data_J6F
#
_chem_comp.id J6F
_chem_comp.name 7-hexyl-3-methyl-8-sulfanylidene-9H-purine-2,6-dione
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H18 N4 O2 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-08-04
_chem_comp.pdbx_modified_date 2023-07-21
_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 282.362
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code J6F
_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 7YL1
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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
J6F C4 C1 C 0 1 N N N N N N 4.637 26.767 32.137 -2.184 -0.495 -0.186 C4 J6F 1
J6F C5 C2 C 0 1 N N N N N N 4.811 28.100 31.914 -1.128 0.196 0.343 C5 J6F 2
J6F C6 C3 C 0 1 N N N N N N 5.855 28.752 32.470 -1.262 1.577 0.586 C6 J6F 3
J6F C8 C4 C 0 1 N N N N N N 3.059 27.443 30.857 -0.527 -1.926 0.115 C8 J6F 4
J6F N1 N1 N 0 1 N N N N N N 6.763 28.046 33.272 -2.427 2.190 0.292 N1 J6F 5
J6F N3 N2 N 0 1 N N N N N N 5.501 26.056 32.927 -3.353 0.174 -0.469 N3 J6F 6
J6F CAA C5 C 0 1 N N N N N N 0.338 34.184 33.817 6.855 1.339 -1.189 CAA J6F 7
J6F CAF C6 C 0 1 N N N N N N 1.584 33.679 33.057 5.906 0.958 -0.052 CAF J6F 8
J6F CAG C7 C 0 1 N N N N N N 1.213 32.548 32.092 4.521 0.648 -0.625 CAG J6F 9
J6F CAH C8 C 0 1 N N N N N N 2.498 32.010 31.449 3.572 0.268 0.513 CAH J6F 10
J6F CAI C9 C 0 1 N N N N N N 2.312 30.515 31.159 2.188 -0.042 -0.060 CAI J6F 11
J6F CAJ C10 C 0 1 N N N N N N 3.607 29.903 30.600 1.238 -0.423 1.077 CAJ J6F 12
J6F N7 N3 N 0 1 N N N N N N 3.820 28.511 31.108 -0.087 -0.720 0.529 N7 J6F 13
J6F O6 O1 O 0 1 N N N N N N 6.051 29.958 32.292 -0.334 2.212 1.058 O6 J6F 14
J6F C2 C11 C 0 1 N N N N N N 6.552 26.668 33.498 -3.454 1.494 -0.228 C2 J6F 15
J6F O2 O2 O 0 1 N N N N N N 7.324 26.010 34.207 -4.495 2.069 -0.484 O2 J6F 16
J6F CAB C12 C 0 1 N N N N N N 5.319 24.588 33.170 -4.490 -0.554 -1.037 CAB J6F 17
J6F N9 N4 N 0 1 N N N N N N 3.534 26.370 31.480 -1.793 -1.802 -0.325 N9 J6F 18
J6F S8 S1 S 0 1 N N N N N N 1.652 27.405 29.856 0.379 -3.378 0.144 S8 J6F 19
J6F H1 H1 H 0 1 N N N N N N 7.549 28.512 33.678 -2.525 3.141 0.457 H1 J6F 20
J6F H2 H2 H 0 1 N N N N N N 0.629 34.994 34.502 7.841 1.560 -0.781 H2 J6F 21
J6F H3 H3 H 0 1 N N N N N N -0.403 34.562 33.097 6.930 0.510 -1.893 H3 J6F 22
J6F H4 H4 H 0 1 N N N N N N -0.100 33.356 34.393 6.470 2.219 -1.705 H4 J6F 23
J6F H5 H5 H 0 1 N N N N N N 2.322 33.306 33.782 6.291 0.078 0.464 H5 J6F 24
J6F H6 H6 H 0 1 N N N N N N 2.020 34.512 32.486 5.831 1.787 0.652 H6 J6F 25
