93 C11 C 9.997 -2.089 6 H93 C13 C 9.588 0.544 7 H93 C14 C 8.708 1.759 8 H93 C15 C 9.592 2.971 9 H93 C16 C 11.018 2.505 10 H93 C18 C 12.233 3.385 11 H93 N02 N 5.104 -2.839 12 H93 N07 N 6.404 -0.589 13 H93 N09 N 3.805 -0.589 14 H93 N10 N 9.122 -0.882 15 H93 N12 N 9.122 -3.296 16 H93 O04 O 6.404 -5.089 17 H93 O17 O 11.015 1.005 18 H93 O19 O 13.602 2.772 19 H93 O20 O 9.131 4.399 20 H93 O21 O 7.208 1.762 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 H93 N09 C08 SINGLE NONE 1 H93 C01 N02 SINGLE NONE 2 H93 O19 C18 SINGLE NONE 3 H93 C08 N02 SINGLE NONE 4 H93 C08 N07 DOUBLE NONE 5 H93 N02 C03 SINGLE NONE 6 H93 C16 C18 SINGLE BEGINWEDGE 7 H93 N07 C06 SINGLE NONE 8 H93 C03 O04 DOUBLE NONE 9 H93 C03 C05 SINGLE NONE 10 H93 C16 O17 SINGLE NONE 11 H93 C16 C15 SINGLE NONE 12 H93 C06 C05 DOUBLE NONE 13 H93 C06 N10 SINGLE NONE 14 H93 O17 C13 SINGLE NONE 15 H93 C05 N12 SINGLE NONE 16 H93 C15 C14 SINGLE NONE 17 H93 C15 O20 SINGLE BEGINDASH 18 H93 C14 C13 SINGLE NONE 19 H93 C14 O21 SINGLE BEGINDASH 20 H93 C13 N10 SINGLE BEGINWEDGE 21 H93 N10 C11 SINGLE NONE 22 H93 N12 C11 DOUBLE 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 H93 MurckoScaffold S1 scaffold 'O=c1[nH]cnc2c1ncn2[C@H]1CCCO1' InChI=1S/C9H10N4O2/c14-9-7-8(10-4-11-9)13(5-12-7)6-2-1-3-15-6/h4-6H,1-3H2,(H,10,11,14)/t6-/m1/s1 JBXHFRZBULGPSC-ZCFIWIBFSA-N H93 imidazole F1 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N H93 purine F2 fragment 'c1ncc2[nH]cnc2n1' InChI=1S/C5H4N4/c1-4-5(8-2-6-1)9-3-7-4/h1-3H,(H,6,7,8,9) KDCGOANMDULRCW-UHFFFAOYSA-N H93 pyrimidine F3 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N H93 ribose F4 fragment OCC1OCC(O)C1O InChI=1S/C5H10O4/c6-1-4-5(8)3(7)2-9-4/h3-8H,1-2H2 KZVAAIRBJJYZOW-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 H93 C03 S1 1 H93 C05 S1 1 H93 C06 S1 1 H93 C08 S1 1 H93 C11 S1 1 H93 C13 S1 1 H93 C14 S1 1 H93 C15 S1 1 H93 C16 S1 1 H93 N02 S1 1 H93 N07 S1 1 H93 N10 S1 1 H93 N12 S1 1 H93 O04 S1 1 H93 O17 S1 1 H93 C05 F1 1 H93 C06 F1 1 H93 N10 F1 1 H93 C11 F1 1 H93 N12 F1 1 H93 N12 F2 1 H93 C11 F2 1 H93 N10 F2 1 H93 C06 F2 1 H93 C05 F2 1 H93 C03 F2 1 H93 N02 F2 1 H93 C08 F2 1 H93 N07 F2 1 H93 C05 F3 1 H93 C03 F3 1 H93 N02 F3 1 H93 C08 F3 1 H93 N07 F3 1 H93 C06 F3 1 H93 C14 F4 1 H93 C15 F4 1 H93 C16 F4 1 H93 O17 F4 1 H93 C13 F4 1 H93 C18 F4 1 H93 O19 F4 1 H93 O20 F4 1 H93 O21 F4 1 # _pdbe_chem_comp_rdkit_properties.comp_id H93 _pdbe_chem_comp_rdkit_properties.exactmw 297.107 _pdbe_chem_comp_rdkit_properties.amw 297.271 _pdbe_chem_comp_rdkit_properties.lipinskiHBA 10 _pdbe_chem_comp_rdkit_properties.lipinskiHBD 5 _pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7 _pdbe_chem_comp_rdkit_properties.NumHBD 4 _pdbe_chem_comp_rdkit_properties.NumHBA 10 _pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 21 _pdbe_chem_comp_rdkit_properties.NumAtoms 36 _pdbe_chem_comp_rdkit_properties.NumHeteroatoms 10 _pdbe_chem_comp_rdkit_properties.NumAmideBonds 0 _pdbe_chem_comp_rdkit_properties.FractionCSP3 0.545 _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 3 _pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2 _pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1 _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 4 _pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0 _pdbe_chem_comp_rdkit_properties.labuteASA 139.033 _pdbe_chem_comp_rdkit_properties.tpsa 148.650 _pdbe_chem_comp_rdkit_properties.CrippenClogP -2.585 _pdbe_chem_comp_rdkit_properties.CrippenMR 67.269 _pdbe_chem_comp_rdkit_properties.chi0v 9.777 _pdbe_chem_comp_rdkit_properties.chi1v 5.184 _pdbe_chem_comp_rdkit_properties.chi2v 2.598 _pdbe_chem_comp_rdkit_properties.chi3v 2.598 _pdbe_chem_comp_rdkit_properties.chi4v 1.637 _pdbe_chem_comp_rdkit_properties.chi0n 24.777 _pdbe_chem_comp_rdkit_properties.chi1n 12.304 _pdbe_chem_comp_rdkit_properties.chi2n 2.598 _pdbe_chem_comp_rdkit_properties.chi3n 2.598 _pdbe_chem_comp_rdkit_properties.chi4n 1.637 _pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.010 _pdbe_chem_comp_rdkit_properties.kappa1 4.745 _pdbe_chem_comp_rdkit_properties.kappa2 4.771 _pdbe_chem_comp_rdkit_properties.kappa3 1.917 _pdbe_chem_comp_rdkit_properties.Phi 1.078 # 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 H93 UniChem ChEMBL CHEMBL3246759 H93 UniChem PDBe H93 H93 UniChem ChEBI 19062 H93 UniChem ZINC ZINC000005344125 H93 UniChem HMDB HMDB0001563 H93 UniChem 'PubChem TPHARMA' 125317692 H93 UniChem NMRShiftDB 60021782 H93 UniChem Nikkaji J130.841F H93 UniChem MetaboLights MTBLC19062 H93 UniChem ChemicalBook CB5496545 H93 UniChem MedChemExpress HY-113136 H93 UniChem 'Probes And Drugs' PD102008 H93 UniChem PubChem 96373 H93 UniChem eMolecules 1109452 H93 UniChem SureChEMBL SCHEMBL62505 H93 UniChem 'PubChem TPHARMA' 14849417 # 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 H93 C01 -5.108 -0.917 0.277 ETKDGv3 1 H93 C03 -3.467 0.966 0.702 ETKDGv3 2 H93 C05 -2.078 1.402 0.695 ETKDGv3 3 H93 C06 -1.140 0.596 0.288 ETKDGv3 4 H93 C08 -2.624 -1.210 -0.184 ETKDGv3 5 H93 C11 -0.284 2.583 0.697 ETKDGv3 6 H93 C13 1.265 0.944 -0.559 ETKDGv3 7 H93 C14 2.549 1.520 0.031 ETKDGv3 8 H93 C15 3.580 0.474 -0.321 ETKDGv3 9 H93 C16 2.743 -0.805 -0.407 ETKDGv3 10 H93 C18 2.801 -1.612 0.900 ETKDGv3 11 H93 N02 -3.740 -0.388 0.272 ETKDGv3 12 H93 N07 -1.406 -0.734 -0.175 ETKDGv3 13 H93 N09 -2.834 -2.545 -0.657 ETKDGv3 14 H93 N10 0.111 1.265 0.283 ETKDGv3 15 H93 N12 -1.553 2.697 0.959 ETKDGv3 16 H93 O04 -4.386 1.749 1.064 ETKDGv3 17 H93 O17 1.401 -0.458 -0.679 ETKDGv3 18 H93 O19 1.994 -2.755 0.806 ETKDGv3 19 H93 O20 4.217 0.749 -1.548 ETKDGv3 20 H93 O21 2.847 2.773 -0.528 ETKDGv3 21 H93 H1 -5.154 -1.834 0.900 ETKDGv3 22 H93 H2 -5.832 -0.188 0.697 ETKDGv3 23 H93 H3 -5.421 -1.154 -0.762 ETKDGv3 24 H93 H4 0.400 3.418 0.766 ETKDGv3 25 H93 H5 1.093 1.361 -1.576 ETKDGv3 26 H93 H6 2.462 1.596 1.142 ETKDGv3 27 H93 H7 4.360 0.415 0.471 ETKDGv3 28 H93 H8 3.122 -1.451 -1.229 ETKDGv3 29 H93 H9 2.429 -0.988 1.742 ETKDGv3 30 H93 H10 3.852 -1.903 1.128 ETKDGv3 31 H93 H11 -3.783 -2.974 -0.708 ETKDGv3 32 H93 H12 -2.021 -3.119 -0.975 ETKDGv3 33 H93 H13 2.487 -3.404 0.239 ETKDGv3 34 H93 H14 3.524 0.780 -2.260 ETKDGv3 35 H93 H15 3.593 3.149 0.009 ETKDGv3 36 #