data_HRD
#
_chem_comp.id HRD
_chem_comp.name 2,6-bis(methylamino)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H12 N6 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2011-05-04
_chem_comp.pdbx_modified_date 2012-04-20
_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 244.253
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code HRD
_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 ?
_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
HRD N1 N1 N 0 1 Y N N N N N 17.422 17.604 17.378 2.634 -1.467 -0.000 N1 HRD 1
HRD N3 N3 N 0 1 Y N N N N N 19.483 17.961 18.190 2.983 0.698 -0.001 N3 HRD 2
HRD C4 C4 C 0 1 Y N N N N N 18.711 17.897 17.085 3.560 -0.539 -0.000 C4 HRD 3
HRD C5 C5 C 0 1 N N N N N N 18.296 18.028 14.681 5.857 0.346 0.001 C5 HRD 4
HRD C6 C6 C 0 1 Y N N N N N 18.662 17.690 19.225 1.607 0.508 -0.001 C6 HRD 5
HRD C7 C7 C 0 1 Y N N N N N 18.957 17.633 20.593 0.530 1.370 -0.001 C7 HRD 6
HRD C8 C8 C 0 1 Y N N N N N 17.873 17.340 21.436 -0.764 0.854 0.000 C8 HRD 7
HRD C10 C10 C 0 1 N N N N N N 15.789 16.775 23.161 -3.279 -0.213 0.000 C10 HRD 8
HRD C1 C1 C 0 1 Y N N N N N 16.573 17.129 20.944 -0.977 -0.547 0.001 C1 HRD 9
HRD C2 C2 C 0 1 Y N N N N N 16.306 17.190 19.569 0.112 -1.410 -0.001 C2 HRD 10
HRD C3 C3 C 0 1 Y N N N N N 17.388 17.482 18.729 1.406 -0.889 -0.001 C3 HRD 11
HRD N2 N2 N 0 1 N N N N N N 19.178 18.100 15.834 4.916 -0.777 0.001 N2 HRD 12
HRD C9 C9 C 0 1 N N N N N N 18.023 17.280 22.818 -1.941 1.732 0.000 C9 HRD 13
HRD O1 O1 O 0 1 N N N N N N 19.238 17.476 23.405 -1.823 2.944 -0.000 O1 HRD 14
HRD N4 N4 N 0 1 N N N N N N 17.014 16.995 23.669 -3.160 1.147 0.001 N4 HRD 15
HRD N5 N5 N 0 1 N N N N N N 14.811 16.507 24.064 -4.539 -0.759 0.000 N5 HRD 16
HRD C11 C11 C 0 1 N N N N N N 13.458 16.295 23.567 -4.706 -2.215 -0.000 C11 HRD 17
HRD N6 N6 N 0 1 N N N N N N 15.598 16.839 21.827 -2.250 -1.020 0.001 N6 HRD 18
HRD H5 H5 H 0 1 N N N N N N 18.873 18.223 13.765 5.696 0.954 0.891 H5 HRD 19
HRD H5A H5A H 0 1 N N N N N N 17.847 17.025 14.625 6.878 -0.036 0.002 H5A HRD 20
HRD H7 H7 H 0 1 N N N N N N 19.953 17.803 20.974 0.689 2.439 -0.000 H7 HRD 21
HRD H2 H2 H 0 1 N N N N N N 15.314 17.020 19.177 -0.042 -2.479 -0.001 H2 HRD 22
HRD H11 H11 H 0 1 N N N N N N 12.784 16.090 24.412 -4.237 -2.634 -0.890 H11 HRD 23
HRD H11A H11A H 0 0 N N N N N N 13.117 17.196 23.037 -4.237 -2.635 0.890 H11A HRD 24
HRD H9 H9 H 0 1 N N N N N N 17.500 18.781 14.781 5.697 0.954 -0.889 H9 HRD 25
