data_J9B
#
_chem_comp.id J9B
_chem_comp.name "2-chloranyl-9-[(3-chlorophenyl)methyl]-~{N}-methyl-purin-6-amine"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C13 H11 Cl2 N5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2023-08-07
_chem_comp.pdbx_modified_date 2023-12-01
_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 308.166
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code J9B
_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 8Q4M
_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
J9B C10 C1 C 0 1 N N N N N N -23.413 30.542 -23.149 -1.169 -1.531 1.668 C10 J9B 1
J9B C13 C2 C 0 1 Y N N N N N -26.426 32.172 -25.248 -3.517 0.575 -0.409 C13 J9B 2
J9B C15 C3 C 0 1 Y N N N N N -25.701 33.293 -25.988 -4.262 -0.397 -1.053 C15 J9B 3
J9B C17 C4 C 0 1 Y N N N N N -23.429 32.578 -24.835 -3.010 -2.101 0.070 C17 J9B 4
J9B C02 C5 C 0 1 Y N N N N N -25.299 26.368 -23.518 2.031 1.363 0.429 C02 J9B 5
J9B C04 C6 C 0 1 Y N N N N N -23.300 25.919 -24.913 3.090 -0.464 -0.505 C04 J9B 6
J9B C06 C7 C 0 1 N N N N N N -22.923 23.656 -25.886 5.252 -0.145 -1.650 C06 J9B 7
J9B C07 C8 C 0 1 Y N N N N N -22.822 27.360 -24.676 2.029 -1.276 -0.067 C07 J9B 8
J9B C08 C9 C 0 1 Y N N N N N -23.563 28.200 -23.919 0.975 -0.669 0.635 C08 J9B 9
J9B C11 C10 C 0 1 Y N N N N N -24.165 31.461 -24.101 -2.261 -1.131 0.710 C11 J9B 10
J9B C12 C11 C 0 1 Y N N N N N -25.660 31.253 -24.302 -2.515 0.207 0.471 C12 J9B 11
J9B C16 C12 C 0 1 Y N N N N N -24.204 33.499 -25.777 -4.008 -1.734 -0.814 C16 J9B 12
J9B C18 C13 C 0 1 Y N N N N N -21.810 29.284 -24.592 0.606 -2.833 0.434 C18 J9B 13
J9B N03 N1 N 0 1 Y N N N N N -24.516 25.475 -24.328 3.045 0.836 -0.235 N03 J9B 14
J9B N05 N2 N 0 1 N N N N N N -22.510 25.036 -25.724 4.156 -1.007 -1.200 N05 J9B 15
J9B N09 N3 N 0 1 Y N N N N N -22.941 29.380 -23.865 0.093 -1.675 0.937 N09 J9B 16
J9B N19 N4 N 0 1 Y N N N N N -21.739 28.034 -25.094 1.742 -2.597 -0.155 N19 J9B 17
J9B N20 N5 N 0 1 Y N N N N N -24.847 27.738 -23.295 1.016 0.641 0.858 N20 J9B 18
J9B CL01 CL1 CL 0 0 N N N N N N -26.827 25.825 -22.776 2.040 3.069 0.753 CL01 J9B 19
J9B CL14 CL2 CL 0 0 N N N N N N -28.175 31.923 -25.478 -3.836 2.254 -0.709 CL14 J9B 20
J9B H101 H1 H 0 0 N N N N N N -24.086 30.224 -22.339 -1.060 -0.765 2.435 H101 J9B 21
J9B H102 H2 H 0 0 N N N N N N -22.555 31.081 -22.721 -1.428 -2.481 2.137 H102 J9B 22
J9B H151 H3 H 0 0 N N N N N N -26.247 33.939 -26.660 -5.042 -0.111 -1.743 H151 J9B 23
