data_05Z
#
_chem_comp.id 05Z
_chem_comp.name 6-benzylthio-2-chloropurine
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H9 Cl N4 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms 2-chloranyl-6-phenylmethylsulfanyl-7H-purine
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2021-05-28
_chem_comp.pdbx_modified_date 2022-04-29
_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 276.745
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 05Z
_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 7OOY
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
#
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
05Z C10 C1 C 0 1 Y N N N N N -30.662 0.190 27.047 3.138 -0.311 0.001 C10 05Z 1
05Z C11 C2 C 0 1 Y N N N N N -29.841 -0.008 25.938 3.817 -0.182 1.197 C11 05Z 2
05Z C12 C3 C 0 1 Y N N N N N -30.041 0.704 24.759 5.175 0.075 1.197 C12 05Z 3
05Z C13 C4 C 0 1 Y N N N N N -31.081 1.610 24.688 5.854 0.202 -0.001 C13 05Z 4
05Z C14 C5 C 0 1 Y N N N N N -31.908 1.808 25.786 5.175 0.072 -1.197 C14 05Z 5
05Z C15 C6 C 0 1 Y N N N N N -31.703 1.103 26.965 3.818 -0.190 -1.197 C15 05Z 6
05Z C2 C7 C 0 1 Y N N N N N -29.193 -2.921 31.680 -2.389 -1.403 0.004 C2 05Z 7
05Z C4 C8 C 0 1 Y N N N N N -28.804 -1.192 33.194 -3.290 0.718 0.001 C4 05Z 8
05Z C5 C9 C 0 1 Y N N N N N -29.458 -0.318 32.352 -1.990 1.249 -0.001 C5 05Z 9
05Z C6 C10 C 0 1 Y N N N N N -29.989 -0.847 31.131 -0.906 0.368 0.000 C6 05Z 10
05Z C8 C11 C 0 1 Y N N N N N -28.789 0.779 34.123 -3.465 2.879 -0.002 C8 05Z 11
05Z C9 C12 C 0 1 N N N N N N -30.411 -0.622 28.325 1.657 -0.590 0.001 C9 05Z 12
05Z N1 N1 N 0 1 Y N N N N N -29.823 -2.123 30.830 -1.151 -0.940 0.002 N1 05Z 13
05Z N3 N2 N 0 1 Y N N N N N -28.687 -2.509 32.837 -3.440 -0.611 0.003 N3 05Z 14
05Z N7 N3 N 0 1 Y N N N N N -29.432 0.895 32.958 -2.138 2.621 -0.002 N7 05Z 15
05Z N9 N4 N 0 1 Y N N N N N -28.397 -0.479 34.294 -4.139 1.763 -0.000 N9 05Z 16
05Z S1 S1 S 0 1 N N N N N N -30.835 0.176 29.910 0.748 0.975 -0.001 S1 05Z 17
05Z CL1 CL1 CL 0 0 N N N N N N -29.042 -4.607 31.194 -2.639 -3.121 -0.001 CL1 05Z 18
05Z H1 H1 H 0 1 N N N N N N -29.036 -0.726 25.995 3.286 -0.281 2.133 H1 05Z 19
05Z H2 H2 H 0 1 N N N N N N -29.391 0.550 23.910 5.706 0.176 2.132 H2 05Z 20
05Z H3 H3 H 0 1 N N N N N N -31.251 2.165 23.777 6.915 0.403 -0.001 H3 05Z 21
05Z H4 H4 H 0 1 N N N N N N -32.719 2.518 25.722 5.705 0.172 -2.133 H4 05Z 22
05Z H5 H5 H 0 1 N N N N N N -32.351 1.265 27.814 3.287 -0.292 -2.132 H5 05Z 23
05Z H7 H7 H 0 1 N N N N N N -31.001 -1.548 28.251 1.395 -1.164 -0.888 H7 05Z 24
05Z H8 H8 H 0 1 N N N N N N -29.340 -0.871 28.355 1.395 -1.161 0.892 H8 05Z 25
05Z H6 H6 H 0 1 N N N N N N -28.614 1.585 34.820 -3.902 3.867 -0.003 H6 05Z 26
05Z H9 H9 H 0 1 N N N N N N -29.829 1.737 32.593 -1.423 3.276 -0.003 H9 05Z 27
#
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
05Z C13 C12 SING Y N 1
05Z C13 C14 DOUB Y N 2
05Z C12 C11 DOUB Y N 3
05Z C14 C15 SING Y N 4
05Z C11 C10 SING Y N 5
05Z C15 C10 DOUB Y N 6
05Z C10 C9 SING N N 7
05Z C9 S1 SING N N 8
05Z S1 C6 SING N N 9
05Z N1 C6 DOUB Y N 10