HRD H10 H10 H 0 1 N N N N N N 19.875 17.398 15.687 5.248 -1.689 0.001 H10 HRD 26
HRD H111 H111 H 0 0 N N N N N N 15.014 16.457 25.042 -5.318 -0.182 0.000 H111 HRD 27
HRD H12 H12 H 0 1 N N N N N N 13.451 15.439 22.877 -5.768 -2.459 -0.000 H12 HRD 28
HRD H13 H13 H 0 1 N N N N N N 17.174 16.949 24.655 -3.958 1.699 0.001 H13 HRD 29
HRD H121 H121 H 0 0 N N N N N N 20.461 18.167 18.233 3.447 1.549 -0.001 H121 HRD 30
#
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
HRD N1 C3 SING Y N 1
HRD N3 C6 SING Y N 2
HRD C4 N1 DOUB Y N 3
HRD C4 N3 SING Y N 4
HRD C5 N2 SING N N 5
HRD C5 H5 SING N N 6
HRD C5 H5A SING N N 7
HRD C5 H9 SING N N 8
HRD C6 C7 SING Y N 9
HRD C7 C8 DOUB Y N 10
HRD C7 H7 SING N N 11
HRD C8 C9 SING N N 12
HRD C10 N4 SING N N 13
HRD C10 N5 SING N N 14
HRD C1 C8 SING Y N 15
HRD C1 N6 SING N N 16
HRD C2 C1 DOUB Y N 17
HRD C2 H2 SING N N 18
HRD C3 C6 DOUB Y N 19
HRD C3 C2 SING Y N 20
HRD N2 C4 SING N N 21
HRD N2 H10 SING N N 22
HRD C9 O1 DOUB N N 23
HRD C9 N4 SING N N 24
HRD N4 H13 SING N N 25
HRD N5 H111 SING N N 26
HRD C11 N5 SING N N 27
HRD C11 H11 SING N N 28
HRD C11 H11A SING N N 29
HRD C11 H12 SING N N 30
HRD N6 C10 DOUB N N 31
HRD N3 H121 SING N N 32
#
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
HRD SMILES ACDLabs 12.01 O=C2c3cc1nc(nc1cc3N=C(NC)N2)NC
HRD SMILES_CANONICAL CACTVS 3.370 CNC1=Nc2cc3nc(NC)[nH]c3cc2C(=O)N1
HRD SMILES CACTVS 3.370 CNC1=Nc2cc3nc(NC)[nH]c3cc2C(=O)N1
HRD SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 CNc1[nH]c2cc3c(cc2n1)N=C(NC3=O)NC
HRD SMILES "OpenEye OEToolkits" 1.7.2 CNc1[nH]c2cc3c(cc2n1)N=C(NC3=O)NC
HRD InChI InChI 1.03 InChI=1S/C11H12N6O/c1-12-10-15-7-3-5-6(4-8(7)16-10)14-11(13-2)17-9(5)18/h3-4H,1-2H3,(H2,12,15,16)(H2,13,14,17,18)
HRD InChIKey InChI 1.03 YOTQNVNIJNKFAK-UHFFFAOYSA-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
HRD "SYSTEMATIC NAME" ACDLabs 12.01 2,6-bis(methylamino)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one
HRD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 2,6-bis(methylamino)-1,7-dihydroimidazo[4,5-g]quinazolin-8-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
HRD 'Create component' 2011-05-04 RCSB
HRD 'Modify aromatic_flag' 2011-06-04 RCSB
HRD 'Modify descriptor' 2011-06-04 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
HRD N1 N 12.316 -1.492 1
HRD N3 N 12.316 0.922 2
HRD C4 C 13.191 -0.285 3
HRD C5 C 15.441 -1.584 4
HRD C6 C 10.896 0.465 5
HRD C7 C 9.597 1.215 6
