data_WSD
#
_chem_comp.id WSD
_chem_comp.name 6-acetyl-2-amino-7,7-dimethyl-7,8-dihydropteridin-4(3H)-one
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H13 N5 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2014-03-20
_chem_comp.pdbx_modified_date 2014-05-23
_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 235.243
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code WSD
_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 4CUL
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
WSD O4A O4A O 0 1 N N N N N N 0.105 3.604 58.572 -1.623 -2.638 0.273 O4A WSD 1
WSD C04 C04 C 0 1 N N N N N N 0.944 4.416 58.121 -1.779 -1.440 0.117 C04 WSD 2
WSD C4A C4A C 0 1 N N N N N N 1.578 4.204 56.889 -0.665 -0.577 -0.068 C4A WSD 3
WSD N05 N05 N 0 1 N N N N N N 1.337 3.116 56.117 0.585 -1.042 -0.070 N05 WSD 4
WSD N03 N03 N 0 1 N N N N N N 1.223 5.533 58.848 -3.016 -0.896 0.110 N03 WSD 5
WSD C02 C02 C 0 1 N N N N N N 2.116 6.456 58.398 -3.182 0.441 -0.075 C02 WSD 6
WSD N02 N02 N 0 1 N N N N N N 2.373 7.574 59.130 -4.447 0.957 -0.069 N02 WSD 7
WSD N01 N01 N 0 1 N N N N N N 2.760 6.251 57.208 -2.160 1.257 -0.259 N01 WSD 8
WSD C8A C8A C 0 1 N N N N N N 2.495 5.160 56.449 -0.914 0.801 -0.272 C8A WSD 9
WSD N08 N08 N 0 1 N N N N N N 3.135 4.999 55.287 0.159 1.635 -0.490 N08 WSD 10
WSD C07 C07 C 0 1 N N N N N N 3.261 3.685 54.668 1.447 1.249 0.109 C07 WSD 11
WSD C12 C12 C 0 1 N N N N N N 3.482 3.934 53.180 2.586 1.960 -0.624 C12 WSD 12
WSD C11 C11 C 0 1 N N N N N N 4.475 2.936 55.220 1.464 1.645 1.587 C11 WSD 13
WSD C06 C06 C 0 1 N N N N N N 1.978 2.932 54.932 1.618 -0.243 -0.017 C06 WSD 14
WSD C09 C09 C 0 1 N N N N N N 1.625 1.743 54.077 2.916 -0.787 -0.080 C09 WSD 15
WSD O09 O09 O 0 1 N N N N N N 2.369 1.420 53.148 3.884 -0.070 0.079 O09 WSD 16
WSD C10 C10 C 0 1 N N N N N N 0.296 1.051 54.312 3.105 -2.259 -0.344 C10 WSD 17
WSD H021 H021 H 0 0 N N N N N N 3.034 8.248 58.799 -5.208 0.372 0.065 H021 WSD 18
WSD H022 H022 H 0 0 N N N N N N 1.901 7.722 59.999 -4.583 1.909 -0.199 H022 WSD 19
WSD H08 H08 H 0 1 N N N N N N 2.666 5.581 54.623 0.070 2.444 -1.017 H08 WSD 20
WSD H121 H121 H 0 0 N N N N N N 3.585 2.971 52.658 2.362 3.023 -0.701 H121 WSD 21
WSD H122 H122 H 0 0 N N N N N N 2.623 4.484 52.769 3.516 1.824 -0.071 H122 WSD 22
WSD H123 H123 H 0 0 N N N N N N 4.398 4.527 53.040 2.694 1.538 -1.623 H123 WSD 23
WSD H111 H111 H 0 0 N N N N N N 4.548 1.950 54.738 0.654 1.135 2.109 H111 WSD 24
WSD H112 H112 H 0 0 N N N N N N 5.388 3.514 55.012 2.418 1.359 2.029 H112 WSD 25
WSD H113 H113 H 0 0 N N N N N N 4.363 2.806 56.306 1.331 2.724 1.676 H113 WSD 26
WSD H101 H101 H 0 0 N N N N N N 0.148 0.272 53.550 2.131 -2.735 -0.459 H101 WSD 27
WSD H102 H102 H 0 0 N N N N N N 0.294 0.591 55.311 3.685 -2.393 -1.258 H102 WSD 28
WSD H103 H103 H 0 0 N N N N N N -0.518 1.788 54.245 3.635 -2.714 0.493 H103 WSD 29
WSD H03 H03 H 0 1 N N N N N N 0.765 5.677 59.725 -3.792 -1.464 0.237 H03 WSD 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
WSD O4A C04 DOUB N N 1