05Z N1 C2 SING Y N 11
05Z C6 C5 SING Y N 12
05Z CL1 C2 SING N N 13
05Z C2 N3 DOUB Y N 14
05Z C5 N7 SING Y N 15
05Z C5 C4 DOUB Y N 16
05Z N3 C4 SING Y N 17
05Z N7 C8 SING Y N 18
05Z C4 N9 SING Y N 19
05Z C8 N9 DOUB Y N 20
05Z C11 H1 SING N N 21
05Z C12 H2 SING N N 22
05Z C13 H3 SING N N 23
05Z C14 H4 SING N N 24
05Z C15 H5 SING N N 25
05Z C9 H7 SING N N 26
05Z C9 H8 SING N N 27
05Z C8 H6 SING N N 28
05Z N7 H9 SING N N 29
#
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
05Z InChI InChI 1.03 InChI=1S/C12H9ClN4S/c13-12-16-10-9(14-7-15-10)11(17-12)18-6-8-4-2-1-3-5-8/h1-5,7H,6H2,(H,14,15,16,17)
05Z InChIKey InChI 1.03 CLBBDQGSXQEBIT-UHFFFAOYSA-N
05Z SMILES_CANONICAL CACTVS 3.385 Clc1nc(SCc2ccccc2)c3[nH]cnc3n1
05Z SMILES CACTVS 3.385 Clc1nc(SCc2ccccc2)c3[nH]cnc3n1
05Z SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1ccc(cc1)CSc2c3c(nc[nH]3)nc(n2)Cl
05Z SMILES "OpenEye OEToolkits" 2.0.7 c1ccc(cc1)CSc2c3c(nc[nH]3)nc(n2)Cl
#
_pdbx_chem_comp_identifier.comp_id 05Z
_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-chloranyl-6-(phenylmethylsulfanyl)-7~{H}-purine
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id 05Z
_pdbx_chem_comp_synonyms.name 2-chloranyl-6-phenylmethylsulfanyl-7H-purine
_pdbx_chem_comp_synonyms.provenance PDB
_pdbx_chem_comp_synonyms.type ?
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
05Z 'Create component' 2021-05-28 PDBE
05Z 'Initial release' 2022-05-04 RCSB
#
_pdbe_chem_comp_synonyms.comp_id 05Z
_pdbe_chem_comp_synonyms.name 2-chloranyl-6-phenylmethylsulfanyl-7H-purine
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
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
05Z C10 C 4.299 1.875 1
05Z C11 C 5.598 2.625 2
05Z C12 C 5.598 4.125 3
05Z C13 C 4.299 4.875 4
05Z C14 C 3.000 4.125 5
05Z C15 C 3.000 2.625 6
05Z C2 C 4.299 -4.125 7
05Z C4 C 6.897 -4.125 8
05Z C5 C 6.897 -2.625 9
05Z C6 C 5.598 -1.875 10
05Z C8 C 9.192 -3.375 11
05Z C9 C 4.299 0.375 12
05Z N1 N 4.299 -2.625 13
05Z N3 N 5.598 -4.875 14
05Z N7 N 8.316 -2.168 15
05Z N9 N 8.316 -4.582 16
05Z S1 S 5.598 -0.375 17
05Z CL1 Cl 3.000 -4.875 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
05Z C13 C12 SINGLE NONE 1
05Z C13 C14 DOUBLE NONE 2
05Z C12 C11 DOUBLE NONE 3
05Z C14 C15 SINGLE NONE 4
05Z C11 C10 SINGLE NONE 5
05Z C15 C10 DOUBLE NONE 6
05Z C10 C9 SINGLE NONE 7
05Z C9 S1 SINGLE NONE 8
05Z S1 C6 SINGLE NONE 9
05Z N1 C6 SINGLE NONE 10
05Z N1 C2 DOUBLE NONE 11
05Z C6 C5 DOUBLE NONE 12
05Z CL1 C2 SINGLE NONE 13
05Z C2 N3 SINGLE NONE 14
05Z C5 N7 SINGLE NONE 15
05Z C5 C4 SINGLE NONE 16
05Z N3 C4 DOUBLE NONE 17
05Z N7 C8 SINGLE NONE 18
05Z C4 N9 SINGLE NONE 19
05Z C8 N9 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
05Z MurckoScaffold S1 scaffold 'c1ccc(CSc2ncnc3nc[nH]c23)cc1' InChI=1S/C12H10N4S/c1-2-4-9(5-3-1)6-17-12-10-11(14-7-13-10)15-8-16-12/h1-5,7-8H,6H2,(H,13,14,15,16) ULIQGBPQLPCTAJ-UHFFFAOYSA-N
05Z imidazole F1 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
05Z phenyl F2 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
05Z purine F3 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
