data_454
#
_chem_comp.id 454
_chem_comp.name 8,8-diphenyl-2,3,4,8-tetrahydroimidazo[1,5-a]pyrimidin-6-amine
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C18 H18 N4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2009-07-28
_chem_comp.pdbx_modified_date 2011-06-04
_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 290.362
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 454
_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 3IGB
_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
454 C1 C1 C 0 1 Y N N N N N 9.910 -7.744 16.074 -2.981 -3.089 -0.508 C1 454 1
454 N1 N1 N 0 1 N N N N N N 14.176 -6.100 18.639 1.287 -0.241 -1.699 N1 454 2
454 C2 C2 C 0 1 Y N N N N N 10.640 -8.609 16.885 -2.903 -2.568 0.770 C2 454 3
454 N2 N2 N 0 1 N N N N N N 15.364 -5.308 16.713 2.118 -0.373 0.508 N2 454 4
454 C3 C3 C 0 1 Y N N N N N 12.027 -8.466 16.991 -1.986 -1.574 1.056 C3 454 5
454 N3 N3 N 0 1 N N N N N N 14.841 -6.816 15.137 0.309 -0.121 1.775 N3 454 6
454 C4 C4 C 0 1 Y N N N N N 12.717 -7.455 16.286 -1.146 -1.102 0.065 C4 454 7
454 N4 N4 N 0 1 N N N N N N 16.362 -5.082 14.568 2.344 -0.472 2.910 N4 454 8
454 C5 C5 C 0 1 Y N N N N N 11.957 -6.595 15.475 -1.223 -1.624 -1.213 C5 454 9
454 C6 C6 C 0 1 Y N N N N N 10.572 -6.742 15.372 -2.141 -2.617 -1.500 C6 454 10
454 C7 C7 C 0 1 N N N N N N 14.243 -7.339 16.447 -0.147 -0.018 0.377 C7 454 11
454 C8 C8 C 0 1 N N N N N N 14.670 -6.229 17.451 1.112 -0.212 -0.427 C8 454 12
454 C9 C9 C 0 1 N N N N N N 14.539 -4.850 19.342 2.635 -0.481 -2.231 C9 454 13
454 C10 C10 C 0 1 N N N N N N 15.813 -4.193 18.783 3.691 0.078 -1.276 C10 454 14
454 C11 C11 C 0 1 N N N N N N 15.660 -4.006 17.278 3.523 -0.558 0.112 C11 454 15
454 C12 C12 C 0 1 N N N N N N 15.533 -5.740 15.424 1.593 -0.323 1.768 C12 454 16
454 C13 C13 C 0 1 Y N N N N N 14.928 -8.675 16.779 -0.743 1.341 0.113 C13 454 17
454 C14 C14 C 0 1 Y N N N N N 14.862 -9.742 15.868 -1.392 2.019 1.128 C14 454 18
454 C15 C15 C 0 1 Y N N N N N 15.477 -10.965 16.136 -1.939 3.265 0.886 C15 454 19
454 C16 C16 C 0 1 Y N N N N N 16.165 -11.141 17.331 -1.836 3.834 -0.370 C16 454 20
454 C17 C17 C 0 1 Y N N N N N 16.247 -10.095 18.244 -1.185 3.156 -1.383 C17 454 21
454 C18 C18 C 0 1 Y N N N N N 15.630 -8.872 17.973 -0.634 1.912 -1.141 C18 454 22
454 H1 H1 H 0 1 N N N N N N 8.838 -7.850 15.991 -3.695 -3.868 -0.731 H1 454 23
454 H2 H2 H 0 1 N N N N N N 10.135 -9.391 17.433 -3.559 -2.936 1.544 H2 454 24
454 H3 H3 H 0 1 N N N N N N 12.582 -9.142 17.625 -1.926 -1.166 2.054 H3 454 25
454 HN4 HN4 H 0 1 N N N N N N 16.481 -5.415 13.633 3.300 -0.621 2.845 HN4 454 26
454 HN4A HN4A H 0 0 N N N N N N 16.852 -4.266 14.875 1.917 -0.427 3.780 HN4A 454 27
454 H5 H5 H 0 1 N N N N N N 12.451 -5.809 14.923 -0.568 -1.255 -1.988 H5 454 28