J6F H7 H7 H 0 1 N N N N N N 0.541 32.933 31.311 4.136 1.528 -1.140 H7 J6F 26
J6F H8 H8 H 0 1 N N N N N N 0.709 31.741 32.644 4.596 -0.181 -1.328 H8 J6F 27
J6F H9 H9 H 0 1 N N N N N N 3.344 32.151 32.138 3.957 -0.612 1.028 H9 J6F 28
J6F H10 H10 H 0 1 N N N N N N 2.696 32.548 30.510 3.497 1.097 1.216 H10 J6F 29
J6F H11 H11 H 0 1 N N N N N N 1.505 30.388 30.422 1.802 0.838 -0.576 H11 J6F 30
J6F H12 H12 H 0 1 N N N N N N 2.041 29.998 32.091 2.263 -0.871 -0.764 H12 J6F 31
J6F H13 H13 H 0 1 N N N N N N 4.459 30.529 30.905 1.623 -1.303 1.593 H13 J6F 32
J6F H14 H14 H 0 1 N N N N N N 3.545 29.877 29.502 1.163 0.406 1.781 H14 J6F 33
J6F H15 H15 H 0 1 N N N N N N 6.121 24.223 33.829 -5.117 -0.935 -0.230 H15 J6F 34
J6F H16 H16 H 0 1 N N N N N N 4.344 24.414 33.648 -5.075 0.118 -1.665 H16 J6F 35
J6F H17 H17 H 0 1 N N N N N N 5.359 24.050 32.211 -4.126 -1.387 -1.638 H17 J6F 36
J6F H18 H18 H 0 1 N N N N N N 3.147 25.448 31.463 -2.342 -2.521 -0.677 H18 J6F 37
#
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
J6F S8 C8 DOUB N N 1
J6F CAJ N7 SING N N 2
J6F CAJ CAI SING N N 3
J6F C8 N7 SING N N 4
J6F C8 N9 SING N N 5
J6F N7 C5 SING N N 6
J6F CAI CAH SING N N 7
J6F CAH CAG SING N N 8
J6F N9 C4 SING N N 9
J6F C5 C4 DOUB N N 10
J6F C5 C6 SING N N 11
J6F CAG CAF SING N N 12
J6F C4 N3 SING N N 13
J6F O6 C6 DOUB N N 14
J6F C6 N1 SING N N 15
J6F N3 CAB SING N N 16
J6F N3 C2 SING N N 17
J6F CAF CAA SING N N 18
J6F N1 C2 SING N N 19
J6F C2 O2 DOUB N N 20
J6F N1 H1 SING N N 21
J6F CAA H2 SING N N 22
J6F CAA H3 SING N N 23
J6F CAA H4 SING N N 24
J6F CAF H5 SING N N 25
J6F CAF H6 SING N N 26
J6F CAG H7 SING N N 27
J6F CAG H8 SING N N 28
J6F CAH H9 SING N N 29
J6F CAH H10 SING N N 30
J6F CAI H11 SING N N 31
J6F CAI H12 SING N N 32
J6F CAJ H13 SING N N 33
J6F CAJ H14 SING N N 34
J6F CAB H15 SING N N 35
J6F CAB H16 SING N N 36
J6F CAB H17 SING N N 37
J6F N9 H18 SING N N 38
#
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
J6F InChI InChI 1.06 InChI=1S/C12H18N4O2S/c1-3-4-5-6-7-16-8-9(13-12(16)19)15(2)11(18)14-10(8)17/h3-7H2,1-2H3,(H,13,19)(H,14,17,18)
J6F InChIKey InChI 1.06 UXIHCIYDMGYKSF-UHFFFAOYSA-N
J6F SMILES_CANONICAL CACTVS 3.385 CCCCCCN1C(=S)NC2=C1C(=O)NC(=O)N2C
J6F SMILES CACTVS 3.385 CCCCCCN1C(=S)NC2=C1C(=O)NC(=O)N2C
J6F SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CCCCCCN1C2=C(NC1=S)N(C(=O)NC2=O)C
J6F SMILES "OpenEye OEToolkits" 2.0.7 CCCCCCN1C2=C(NC1=S)N(C(=O)NC2=O)C
#
_pdbx_chem_comp_identifier.comp_id J6F
_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 7-hexyl-3-methyl-8-sulfanylidene-9~{H}-purine-2,6-dione