HRD C8 C 8.298 0.465 7
HRD C10 C 5.598 -1.066 8
HRD C1 C 8.298 -1.035 9
HRD C2 C 9.597 -1.785 10
HRD C3 C 10.896 -1.035 11
HRD N2 N 14.691 -0.285 12
HRD C9 C 6.957 1.267 13
HRD O1 O 6.975 2.767 14
HRD N4 N 5.598 0.496 15
HRD N5 N 4.302 -1.821 16
HRD C11 C 3.000 -1.076 17
HRD N6 N 6.957 -1.837 18
#
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
HRD N1 C3 SINGLE NONE 1
HRD N3 C6 SINGLE NONE 2
HRD C4 N1 DOUBLE NONE 3
HRD C4 N3 SINGLE NONE 4
HRD C5 N2 SINGLE NONE 5
HRD C6 C7 SINGLE NONE 6
HRD C7 C8 DOUBLE NONE 7
HRD C8 C9 SINGLE NONE 8
HRD C10 N4 SINGLE NONE 9
HRD C10 N5 SINGLE NONE 10
HRD C1 C8 SINGLE NONE 11
HRD C1 N6 SINGLE NONE 12
HRD C2 C1 DOUBLE NONE 13
HRD C3 C6 DOUBLE NONE 14
HRD C3 C2 SINGLE NONE 15
HRD N2 C4 SINGLE NONE 16
HRD C9 O1 DOUBLE NONE 17
HRD C9 N4 SINGLE NONE 18
HRD C11 N5 SINGLE NONE 19
HRD N6 C10 DOUBLE NONE 20
#
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
HRD MurckoScaffold S1 scaffold 'O=c1[nH]cnc2cc3nc[nH]c3cc12' InChI=1S/C9H6N4O/c14-9-5-1-7-8(12-3-11-7)2-6(5)10-4-13-9/h1-4H,(H,11,12)(H,10,13,14) ZLJSWBSUEOZJDB-UHFFFAOYSA-N
HRD benzimidazole F1 fragment 'c1ccc2[nH]cnc2c1' InChI=1S/C7H6N2/c1-2-4-7-6(3-1)8-5-9-7/h1-5H,(H,8,9) HYZJCKYKOHLVJF-UHFFFAOYSA-N
HRD imidazole F2 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
HRD phenyl F3 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
HRD pyrimidine F4 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
HRD quinazoline F5 fragment c1ccc2ncncc2c1 InChI=1S/C8H6N2/c1-2-4-8-7(3-1)5-9-6-10-8/h1-6H JWVCLYRUEFBMGU-UHFFFAOYSA-N
HRD Z54628578 F6 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
HRD N1 S1 1
HRD N3 S1 1
HRD C4 S1 1
HRD C6 S1 1
HRD C7 S1 1
HRD C8 S1 1
HRD C10 S1 1
HRD C1 S1 1
HRD C2 S1 1
HRD C3 S1 1
HRD C9 S1 1
HRD O1 S1 1
HRD N4 S1 1
HRD N6 S1 1
HRD C6 F1 1
HRD N3 F1 1
HRD C4 F1 1
HRD N1 F1 1
HRD C3 F1 1
HRD C2 F1 1
HRD C1 F1 1
HRD C8 F1 1
HRD C7 F1 1
HRD C6 F2 1
HRD C3 F2 1
HRD N1 F2 1
HRD C4 F2 1
HRD N3 F2 1
HRD C6 F3 1
HRD C7 F3 1
HRD C8 F3 1
HRD C1 F3 1
HRD C2 F3 1
HRD C3 F3 1
HRD C8 F4 1
HRD C9 F4 1
HRD N4 F4 1
HRD C10 F4 1
HRD N6 F4 1
HRD C1 F4 1
HRD C6 F5 1
HRD C3 F5 1
HRD C2 F5 1
HRD C1 F5 1
HRD C8 F5 1
HRD C7 F5 1
HRD C9 F5 1
HRD N4 F5 1
HRD C10 F5 1
HRD N6 F5 1
HRD C11 F6 1
HRD N5 F6 1
HRD C10 F6 1
HRD N4 F6 1
HRD C9 F6 1
HRD C8 F6 1
HRD C1 F6 1
HRD N6 F6 1
#
_pdbe_chem_comp_rdkit_properties.comp_id HRD
_pdbe_chem_comp_rdkit_properties.exactmw 244.107