454 H6 H6 H 0 1 N N N N N N 10.009 -6.071 14.741 -2.202 -3.024 -2.498 H6 454 29
454 H9 H9 H 0 1 N N N N N N 13.707 -4.138 19.233 2.789 -1.554 -2.351 H9 454 30
454 H9A H9A H 0 1 N N N N N N 14.710 -5.087 20.402 2.732 0.005 -3.201 H9A 454 31
454 H10 H10 H 0 1 N N N N N N 15.964 -3.215 19.263 4.685 -0.149 -1.662 H10 454 32
454 H10A H10A H 0 0 N N N N N N 16.681 -4.837 18.988 3.572 1.159 -1.197 H10A 454 33
454 H11 H11 H 0 1 N N N N N N 16.590 -3.607 16.847 4.180 -0.064 0.828 H11 454 34
454 H11A H11A H 0 0 N N N N N N 14.842 -3.303 17.063 3.759 -1.622 0.063 H11A 454 35
454 H14 H14 H 0 1 N N N N N N 14.324 -9.613 14.941 -1.473 1.575 2.109 H14 454 36
454 H15 H15 H 0 1 N N N N N N 15.419 -11.771 15.419 -2.447 3.795 1.679 H15 454 37
454 H16 H16 H 0 1 N N N N N N 16.635 -12.088 17.550 -2.263 4.807 -0.558 H16 454 38
454 H17 H17 H 0 1 N N N N N N 16.791 -10.229 19.167 -1.104 3.600 -2.365 H17 454 39
454 H18 H18 H 0 1 N N N N N N 15.695 -8.070 18.693 -0.123 1.384 -1.932 H18 454 40
#
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
454 C1 C2 DOUB Y N 1
454 C1 C6 SING Y N 2
454 N1 C8 DOUB N N 3
454 N1 C9 SING N N 4
454 C2 C3 SING Y N 5
454 N2 C8 SING N N 6
454 N2 C11 SING N N 7
454 N2 C12 SING N N 8
454 C3 C4 DOUB Y N 9
454 N3 C7 SING N N 10
454 N3 C12 DOUB N N 11
454 C4 C5 SING Y N 12
454 C4 C7 SING N N 13
454 N4 C12 SING N N 14
454 C5 C6 DOUB Y N 15
454 C7 C8 SING N N 16
454 C7 C13 SING N N 17
454 C9 C10 SING N N 18
454 C10 C11 SING N N 19
454 C13 C14 DOUB Y N 20
454 C13 C18 SING Y N 21
454 C14 C15 SING Y N 22
454 C15 C16 DOUB Y N 23
454 C16 C17 SING Y N 24
454 C17 C18 DOUB Y N 25
454 C1 H1 SING N N 26
454 C2 H2 SING N N 27
454 C3 H3 SING N N 28
454 N4 HN4 SING N N 29
454 N4 HN4A SING N N 30
454 C5 H5 SING N N 31
454 C6 H6 SING N N 32
454 C9 H9 SING N N 33
454 C9 H9A SING N N 34
454 C10 H10 SING N N 35
454 C10 H10A SING N N 36
454 C11 H11 SING N N 37
454 C11 H11A SING N N 38
454 C14 H14 SING N N 39
454 C15 H15 SING N N 40
454 C16 H16 SING N N 41
454 C17 H17 SING N N 42
454 C18 H18 SING N N 43
#
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
454 SMILES ACDLabs 11.02 N2=C(N)N1C(=NCCC1)C2(c3ccccc3)c4ccccc4
454 SMILES_CANONICAL CACTVS 3.352 NC1=NC(c2ccccc2)(c3ccccc3)C4=NCCCN14
454 SMILES CACTVS 3.352 NC1=NC(c2ccccc2)(c3ccccc3)C4=NCCCN14
454 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 c1ccc(cc1)C2(C3=NCCCN3C(=N2)N)c4ccccc4
454 SMILES "OpenEye OEToolkits" 1.7.0 c1ccc(cc1)C2(C3=NCCCN3C(=N2)N)c4ccccc4
454 InChI InChI 1.03 InChI=1S/C18H18N4/c19-17-21-18(14-8-3-1-4-9-14,15-10-5-2-6-11-15)16-20-12-7-13-22(16)17/h1-6,8-11H,7,12-13H2,(H2,19,21)
454 InChIKey InChI 1.03 UFWSJOVQEPTPNE-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
454 "SYSTEMATIC NAME" ACDLabs 11.02 8,8-diphenyl-2,3,4,8-tetrahydroimidazo[1,5-a]pyrimidin-6-amine
