data_05Q
#
_chem_comp.id 05Q
_chem_comp.name 6-benzyloxo-2-chloropurine
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H9 Cl N4 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms 2-chloranyl-6-phenylmethoxy-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 260.679
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 05Q
_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 7OOZ
_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
05Q C6 C1 C 0 1 Y N N N N N -29.219 -1.551 -2.726 -0.643 0.192 0.004 C6 05Q 1
05Q C11 C2 C 0 1 Y N N N N N -28.540 -4.849 -0.791 3.627 -0.303 1.196 C11 05Q 2
05Q C15 C3 C 0 1 Y N N N N N -30.628 -3.943 -0.089 3.625 -0.297 -1.198 C15 05Q 3
05Q C14 C4 C 0 1 Y N N N N N -31.154 -5.223 -0.007 4.965 0.041 -1.198 C14 05Q 4
05Q C2 C5 C 0 1 Y N N N N N -31.287 -0.760 -3.212 -2.497 -1.184 0.001 C2 05Q 5
05Q C4 C6 C 0 1 Y N N N N N -29.710 -0.394 -4.729 -2.879 1.087 -0.003 C4 05Q 6
05Q C5 C7 C 0 1 Y N N N N N -28.778 -1.039 -3.948 -1.490 1.300 0.002 C5 05Q 7
05Q C8 C8 C 0 1 Y N N N N N -27.765 -0.386 -5.708 -2.543 3.229 -0.001 C8 05Q 8
05Q C9 C9 C 0 1 N N N N N N -28.739 -2.363 -0.564 1.495 -0.839 -0.001 C9 05Q 9
05Q C10 C10 C 0 1 Y N N N N N -29.317 -3.748 -0.482 2.956 -0.470 -0.001 C10 05Q 10
05Q C13 C11 C 0 1 Y N N N N N -30.374 -6.311 -0.332 5.636 0.208 -0.001 C13 05Q 11
05Q C12 C12 C 0 1 Y N N N N N -29.070 -6.129 -0.724 4.967 0.036 1.196 C12 05Q 12
05Q N1 N1 N 0 1 Y N N N N N -30.485 -1.392 -2.367 -1.185 -1.021 0.001 N1 05Q 13
05Q N3 N2 N 0 1 Y N N N N N -31.002 -0.246 -4.395 -3.335 -0.169 0.004 N3 05Q 14
05Q N9 N3 N 0 1 Y N N N N N -29.061 0.007 -5.859 -3.460 2.302 -0.003 N9 05Q 15
05Q N7 N4 N 0 1 Y N N N N N -27.543 -1.023 -4.580 -1.313 2.668 0.003 N7 05Q 16
05Q O1 O1 O 0 1 N N N N N N -28.321 -2.142 -1.920 0.703 0.350 0.003 O1 05Q 17
05Q CL1 CL1 CL 0 0 N N N N N N -32.945 -0.579 -2.709 -3.138 -2.797 -0.002 CL1 05Q 18
05Q H1 H1 H 0 1 N N N N N N -27.511 -4.711 -1.087 3.103 -0.434 2.132 H1 05Q 19
05Q H5 H5 H 0 1 N N N N N N -31.247 -3.092 0.156 3.101 -0.428 -2.133 H5 05Q 20
05Q H4 H4 H 0 1 N N N N N N -32.176 -5.367 0.312 5.488 0.175 -2.134 H4 05Q 21
05Q H3 H3 H 0 1 N N N N N N -30.788 -7.307 -0.279 6.683 0.472 -0.001 H3 05Q 22
05Q H2 H2 H 0 1 N N N N N N -28.458 -6.982 -0.980 5.491 0.166 2.131 H2 05Q 23
05Q H6 H6 H 0 1 N N N N N N -26.997 -0.193 -6.442 -2.739 4.292 -0.002 H6 05Q 24
05Q H7 H7 H 0 1 N N N N N N -27.876 -2.277 0.112 1.268 -1.424 -0.892 H7 05Q 25
05Q H8 H8 H 0 1 N N N N N N -29.501 -1.622 -0.282 1.270 -1.429 0.888 H8 05Q 26
05Q H9 H9 H 0 1 N N N N N N -26.680 -1.408 -4.252 -0.465 3.139 0.006 H9 05Q 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
05Q N9 C8 DOUB Y N 1
05Q N9 C4 SING Y N 2
05Q C8 N7 SING Y N 3
05Q C4 N3 SING Y N 4
05Q C4 C5 DOUB Y N 5
05Q N7 C5 SING Y N 6
05Q N3 C2 DOUB Y N 7
05Q C5 C6 SING Y N 8
05Q C2 CL1 SING N N 9
05Q C2 N1 SING Y N 10
05Q C6 N1 DOUB Y N 11
05Q C6 O1 SING N N 12
05Q O1 C9 SING N N 13