05Z pyrimidine F4 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
05Z C10 S1 1
05Z C11 S1 1
05Z C12 S1 1
05Z C13 S1 1
05Z C14 S1 1
05Z C15 S1 1
05Z C2 S1 1
05Z C4 S1 1
05Z C5 S1 1
05Z C6 S1 1
05Z C8 S1 1
05Z C9 S1 1
05Z N1 S1 1
05Z N3 S1 1
05Z N7 S1 1
05Z N9 S1 1
05Z S1 S1 1
05Z C4 F1 1
05Z C5 F1 1
05Z N7 F1 1
05Z C8 F1 1
05Z N9 F1 1
05Z C10 F2 1
05Z C11 F2 1
05Z C12 F2 1
05Z C13 F2 1
05Z C14 F2 1
05Z C15 F2 1
05Z N7 F3 1
05Z C8 F3 1
05Z N9 F3 1
05Z C4 F3 1
05Z C5 F3 1
05Z C6 F3 1
05Z N1 F3 1
05Z C2 F3 1
05Z N3 F3 1
05Z C5 F4 1
05Z C6 F4 1
05Z N1 F4 1
05Z C2 F4 1
05Z N3 F4 1
05Z C4 F4 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 05Z
_pdbe_chem_comp_rdkit_properties.exactmw 276.024
_pdbe_chem_comp_rdkit_properties.amw 276.752
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 18
_pdbe_chem_comp_rdkit_properties.NumAtoms 27
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.083
_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 125.532
_pdbe_chem_comp_rdkit_properties.tpsa 54.460
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.707
_pdbe_chem_comp_rdkit_properties.CrippenMR 70.795
_pdbe_chem_comp_rdkit_properties.chi0v 10.147
_pdbe_chem_comp_rdkit_properties.chi1v 5.831
_pdbe_chem_comp_rdkit_properties.chi2v 2.827
_pdbe_chem_comp_rdkit_properties.chi3v 2.827
_pdbe_chem_comp_rdkit_properties.chi4v 2.049
_pdbe_chem_comp_rdkit_properties.chi0n 17.575
_pdbe_chem_comp_rdkit_properties.chi1n 9.083
_pdbe_chem_comp_rdkit_properties.chi2n 1.874
_pdbe_chem_comp_rdkit_properties.chi3n 1.874
_pdbe_chem_comp_rdkit_properties.chi4n 1.167
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.590
_pdbe_chem_comp_rdkit_properties.kappa1 5.187
_pdbe_chem_comp_rdkit_properties.kappa2 4.956
_pdbe_chem_comp_rdkit_properties.kappa3 2.321
_pdbe_chem_comp_rdkit_properties.Phi 1.428
#
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
05Z UniChem PDBe 05Z
05Z UniChem 'PubChem TPHARMA' 14947889
05Z UniChem PubChem 9970705
05Z UniChem Nikkaji J1.169.656B
#
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
05Z C10 -1.378 -1.059 -0.497 ETKDGv3 1
05Z C11 -0.956 0.020 -1.426 ETKDGv3 2
05Z C12 -1.852 0.903 -1.885 ETKDGv3 3
05Z C13 -3.267 0.803 -1.475 ETKDGv3 4
05Z C14 -3.655 -0.168 -0.639 ETKDGv3 5
05Z C15 -2.668 -1.140 -0.124 ETKDGv3 6
05Z C2 0.604 2.317 1.110 ETKDGv3 7
05Z C4 2.681 1.277 0.754 ETKDGv3 8
05Z C5 2.108 0.034 1.113 ETKDGv3 9
05Z C6 0.820 -0.056 1.434 ETKDGv3 10
05Z C8 4.224 -0.204 0.450 ETKDGv3 11
05Z C9 -0.359 -2.016 0.057 ETKDGv3 12
05Z N1 0.057 1.171 1.444 ETKDGv3 13
05Z N3 1.997 2.379 0.718 ETKDGv3 14
05Z N7 3.093 -0.960 0.925 ETKDGv3 15
05Z N9 4.023 1.084 0.336 ETKDGv3 16
05Z S1 0.033 -1.626 1.800 ETKDGv3 17
05Z CL1 -0.364 3.775 1.112 ETKDGv3 18
05Z H1 0.081 0.106 -1.726 ETKDGv3 19
05Z H2 -1.541 1.694 -2.556 ETKDGv3 20
05Z H3 -3.988 1.518 -1.850 ETKDGv3 21
05Z H4 -4.691 -0.241 -0.336 ETKDGv3 22
05Z H5 -2.996 -1.909 0.565 ETKDGv3 23
05Z H7 0.573 -1.995 -0.549 ETKDGv3 24
05Z H8 -0.757 -3.051 0.009 ETKDGv3 25
05Z H6 5.169 -0.664 0.195 ETKDGv3 26
05Z H9 3.009 -1.994 1.041 ETKDGv3 27
#