454 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 8,8-diphenyl-3,4-dihydro-2H-imidazo[1,5-a]pyrimidin-6-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
454 'Create component' 2009-07-28 RCSB
454 'Modify aromatic_flag' 2011-06-04 RCSB
454 '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
454 C1 C 11.494 -0.588 1
454 N1 N 4.299 -0.418 2
454 C2 C 10.614 -1.803 3
454 N2 N 5.598 1.832 4
454 C3 C 9.122 -1.649 5
454 N3 N 7.893 1.082 6
454 C4 C 8.509 -0.279 7
454 N4 N 7.483 3.715 8
454 C5 C 9.389 0.936 9
454 C6 C 10.881 0.782 10
454 C7 C 7.018 -0.125 11
454 C8 C 5.598 0.332 12
454 C9 C 3.000 0.332 13
454 C10 C 3.000 1.832 14
454 C11 C 4.299 2.582 15
454 C12 C 7.018 2.289 16
454 C13 C 6.556 -1.552 17
454 C14 C 5.090 -1.867 18
454 C15 C 4.629 -3.294 19
454 C16 C 5.634 -4.407 20
454 C17 C 7.101 -4.093 21
454 C18 C 7.562 -2.665 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
454 C1 C2 DOUBLE NONE 1
454 C1 C6 SINGLE NONE 2
454 N1 C8 DOUBLE NONE 3
454 N1 C9 SINGLE NONE 4
454 C2 C3 SINGLE NONE 5
454 N2 C8 SINGLE NONE 6
454 N2 C11 SINGLE NONE 7
454 N2 C12 SINGLE NONE 8
454 C3 C4 DOUBLE NONE 9
454 N3 C7 SINGLE NONE 10
454 N3 C12 DOUBLE NONE 11
454 C4 C5 SINGLE NONE 12
454 C4 C7 SINGLE NONE 13
454 N4 C12 SINGLE NONE 14
454 C5 C6 DOUBLE NONE 15
454 C7 C8 SINGLE NONE 16
454 C7 C13 SINGLE NONE 17
454 C9 C10 SINGLE NONE 18
454 C10 C11 SINGLE NONE 19
454 C13 C14 DOUBLE NONE 20
454 C13 C18 SINGLE NONE 21
454 C14 C15 SINGLE NONE 22
454 C15 C16 DOUBLE NONE 23
454 C16 C17 SINGLE NONE 24
454 C17 C18 DOUBLE 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
454 MurckoScaffold S1 scaffold C1=NC(c2ccccc2)(c2ccccc2)C2=NCCCN12 InChI=1S/C18H17N3/c1-3-8-15(9-4-1)18(16-10-5-2-6-11-16)17-19-12-7-13-21(17)14-20-18/h1-6,8-11,14H,7,12-13H2 URKBKXCPKMDZFC-UHFFFAOYSA-N
454 phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-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
454 C1 S1 1
454 N1 S1 1
454 C2 S1 1
454 N2 S1 1
454 C3 S1 1
454 N3 S1 1
454 C4 S1 1
454 C5 S1 1
454 C6 S1 1
454 C7 S1 1
454 C8 S1 1
454 C9 S1 1
454 C10 S1 1
454 C11 S1 1
454 C12 S1 1
454 C13 S1 1
454 C14 S1 1
454 C15 S1 1
454 C16 S1 1
454 C17 S1 1
454 C18 S1 1
454 C1 F1 1
454 C2 F1 1
454 C3 F1 1
454 C4 F1 1
454 C5 F1 1
454 C6 F1 1
454 C13 F1 2
454 C14 F1 2
454 C15 F1 2
454 C16 F1 2
454 C17 F1 2
454 C18 F1 2
#
_pdbe_chem_comp_rdkit_properties.comp_id 454
_pdbe_chem_comp_rdkit_properties.exactmw 290.153
_pdbe_chem_comp_rdkit_properties.amw 290.370
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 22
_pdbe_chem_comp_rdkit_properties.NumAtoms 40
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.222
_pdbe_chem_comp_rdkit_properties.NumRings 4
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2
_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 154.962