WSD C04 C4A SING N N 2
WSD C04 N03 SING N N 3
WSD C4A N05 SING N N 4
WSD C4A C8A DOUB N N 5
WSD N05 C06 DOUB N N 6
WSD N03 C02 SING N N 7
WSD C02 N02 SING N N 8
WSD C02 N01 DOUB N N 9
WSD N01 C8A SING N N 10
WSD C8A N08 SING N N 11
WSD N08 C07 SING N N 12
WSD C07 C12 SING N N 13
WSD C07 C11 SING N N 14
WSD C07 C06 SING N N 15
WSD C06 C09 SING N N 16
WSD C09 O09 DOUB N N 17
WSD C09 C10 SING N N 18
WSD N02 H021 SING N N 19
WSD N02 H022 SING N N 20
WSD N08 H08 SING N N 21
WSD C12 H121 SING N N 22
WSD C12 H122 SING N N 23
WSD C12 H123 SING N N 24
WSD C11 H111 SING N N 25
WSD C11 H112 SING N N 26
WSD C11 H113 SING N N 27
WSD C10 H101 SING N N 28
WSD C10 H102 SING N N 29
WSD C10 H103 SING N N 30
WSD N03 H03 SING N N 31
#
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
WSD SMILES ACDLabs 12.01 O=C2NC(=NC1=C2N=C(C(=O)C)C(N1)(C)C)N
WSD InChI InChI 1.03 InChI=1S/C10H13N5O2/c1-4(16)6-10(2,3)15-7-5(12-6)8(17)14-9(11)13-7/h1-3H3,(H4,11,13,14,15,17)
WSD InChIKey InChI 1.03 WLVJPLIOOQQZAE-UHFFFAOYSA-N
WSD SMILES_CANONICAL CACTVS 3.385 CC(=O)C1=NC2=C(NC1(C)C)N=C(N)NC2=O
WSD SMILES CACTVS 3.385 CC(=O)C1=NC2=C(NC1(C)C)N=C(N)NC2=O
WSD SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 CC(=O)C1=NC2=C(NC1(C)C)N=C(NC2=O)N
WSD SMILES "OpenEye OEToolkits" 1.7.6 CC(=O)C1=NC2=C(NC1(C)C)N=C(NC2=O)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
WSD "SYSTEMATIC NAME" ACDLabs 12.01 6-acetyl-2-amino-7,7-dimethyl-7,8-dihydropteridin-4(3H)-one
WSD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 2-azanyl-6-ethanoyl-7,7-dimethyl-3,8-dihydropteridin-4-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
WSD 'Create component' 2014-03-20 EBI
WSD 'Modify model coordinates code' 2014-03-25 EBI
WSD 'Initial release' 2014-05-28 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
WSD O4A O 9.520 2.767 1
WSD C04 C 9.537 1.267 2
WSD C4A C 8.196 0.465 3
WSD N05 N 6.897 1.215 4
WSD N03 N 10.896 0.496 5
WSD C02 C 10.896 -1.066 6
WSD N02 N 12.192 -1.821 7
WSD N01 N 9.537 -1.837 8
WSD C8A C 8.196 -1.035 9
WSD N08 N 6.897 -1.785 10
WSD C07 C 5.598 -1.035 11
WSD C12 C 4.098 -1.035 12
WSD C11 C 4.848 -2.334 13
WSD C06 C 5.598 0.465 14
WSD C09 C 4.299 1.215 15
WSD O09 O 3.000 0.465 16
WSD C10 C 4.299 2.715 17
#
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
WSD O4A C04 DOUBLE NONE 1
WSD C04 C4A SINGLE NONE 2
WSD C04 N03 SINGLE NONE 3
WSD C4A N05 SINGLE NONE 4
WSD C4A C8A DOUBLE NONE 5
WSD N05 C06 DOUBLE NONE 6
WSD N03 C02 SINGLE NONE 7
WSD C02 N02 SINGLE NONE 8
WSD C02 N01 DOUBLE NONE 9
WSD N01 C8A SINGLE NONE 10
WSD C8A N08 SINGLE NONE 11
WSD N08 C07 SINGLE NONE 12
WSD C07 C12 SINGLE NONE 13
WSD C07 C11 SINGLE NONE 14
WSD C07 C06 SINGLE NONE 15
WSD C06 C09 SINGLE NONE 16
WSD C09 O09 DOUBLE NONE 17
WSD C09 C10 SINGLE NONE 18
#
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
WSD MurckoScaffold S1 scaffold 'O=c1[nH]cnc2c1N=CCN2' InChI=1S/C6H6N4O/c11-6-4-5(9-3-10-6)8-2-1-7-4/h1,3H,2H2,(H2,8,9,10,11) RSPZIHWNURGJFC-UHFFFAOYSA-N