J9B H171 H4 H 0 0 N N N N N N -22.368 32.717 -24.690 -2.811 -3.146 0.257 H171 J9B 24
J9B H062 H5 H 0 0 N N N N N N -22.205 23.132 -26.534 5.716 0.332 -0.786 H062 J9B 25
J9B H063 H6 H 0 0 N N N N N N -22.955 23.165 -24.902 5.994 -0.745 -2.175 H063 J9B 26
J9B H061 H7 H 0 0 N N N N N N -23.922 23.624 -26.344 4.861 0.620 -2.321 H061 J9B 27
J9B H121 H8 H 0 0 N N N N N N -26.174 30.461 -23.779 -1.930 0.965 0.970 H121 J9B 28
J9B H161 H9 H 0 0 N N N N N N -23.691 34.297 -26.294 -4.589 -2.493 -1.316 H161 J9B 29
J9B H181 H10 H 0 0 N N N N N N -21.087 30.071 -24.746 0.138 -3.804 0.512 H181 J9B 30
J9B H051 H11 H 0 0 N N N N N N -22.472 25.438 -26.639 4.177 -1.957 -1.390 H051 J9B 31
#
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
J9B CL01 C02 SING N N 1
J9B C02 N20 DOUB Y N 2
J9B C02 N03 SING Y N 3
J9B N03 C04 DOUB Y N 4
J9B C04 N05 SING N N 5
J9B C04 C07 SING Y N 6
J9B N05 C06 SING N N 7
J9B C07 N19 SING Y N 8
J9B C07 C08 DOUB Y N 9
J9B C08 N09 SING Y N 10
J9B C08 N20 SING Y N 11
J9B N09 C10 SING N N 12
J9B N09 C18 SING Y N 13
J9B C10 C11 SING N N 14
J9B C11 C17 DOUB Y N 15
J9B C11 C12 SING Y N 16
J9B C12 C13 DOUB Y N 17
J9B C13 CL14 SING N N 18
J9B C13 C15 SING Y N 19
J9B C15 C16 DOUB Y N 20
J9B C16 C17 SING Y N 21
J9B C18 N19 DOUB Y N 22
J9B C10 H101 SING N N 23
J9B C10 H102 SING N N 24
J9B C15 H151 SING N N 25
J9B C17 H171 SING N N 26
J9B C06 H062 SING N N 27
J9B C06 H063 SING N N 28
J9B C06 H061 SING N N 29
J9B C12 H121 SING N N 30
J9B C16 H161 SING N N 31
J9B C18 H181 SING N N 32
J9B N05 H051 SING N N 33
#
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
J9B InChI InChI 1.06 "InChI=1S/C13H11Cl2N5/c1-16-11-10-12(19-13(15)18-11)20(7-17-10)6-8-3-2-4-9(14)5-8/h2-5,7H,6H2,1H3,(H,16,18,19)"
J9B InChIKey InChI 1.06 HBDBUHLHHMNOIL-UHFFFAOYSA-N
J9B SMILES_CANONICAL CACTVS 3.385 "CNc1nc(Cl)nc2n(Cc3cccc(Cl)c3)cnc12"
J9B SMILES CACTVS 3.385 "CNc1nc(Cl)nc2n(Cc3cccc(Cl)c3)cnc12"
J9B SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CNc1c2c(nc(n1)Cl)n(cn2)Cc3cccc(c3)Cl"
J9B SMILES "OpenEye OEToolkits" 2.0.7 "CNc1c2c(nc(n1)Cl)n(cn2)Cc3cccc(c3)Cl"
#
_pdbx_chem_comp_identifier.comp_id J9B
_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-9-[(3-chlorophenyl)methyl]-~{N}-methyl-purin-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
J9B 'Create component' 2023-08-07 PDBE
J9B 'Initial release' 2023-12-06 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.09.6 'Core functionality.'