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
J6F 'Create component' 2022-08-04 PDBJ
J6F 'Initial release' 2023-07-26 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 '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
J6F C4 C 6.897 -2.456 1
J6F C5 C 6.897 -0.956 2
J6F C6 C 5.598 -0.206 3
J6F C8 C 9.192 -1.706 4
J6F N1 N 4.299 -0.956 5
J6F N3 N 5.598 -3.206 6
J6F CAA C 14.118 4.706 7
J6F CAF C 12.650 4.397 8
J6F CAG C 12.184 2.971 9
J6F CAH C 10.716 2.662 10
J6F CAI C 10.250 1.236 11
J6F CAJ C 8.783 0.927 12
J6F N7 N 8.316 -0.499 13
J6F O6 O 5.598 1.294 14
J6F C2 C 4.299 -2.456 15
J6F O2 O 3.000 -3.206 16
J6F CAB C 5.598 -4.706 17
J6F N9 N 8.316 -2.913 18
J6F S8 S 10.692 -1.706 19
#
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
J6F S8 C8 DOUBLE NONE 1
J6F CAJ N7 SINGLE NONE 2
J6F CAJ CAI SINGLE NONE 3
J6F C8 N7 SINGLE NONE 4
J6F C8 N9 SINGLE NONE 5
J6F N7 C5 SINGLE NONE 6
J6F CAI CAH SINGLE NONE 7
J6F CAH CAG SINGLE NONE 8
J6F N9 C4 SINGLE NONE 9
J6F C5 C4 DOUBLE NONE 10
J6F C5 C6 SINGLE NONE 11
J6F CAG CAF SINGLE NONE 12
J6F C4 N3 SINGLE NONE 13
J6F O6 C6 DOUBLE NONE 14
J6F C6 N1 SINGLE NONE 15
J6F N3 CAB SINGLE NONE 16
J6F N3 C2 SINGLE NONE 17
J6F CAF CAA SINGLE NONE 18
J6F N1 C2 SINGLE NONE 19
J6F C2 O2 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
J6F MurckoScaffold S1 scaffold 'O=c1[nH]c(=O)c2[nH]c(=S)[nH]c2[nH]1' InChI=1S/C5H4N4O2S/c10-3-1-2(7-4(11)9-3)8-5(12)6-1/h(H4,6,7,8,9,10,11,12) KFQXXACDWBTCDT-UHFFFAOYSA-N
J6F imidazole F1 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
J6F purine F2 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
J6F pyrimidine F3 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
J6F C4 S1 1
J6F C5 S1 1
J6F C6 S1 1
J6F C8 S1 1
J6F N1 S1 1
J6F N3 S1 1
J6F N7 S1 1
J6F O6 S1 1
J6F C2 S1 1
J6F O2 S1 1
J6F N9 S1 1
J6F S8 S1 1
J6F C4 F1 1
J6F C5 F1 1
J6F N7 F1 1
J6F C8 F1 1
J6F N9 F1 1
J6F N7 F2 1
J6F C8 F2 1
J6F N9 F2 1
J6F C4 F2 1
J6F C5 F2 1
J6F C6 F2 1
J6F N1 F2 1
J6F C2 F2 1
J6F N3 F2 1
J6F C5 F3 1
J6F C4 F3 1
J6F N3 F3 1
J6F C2 F3 1
J6F N1 F3 1
J6F C6 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id J6F
_pdbe_chem_comp_rdkit_properties.exactmw 282.115
_pdbe_chem_comp_rdkit_properties.amw 282.369
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 19
_pdbe_chem_comp_rdkit_properties.NumAtoms 37
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.583
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_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 140.043