05Q C11 C12 DOUB Y N 14
05Q C11 C10 SING Y N 15
05Q C12 C13 SING Y N 16
05Q C9 C10 SING N N 17
05Q C10 C15 DOUB Y N 18
05Q C13 C14 DOUB Y N 19
05Q C15 C14 SING Y N 20
05Q C11 H1 SING N N 21
05Q C15 H5 SING N N 22
05Q C14 H4 SING N N 23
05Q C13 H3 SING N N 24
05Q C12 H2 SING N N 25
05Q C8 H6 SING N N 26
05Q C9 H7 SING N N 27
05Q C9 H8 SING N N 28
05Q 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
05Q InChI InChI 1.03 InChI=1S/C12H9ClN4O/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)
05Q InChIKey InChI 1.03 XKVATRYEPITAPH-UHFFFAOYSA-N
05Q SMILES_CANONICAL CACTVS 3.385 Clc1nc(OCc2ccccc2)c3[nH]cnc3n1
05Q SMILES CACTVS 3.385 Clc1nc(OCc2ccccc2)c3[nH]cnc3n1
05Q SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1ccc(cc1)COc2c3c(nc[nH]3)nc(n2)Cl
05Q SMILES "OpenEye OEToolkits" 2.0.7 c1ccc(cc1)COc2c3c(nc[nH]3)nc(n2)Cl
#
_pdbx_chem_comp_identifier.comp_id 05Q
_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-phenylmethoxy-7~{H}-purine
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id 05Q
_pdbx_chem_comp_synonyms.name 2-chloranyl-6-phenylmethoxy-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
05Q 'Create component' 2021-05-28 PDBE
05Q 'Initial release' 2022-05-04 RCSB
#
_pdbe_chem_comp_synonyms.comp_id 05Q
_pdbe_chem_comp_synonyms.name 2-chloranyl-6-phenylmethoxy-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
05Q C6 C 5.598 -1.875 1
05Q C11 C 5.598 2.625 2
05Q C15 C 3.000 2.625 3
05Q C14 C 3.000 4.125 4
05Q C2 C 4.299 -4.125 5
05Q C4 C 6.897 -4.125 6
05Q C5 C 6.897 -2.625 7
05Q C8 C 9.192 -3.375 8
05Q C9 C 4.299 0.375 9
05Q C10 C 4.299 1.875 10
05Q C13 C 4.299 4.875 11
05Q C12 C 5.598 4.125 12
05Q N1 N 4.299 -2.625 13
05Q N3 N 5.598 -4.875 14
05Q N9 N 8.316 -4.582 15
05Q N7 N 8.316 -2.168 16
05Q O1 O 5.598 -0.375 17
05Q 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
05Q N9 C8 DOUBLE NONE 1
05Q N9 C4 SINGLE NONE 2
05Q C8 N7 SINGLE NONE 3
05Q C4 N3 SINGLE NONE 4
05Q C4 C5 DOUBLE NONE 5
05Q N7 C5 SINGLE NONE 6
05Q N3 C2 DOUBLE NONE 7
05Q C5 C6 SINGLE NONE 8
05Q C2 CL1 SINGLE NONE 9
05Q C2 N1 SINGLE NONE 10
05Q C6 N1 DOUBLE NONE 11
05Q C6 O1 SINGLE NONE 12
05Q O1 C9 SINGLE NONE 13
05Q C11 C12 DOUBLE NONE 14
05Q C11 C10 SINGLE NONE 15
05Q C12 C13 SINGLE NONE 16
05Q C9 C10 SINGLE NONE 17
05Q C10 C15 DOUBLE NONE 18
05Q C13 C14 DOUBLE NONE 19
05Q C15 C14 SINGLE 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
05Q MurckoScaffold S1 scaffold 'c1ccc(COc2ncnc3nc[nH]c23)cc1' InChI=1S/C12H10N4O/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) ZZZXGPGVDJDFCJ-UHFFFAOYSA-N
05Q imidazole F1 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
05Q inosine F2 fragment 'Oc1ncnc2nc[nH]c12' InChI=1S/C5H4N4O/c10-5-3-4(7-1-6-3)8-2-9-5/h1-2H,(H2,6,7,8,9,10) FDGQSTZJBFJUBT-UHFFFAOYSA-N
05Q phenyl F3 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
05Q purine F4 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
05Q pyrimidine F5 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