pdbeccdutils 0.8.6 '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
J9B C10 C 8.783 2.169 1
J9B C13 C 12.720 1.671 2
J9B C15 C 13.186 3.097 3
J9B C17 C 10.716 3.904 4
J9B C02 C 4.299 0.286 5
J9B C04 C 5.598 -1.964 6
J9B C06 C 4.299 -4.214 7
J9B C07 C 6.897 -1.214 8
J9B C08 C 6.897 0.286 9
J9B C11 C 10.250 2.479 10
J9B C12 C 11.252 1.362 11
J9B C16 C 12.184 4.214 12
J9B C18 C 9.192 -0.464 13
J9B N03 N 4.299 -1.214 14
J9B N05 N 5.598 -3.464 15
J9B N09 N 8.316 0.743 16
J9B N19 N 8.316 -1.671 17
J9B N20 N 5.598 1.036 18
J9B CL01 Cl 3.000 1.036 19
J9B CL14 Cl 13.722 0.555 20
#
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
J9B CL01 C02 SINGLE NONE 1
J9B C02 N20 DOUBLE NONE 2
J9B C02 N03 SINGLE NONE 3
J9B N03 C04 DOUBLE NONE 4
J9B C04 N05 SINGLE NONE 5
J9B C04 C07 SINGLE NONE 6
J9B N05 C06 SINGLE NONE 7
J9B C07 N19 SINGLE NONE 8
J9B C07 C08 DOUBLE NONE 9
J9B C08 N09 SINGLE NONE 10
J9B C08 N20 SINGLE NONE 11
J9B N09 C10 SINGLE NONE 12
J9B N09 C18 SINGLE NONE 13
J9B C10 C11 SINGLE NONE 14
J9B C11 C17 DOUBLE NONE 15
J9B C11 C12 SINGLE NONE 16
J9B C12 C13 DOUBLE NONE 17
J9B C13 CL14 SINGLE NONE 18
J9B C13 C15 SINGLE NONE 19
J9B C15 C16 DOUBLE NONE 20
J9B C16 C17 SINGLE NONE 21
J9B C18 N19 DOUBLE NONE 22
#
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
J9B MurckoScaffold S1 scaffold c1ccc(Cn2cnc3cncnc32)cc1 InChI=1S/C12H10N4/c1-2-4-10(5-3-1)7-16-9-15-11-6-13-8-14-12(11)16/h1-6,8-9H,7H2 MDOUSORGCMUMBO-UHFFFAOYSA-N
J9B adenine F1 fragment 'Nc1ncnc2nc[nH]c12' InChI=1S/C5H5N5/c6-4-3-5(9-1-7-3)10-2-8-4/h1-2H,(H3,6,7,8,9,10) GFFGJBXGBJISGV-UHFFFAOYSA-N
J9B imidazole F2 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
J9B phenyl F3 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
J9B 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
J9B 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
J9B C10 S1 1
J9B C13 S1 1
J9B C15 S1 1
J9B C17 S1 1
J9B C02 S1 1
J9B C04 S1 1
J9B C07 S1 1
J9B C08 S1 1
J9B C11 S1 1
J9B C12 S1 1
J9B C16 S1 1
J9B C18 S1 1
J9B N03 S1 1
J9B N09 S1 1
J9B N19 S1 1
J9B N20 S1 1
J9B N03 F1 1
J9B C04 F1 1
J9B C07 F1 1
J9B C08 F1 1
J9B N20 F1 1
J9B C02 F1 1
J9B N09 F1 1
J9B C18 F1 1
J9B N19 F1 1
J9B N05 F1 1
J9B C07 F2 1
J9B C08 F2 1
J9B N09 F2 1
J9B C18 F2 1
J9B N19 F2 1
J9B C13 F3 1
J9B C12 F3 1
J9B C11 F3 1
J9B C17 F3 1
J9B C16 F3 1
J9B C15 F3 1
J9B N19 F4 1
J9B C18 F4 1
J9B N09 F4 1
J9B C08 F4 1
J9B C07 F4 1
J9B C04 F4 1
J9B N03 F4 1
J9B C02 F4 1
J9B N20 F4 1
J9B C07 F5 1
J9B C04 F5 1
J9B N03 F5 1
J9B C02 F5 1
J9B N20 F5 1
J9B C08 F5 1
#
_pdbe_chem_comp_rdkit_properties.comp_id J9B