_pdbe_chem_comp_rdkit_properties.tpsa 75.580
_pdbe_chem_comp_rdkit_properties.CrippenClogP 3.038
_pdbe_chem_comp_rdkit_properties.CrippenMR 75.136
_pdbe_chem_comp_rdkit_properties.chi0v 9.830
_pdbe_chem_comp_rdkit_properties.chi1v 5.007
_pdbe_chem_comp_rdkit_properties.chi2v 2.260
_pdbe_chem_comp_rdkit_properties.chi3v 2.260
_pdbe_chem_comp_rdkit_properties.chi4v 1.490
_pdbe_chem_comp_rdkit_properties.chi0n 27.014
_pdbe_chem_comp_rdkit_properties.chi1n 13.493
_pdbe_chem_comp_rdkit_properties.chi2n 1.986
_pdbe_chem_comp_rdkit_properties.chi3n 1.986
_pdbe_chem_comp_rdkit_properties.chi4n 1.267
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.630
_pdbe_chem_comp_rdkit_properties.kappa1 3.519
_pdbe_chem_comp_rdkit_properties.kappa2 5.561
_pdbe_chem_comp_rdkit_properties.kappa3 2.555
_pdbe_chem_comp_rdkit_properties.Phi 1.030
#
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
J6F UniChem ChEMBL CHEMBL5574538
J6F UniChem ZINC ZINC000100048327
J6F UniChem eMolecules 1184533
J6F UniChem PubChem 3097501
J6F UniChem Mcule MCULE-7048829286
#
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
J6F C4 2.636 0.634 0.101 ETKDGv3 1
J6F C5 1.805 -0.072 0.856 ETKDGv3 2
J6F C6 2.057 -1.492 1.137 ETKDGv3 3
J6F C8 0.983 2.001 0.701 ETKDGv3 4
J6F N1 3.201 -2.109 0.536 ETKDGv3 5
J6F N3 3.819 0.075 -0.497 ETKDGv3 6
J6F CAA -5.035 0.081 -0.282 ETKDGv3 7
J6F CAF -4.057 -0.974 -0.798 ETKDGv3 8
J6F CAG -2.738 -0.372 -1.315 ETKDGv3 9
J6F CAH -1.920 0.402 -0.266 ETKDGv3 10
J6F CAI -1.417 -0.492 0.879 ETKDGv3 11
J6F CAJ -0.557 0.281 1.890 ETKDGv3 12
J6F N7 0.706 0.731 1.299 ETKDGv3 13
J6F O6 1.300 -2.158 1.891 ETKDGv3 14
J6F C2 4.079 -1.333 -0.296 ETKDGv3 15
J6F O2 5.068 -1.890 -0.845 ETKDGv3 16
J6F CAB 4.669 0.899 -1.358 ETKDGv3 17
J6F N9 2.189 1.978 -0.052 ETKDGv3 18
J6F S8 0.018 3.319 0.815 ETKDGv3 19
J6F H1 3.397 -3.122 0.702 ETKDGv3 20
J6F H2 -4.668 0.523 0.668 ETKDGv3 21
J6F H3 -6.018 -0.394 -0.083 ETKDGv3 22
J6F H4 -5.176 0.884 -1.037 ETKDGv3 23
J6F H5 -3.862 -1.725 -0.005 ETKDGv3 24
J6F H6 -4.542 -1.512 -1.641 ETKDGv3 25
J6F H7 -2.966 0.314 -2.160 ETKDGv3 26
J6F H8 -2.111 -1.193 -1.728 ETKDGv3 27
J6F H9 -1.045 0.838 -0.792 ETKDGv3 28
J6F H10 -2.514 1.248 0.141 ETKDGv3 29
J6F H11 -0.836 -1.341 0.461 ETKDGv3 30
J6F H12 -2.284 -0.909 1.431 ETKDGv3 31
J6F H13 -0.338 -0.375 2.758 ETKDGv3 32
J6F H14 -1.127 1.148 2.286 ETKDGv3 33
J6F H15 5.650 0.414 -1.544 ETKDGv3 34
J6F H16 4.870 1.877 -0.872 ETKDGv3 35
J6F H17 4.161 1.069 -2.330 ETKDGv3 36
J6F H18 2.603 2.745 -0.627 ETKDGv3 37
#