_pdbe_chem_comp_rdkit_properties.amw 244.258
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 18
_pdbe_chem_comp_rdkit_properties.NumAtoms 30
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.182
_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 118.746
_pdbe_chem_comp_rdkit_properties.tpsa 98.490
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.165
_pdbe_chem_comp_rdkit_properties.CrippenMR 65.157
_pdbe_chem_comp_rdkit_properties.chi0v 8.592
_pdbe_chem_comp_rdkit_properties.chi1v 4.637
_pdbe_chem_comp_rdkit_properties.chi2v 2.192
_pdbe_chem_comp_rdkit_properties.chi3v 2.192
_pdbe_chem_comp_rdkit_properties.chi4v 1.468
_pdbe_chem_comp_rdkit_properties.chi0n 20.592
_pdbe_chem_comp_rdkit_properties.chi1n 10.426
_pdbe_chem_comp_rdkit_properties.chi2n 2.192
_pdbe_chem_comp_rdkit_properties.chi3n 2.192
_pdbe_chem_comp_rdkit_properties.chi4n 1.468
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.570
_pdbe_chem_comp_rdkit_properties.kappa1 3.710
_pdbe_chem_comp_rdkit_properties.kappa2 3.726
_pdbe_chem_comp_rdkit_properties.kappa3 1.481
_pdbe_chem_comp_rdkit_properties.Phi 0.768
#
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
HRD UniChem PDBe HRD
HRD UniChem ZINC ZINC000095921287
HRD UniChem PubChem 135566560
#
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
HRD N1 -2.586 1.570 -0.895 ETKDGv3 1
HRD N3 -3.068 -0.419 0.147 ETKDGv3 2
HRD C4 -3.535 0.779 -0.486 ETKDGv3 3
HRD C5 -5.974 0.201 -0.200 ETKDGv3 4
HRD C6 -1.667 -0.250 0.068 ETKDGv3 5
HRD C7 -0.610 -1.152 0.550 ETKDGv3 6
HRD C8 0.672 -0.773 0.360 ETKDGv3 7
HRD C10 3.363 0.170 -0.118 ETKDGv3 8
HRD C1 0.988 0.521 -0.319 ETKDGv3 9
HRD C2 -0.004 1.324 -0.748 ETKDGv3 10
HRD C3 -1.392 0.888 -0.528 ETKDGv3 11
HRD N2 -4.919 1.093 -0.661 ETKDGv3 12
HRD C9 1.817 -1.582 0.793 ETKDGv3 13
HRD O1 1.652 -2.688 1.374 ETKDGv3 14
HRD N4 3.141 -1.094 0.545 ETKDGv3 15
HRD N5 4.695 0.648 -0.360 ETKDGv3 16
HRD C11 5.891 -0.087 0.035 ETKDGv3 17
HRD N6 2.357 0.900 -0.509 ETKDGv3 18
HRD H5 -5.885 -0.782 -0.707 ETKDGv3 19
HRD H5A -6.967 0.638 -0.436 ETKDGv3 20
HRD H7 -0.866 -2.084 1.038 ETKDGv3 21
HRD H2 0.208 2.265 -1.241 ETKDGv3 22
HRD H11 5.913 -1.074 -0.473 ETKDGv3 23
HRD H11A 5.902 -0.227 1.137 ETKDGv3 24
HRD H9 -5.896 0.063 0.899 ETKDGv3 25
HRD H10 -5.182 1.988 -1.133 ETKDGv3 26
HRD H111 4.818 1.567 -0.842 ETKDGv3 27
HRD H12 6.797 0.484 -0.258 ETKDGv3 28
HRD H13 3.947 -1.677 0.858 ETKDGv3 29
HRD H121 -3.610 -1.210 0.560 ETKDGv3 30
#