_pdbe_chem_comp_rdkit_properties.tpsa 53.980
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.253
_pdbe_chem_comp_rdkit_properties.CrippenMR 88.379
_pdbe_chem_comp_rdkit_properties.chi0v 10.789
_pdbe_chem_comp_rdkit_properties.chi1v 6.039
_pdbe_chem_comp_rdkit_properties.chi2v 3.112
_pdbe_chem_comp_rdkit_properties.chi3v 3.112
_pdbe_chem_comp_rdkit_properties.chi4v 2.224
_pdbe_chem_comp_rdkit_properties.chi0n 28.789
_pdbe_chem_comp_rdkit_properties.chi1n 14.933
_pdbe_chem_comp_rdkit_properties.chi2n 3.112
_pdbe_chem_comp_rdkit_properties.chi3n 3.112
_pdbe_chem_comp_rdkit_properties.chi4n 2.224
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.620
_pdbe_chem_comp_rdkit_properties.kappa1 4.015
_pdbe_chem_comp_rdkit_properties.kappa2 4.983
_pdbe_chem_comp_rdkit_properties.kappa3 1.766
_pdbe_chem_comp_rdkit_properties.Phi 0.909
#
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
454 UniChem ChEMBL CHEMBL582044
454 UniChem PDBe 454
454 UniChem ZINC ZINC000034657615
454 UniChem SureChEMBL SCHEMBL3456304
454 UniChem BindingDb 50300710
454 UniChem BRENDA 82368
454 UniChem PubChem 11543843
454 UniChem 'PubChem TPHARMA' 16646008
#
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
454 C1 -3.114 -3.100 0.577 ETKDGv3 1
454 N1 1.170 -0.418 1.522 ETKDGv3 2
454 C2 -2.901 -2.096 1.433 ETKDGv3 3
454 N2 2.039 -0.247 -0.673 ETKDGv3 4
454 C3 -1.958 -1.014 1.087 ETKDGv3 5
454 N3 0.105 0.033 -1.844 ETKDGv3 6
454 C4 -1.315 -1.012 -0.101 ETKDGv3 7
454 N4 2.062 -0.281 -3.177 ETKDGv3 8
454 C5 -1.550 -2.149 -1.037 ETKDGv3 9
454 C6 -2.403 -3.130 -0.715 ETKDGv3 10
454 C7 -0.317 0.095 -0.433 ETKDGv3 11
454 C8 0.988 -0.172 0.260 ETKDGv3 12
454 C9 2.479 -0.848 2.033 ETKDGv3 13
454 C10 3.645 -0.350 1.149 ETKDGv3 14
454 C11 3.388 -0.675 -0.332 ETKDGv3 15
454 C12 1.386 -0.157 -1.927 ETKDGv3 16
454 C13 -0.894 1.484 -0.162 ETKDGv3 17
454 C14 -2.004 1.876 -0.821 ETKDGv3 18
454 C15 -2.595 3.208 -0.584 ETKDGv3 19
454 C16 -2.029 4.047 0.289 ETKDGv3 20
454 C17 -0.811 3.643 1.014 ETKDGv3 21
454 C18 -0.270 2.437 0.805 ETKDGv3 22
454 H1 -3.804 -3.894 0.831 ETKDGv3 23
454 H2 -3.417 -2.075 2.384 ETKDGv3 24
454 H3 -1.791 -0.223 1.808 ETKDGv3 25
454 HN4 1.530 -0.212 -4.072 ETKDGv3 26
454 HN4A 3.092 -0.445 -3.211 ETKDGv3 27
454 H5 -1.034 -2.202 -1.987 ETKDGv3 28
454 H6 -2.570 -3.951 -1.400 ETKDGv3 29
454 H9 2.607 -0.475 3.070 ETKDGv3 30
454 H9A 2.500 -1.959 2.062 ETKDGv3 31
454 H10 4.595 -0.823 1.478 ETKDGv3 32
454 H10A 3.744 0.751 1.268 ETKDGv3 33
454 H11 3.480 -1.770 -0.500 ETKDGv3 34
454 H11A 4.127 -0.143 -0.967 ETKDGv3 35
454 H14 -2.483 1.215 -1.534 ETKDGv3 36
454 H15 -3.489 3.503 -1.119 ETKDGv3 37
454 H16 -2.462 5.024 0.463 ETKDGv3 38
454 H17 -0.353 4.329 1.716 ETKDGv3 39
454 H18 0.628 2.176 1.347 ETKDGv3 40
#