_pdbe_chem_comp_rdkit_properties.exactmw 307.039
_pdbe_chem_comp_rdkit_properties.amw 308.172
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 20
_pdbe_chem_comp_rdkit_properties.NumAtoms 31
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.154
_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 140.647
_pdbe_chem_comp_rdkit_properties.tpsa 55.630
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.359
_pdbe_chem_comp_rdkit_properties.CrippenMR 77.138
_pdbe_chem_comp_rdkit_properties.chi0v 11.004
_pdbe_chem_comp_rdkit_properties.chi1v 5.844
_pdbe_chem_comp_rdkit_properties.chi2v 2.576
_pdbe_chem_comp_rdkit_properties.chi3v 2.576
_pdbe_chem_comp_rdkit_properties.chi4v 1.755
_pdbe_chem_comp_rdkit_properties.chi0n 20.492
_pdbe_chem_comp_rdkit_properties.chi1n 10.535
_pdbe_chem_comp_rdkit_properties.chi2n 2.218
_pdbe_chem_comp_rdkit_properties.chi3n 2.218
_pdbe_chem_comp_rdkit_properties.chi4n 1.453
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.850
_pdbe_chem_comp_rdkit_properties.kappa1 5.502
_pdbe_chem_comp_rdkit_properties.kappa2 5.264
_pdbe_chem_comp_rdkit_properties.kappa3 2.418
_pdbe_chem_comp_rdkit_properties.Phi 1.448
#
_pdbe_chem_comp_external_mappings.comp_id J9B
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PubChem
_pdbe_chem_comp_external_mappings.resource_id 169449356
#
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
J9B C10 -1.479 -1.804 -1.159 ETKDGv3 1
J9B C13 -3.254 1.373 -0.027 ETKDGv3 2
J9B C15 -3.798 0.927 1.273 ETKDGv3 3
J9B C17 -2.808 -1.266 0.860 ETKDGv3 4
J9B C02 1.504 1.421 -1.743 ETKDGv3 5
J9B C04 2.674 0.434 0.113 ETKDGv3 6
J9B C06 4.623 1.565 1.260 ETKDGv3 7
J9B C07 1.738 -0.693 0.001 ETKDGv3 8
J9B C08 0.815 -0.676 -0.922 ETKDGv3 9
J9B C11 -2.320 -0.872 -0.330 ETKDGv3 10
J9B C12 -2.553 0.520 -0.788 ETKDGv3 11
J9B C16 -3.588 -0.326 1.693 ETKDGv3 12
J9B C18 0.451 -2.354 0.460 ETKDGv3 13
J9B N03 2.543 1.423 -0.733 ETKDGv3 14
J9B N05 3.691 0.452 1.123 ETKDGv3 15
J9B N09 -0.087 -1.750 -0.726 ETKDGv3 16
J9B N19 1.522 -1.766 0.910 ETKDGv3 17
J9B N20 0.666 0.422 -1.829 ETKDGv3 18
J9B CL01 1.352 2.779 -2.835 ETKDGv3 19
J9B CL14 -3.523 3.020 -0.567 ETKDGv3 20
J9B H101 -1.541 -1.522 -2.232 ETKDGv3 21
J9B H102 -1.854 -2.847 -1.072 ETKDGv3 22
J9B H151 -4.367 1.614 1.886 ETKDGv3 23
J9B H171 -2.631 -2.270 1.226 ETKDGv3 24
J9B H062 4.064 2.502 1.466 ETKDGv3 25
J9B H063 5.321 1.371 2.101 ETKDGv3 26
J9B H061 5.212 1.680 0.325 ETKDGv3 27
J9B H121 -2.155 0.849 -1.739 ETKDGv3 28
J9B H161 -3.983 -0.653 2.646 ETKDGv3 29
J9B H181 -0.006 -3.198 0.959 ETKDGv3 30
J9B H051 3.771 -0.353 1.783 ETKDGv3 31
#