05Q C6 S1 1
05Q C11 S1 1
05Q C15 S1 1
05Q C14 S1 1
05Q C2 S1 1
05Q C4 S1 1
05Q C5 S1 1
05Q C8 S1 1
05Q C9 S1 1
05Q C10 S1 1
05Q C13 S1 1
05Q C12 S1 1
05Q N1 S1 1
05Q N3 S1 1
05Q N9 S1 1
05Q N7 S1 1
05Q O1 S1 1
05Q C4 F1 1
05Q C5 F1 1
05Q N7 F1 1
05Q C8 F1 1
05Q N9 F1 1
05Q C2 F2 1
05Q N1 F2 1
05Q C6 F2 1
05Q C5 F2 1
05Q C4 F2 1
05Q N3 F2 1
05Q N9 F2 1
05Q C8 F2 1
05Q N7 F2 1
05Q O1 F2 1
05Q C11 F3 1
05Q C12 F3 1
05Q C13 F3 1
05Q C14 F3 1
05Q C15 F3 1
05Q C10 F3 1
05Q N7 F4 1
05Q C8 F4 1
05Q N9 F4 1
05Q C4 F4 1
05Q C5 F4 1
05Q C6 F4 1
05Q N1 F4 1
05Q C2 F4 1
05Q N3 F4 1
05Q C5 F5 1
05Q C4 F5 1
05Q N3 F5 1
05Q C2 F5 1
05Q N1 F5 1
05Q C6 F5 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 05Q
_pdbe_chem_comp_rdkit_properties.exactmw 260.046
_pdbe_chem_comp_rdkit_properties.amw 260.684
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_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 120.523
_pdbe_chem_comp_rdkit_properties.tpsa 63.690
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.640
_pdbe_chem_comp_rdkit_properties.CrippenMR 64.386
_pdbe_chem_comp_rdkit_properties.chi0v 9.331
_pdbe_chem_comp_rdkit_properties.chi1v 5.014
_pdbe_chem_comp_rdkit_properties.chi2v 2.043
_pdbe_chem_comp_rdkit_properties.chi3v 2.043
_pdbe_chem_comp_rdkit_properties.chi4v 1.324
_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 -2.140
_pdbe_chem_comp_rdkit_properties.kappa1 4.854
_pdbe_chem_comp_rdkit_properties.kappa2 4.619
_pdbe_chem_comp_rdkit_properties.kappa3 2.123
_pdbe_chem_comp_rdkit_properties.Phi 1.246
#
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
05Q UniChem PDBe 05Q
05Q UniChem SureChEMBL SCHEMBL4884326
05Q UniChem 'PubChem TPHARMA' 16755269
05Q UniChem PubChem 11651824
05Q UniChem Nikkaji J1.169.655D
05Q UniChem 'EPA CompTox Dashboard' DTXSID90470056
05Q UniChem BRENDA 50564
#
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
05Q C6 -1.292 0.579 -0.113 ETKDGv3 1
05Q C11 2.398 0.669 0.560 ETKDGv3 2
05Q C15 2.088 -0.021 -1.764 ETKDGv3 3
05Q C14 3.121 -1.056 -1.548 ETKDGv3 4
05Q C2 -1.544 -0.133 2.172 ETKDGv3 5
05Q C4 -3.205 -0.687 0.595 ETKDGv3 6
05Q C5 -2.571 -0.084 -0.371 ETKDGv3 7
05Q C8 -4.425 -0.995 -1.140 ETKDGv3 8
05Q C9 0.671 1.845 -0.973 ETKDGv3 9
05Q C10 1.742 0.809 -0.765 ETKDGv3 10
05Q C13 3.711 -1.176 -0.352 ETKDGv3 11
05Q C12 3.331 -0.272 0.753 ETKDGv3 12
05Q N1 -0.825 0.543 1.109 ETKDGv3 13
05Q N3 -2.685 -0.726 1.929 ETKDGv3 14
05Q N9 -4.407 -1.286 0.129 ETKDGv3 15
05Q N7 -3.296 -0.225 -1.575 ETKDGv3 16
05Q O1 -0.601 1.222 -1.146 ETKDGv3 17
05Q CL1 -0.875 -0.162 3.789 ETKDGv3 18
05Q H1 2.123 1.324 1.376 ETKDGv3 19
05Q H5 1.614 0.055 -2.735 ETKDGv3 20
05Q H4 3.397 -1.719 -2.358 ETKDGv3 21
05Q H3 4.466 -1.934 -0.192 ETKDGv3 22
05Q H2 3.807 -0.375 1.719 ETKDGv3 23
05Q H6 -5.220 -1.309 -1.802 ETKDGv3 24
05Q H7 0.631 2.559 -0.122 ETKDGv3 25
05Q H8 0.906 2.433 -1.886 ETKDGv3 26
05Q H9 -3.064 0.122 -2.531 ETKDGv3 27
#