WSD pyrimidine F1 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-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
WSD O4A S1 1
WSD C04 S1 1
WSD C4A S1 1
WSD N05 S1 1
WSD N03 S1 1
WSD C02 S1 1
WSD N01 S1 1
WSD C8A S1 1
WSD N08 S1 1
WSD C07 S1 1
WSD C06 S1 1
WSD C4A F1 1
WSD C04 F1 1
WSD N03 F1 1
WSD C02 F1 1
WSD N01 F1 1
WSD C8A F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id WSD
_pdbe_chem_comp_rdkit_properties.exactmw 235.107
_pdbe_chem_comp_rdkit_properties.amw 235.247
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 17
_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 0.400
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 115.659
_pdbe_chem_comp_rdkit_properties.tpsa 113.230
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.024
_pdbe_chem_comp_rdkit_properties.CrippenMR 62.384
_pdbe_chem_comp_rdkit_properties.chi0v 8.053
_pdbe_chem_comp_rdkit_properties.chi1v 4.171
_pdbe_chem_comp_rdkit_properties.chi2v 1.877
_pdbe_chem_comp_rdkit_properties.chi3v 1.877
_pdbe_chem_comp_rdkit_properties.chi4v 1.207
_pdbe_chem_comp_rdkit_properties.chi0n 21.053
_pdbe_chem_comp_rdkit_properties.chi1n 10.460
_pdbe_chem_comp_rdkit_properties.chi2n 1.877
_pdbe_chem_comp_rdkit_properties.chi3n 1.877
_pdbe_chem_comp_rdkit_properties.chi4n 1.207
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.180
_pdbe_chem_comp_rdkit_properties.kappa1 3.408
_pdbe_chem_comp_rdkit_properties.kappa2 3.407
_pdbe_chem_comp_rdkit_properties.kappa3 1.793
_pdbe_chem_comp_rdkit_properties.Phi 0.683
#
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
WSD UniChem ChEMBL CHEMBL402134
WSD UniChem PDBe WSD
WSD UniChem ZINC ZINC000029128568
WSD UniChem SureChEMBL SCHEMBL21002237
WSD UniChem 'PubChem TPHARMA' 16755012
WSD UniChem PubChem 135424781
WSD UniChem SureChEMBL SCHEMBL4108709
#
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
WSD O4A -1.808 1.052 2.863 ETKDGv3 1
WSD C04 -2.055 0.539 1.740 ETKDGv3 2
WSD C4A -0.974 0.241 0.791 ETKDGv3 3
WSD N05 0.386 0.527 1.122 ETKDGv3 4
WSD N03 -3.400 0.235 1.363 ETKDGv3 5
WSD C02 -3.646 -0.348 0.075 ETKDGv3 6
WSD N02 -4.979 -0.662 -0.326 ETKDGv3 7
WSD N01 -2.652 -0.593 -0.730 ETKDGv3 8
WSD C8A -1.283 -0.302 -0.388 ETKDGv3 9
WSD N08 -0.241 -0.597 -1.319 ETKDGv3 10
WSD C07 1.185 -0.334 -1.055 ETKDGv3 11
WSD C12 1.688 0.628 -2.148 ETKDGv3 12
WSD C11 1.928 -1.679 -1.148 ETKDGv3 13
WSD C06 1.398 0.292 0.337 ETKDGv3 14
WSD C09 2.751 0.652 0.842 ETKDGv3 15
WSD O09 3.778 0.455 0.139 ETKDGv3 16
WSD C10 2.922 1.259 2.202 ETKDGv3 17
WSD H021 -5.783 -0.469 0.311 ETKDGv3 18
WSD H022 -5.165 -1.086 -1.262 ETKDGv3 19
WSD H08 -0.514 -1.022 -2.234 ETKDGv3 20
WSD H121 1.185 1.614 -2.050 ETKDGv3 21
WSD H122 2.784 0.782 -2.095 ETKDGv3 22
WSD H123 1.457 0.220 -3.156 ETKDGv3 23
WSD H111 3.028 -1.552 -1.083 ETKDGv3 24
WSD H112 1.707 -2.176 -2.118 ETKDGv3 25
WSD H113 1.599 -2.354 -0.330 ETKDGv3 26
WSD H101 2.363 2.217 2.258 ETKDGv3 27
WSD H102 3.995 1.461 2.409 ETKDGv3 28
WSD H103 2.536 0.562 2.975 ETKDGv3 29
WSD H03 -4.190 0.436 2.016 ETKDGv3 30
#