data_JFS
#
_chem_comp.id JFS
_chem_comp.name '[4-(1H-benzimidazol-1-yl)phenyl]methanol'
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C14 H12 N2 O'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2018-09-10
_chem_comp.pdbx_modified_date 2024-09-27
_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 224.258
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code JFS
_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 5QDK
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_chem_comp.pdbx_pcm Y
#
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
JFS C10 C1 C 0 1 Y N N N N N 32.739 -12.309 -29.503 0.566 -0.372 0.021 C10 JFS 1
JFS C13 C2 C 0 1 Y N N N N N 34.458 -14.591 -29.350 3.233 0.335 0.225 C13 JFS 2
JFS C15 C3 C 0 1 Y N N N N N 32.877 -13.170 -30.582 1.061 0.694 -0.717 C15 JFS 3
JFS C01 C4 C 0 1 Y N N N N N 28.826 -9.442 -27.514 -4.402 1.230 0.131 C01 JFS 4
JFS C02 C5 C 0 1 Y N N N N N 29.401 -10.537 -26.902 -3.278 2.026 0.305 C02 JFS 5
JFS C03 C6 C 0 1 Y N N N N N 30.433 -11.182 -27.528 -2.016 1.474 0.253 C03 JFS 6
JFS C04 C7 C 0 1 Y N N N N N 30.904 -10.785 -28.723 -1.870 0.112 0.023 C04 JFS 7
JFS C05 C8 C 0 1 Y N N N N N 30.277 -9.640 -29.358 -3.008 -0.693 -0.154 C05 JFS 8
JFS C06 C9 C 0 1 Y N N N N N 29.266 -9.035 -28.692 -4.278 -0.112 -0.091 C06 JFS 9
JFS N07 N1 N 0 1 Y N N N N N 30.906 -9.400 -30.574 -2.568 -1.961 -0.357 N07 JFS 10
JFS C08 C10 C 0 1 Y N N N N N 31.801 -10.332 -30.682 -1.268 -1.987 -0.318 C08 JFS 11
JFS N09 N2 N 0 1 Y N N N N N 31.864 -11.199 -29.626 -0.783 -0.734 -0.086 N09 JFS 12
JFS C11 C11 C 0 1 Y N N N N N 33.450 -12.593 -28.362 1.412 -1.083 0.862 C11 JFS 13
JFS C12 C12 C 0 1 Y N N N N N 34.280 -13.678 -28.310 2.743 -0.728 0.961 C12 JFS 14
JFS C14 C13 C 0 1 Y N N N N N 33.702 -14.277 -30.509 2.393 1.045 -0.613 C14 JFS 15
JFS C16 C14 C 0 1 N N N N N N 35.426 -15.812 -29.260 4.686 0.721 0.336 C16 JFS 16
JFS O17 O1 O 0 1 N N N N N N 35.104 -16.842 -30.130 5.445 0.004 -0.640 O17 JFS 17
JFS H151 H1 H 0 0 N N N N N N 32.332 -12.972 -31.493 0.406 1.249 -1.372 H151 JFS 18
JFS H011 H2 H 0 0 N N N N N N 28.016 -8.917 -27.030 -5.384 1.676 0.174 H011 JFS 19
JFS H021 H3 H 0 0 N N N N N N 29.042 -10.880 -25.943 -3.393 3.085 0.483 H021 JFS 20
JFS H031 H4 H 0 0 N N N N N N 30.884 -12.037 -27.047 -1.145 2.097 0.389 H031 JFS 21
JFS H061 H5 H 0 0 N N N N N N 28.795 -8.176 -29.146 -5.159 -0.722 -0.225 H061 JFS 22
JFS H081 H6 H 0 0 N N N N N N 32.449 -10.417 -31.542 -0.662 -2.871 -0.449 H081 JFS 23
JFS H111 H7 H 0 0 N N N N N N 33.352 -11.953 -27.498 1.030 -1.913 1.438 H111 JFS 24
JFS H121 H8 H 0 0 N N N N N N 34.837 -13.840 -27.399 3.402 -1.280 1.615 H121 JFS 25
JFS H141 H9 H 0 0 N N N N N N 33.774 -14.928 -31.368 2.779 1.875 -1.187 H141 JFS 26
JFS H162 H10 H 0 0 N N N N N N 35.397 -16.203 -28.232 4.792 1.792 0.164 H162 JFS 27
JFS H161 H11 H 0 0 N N N N N N 36.444 -15.466 -29.492 5.052 0.475 1.333 H161 JFS 28
JFS H171 H12 H 0 0 N N N N N N 35.728 -17.551 -30.027 6.391 0.204 -0.626 H171 JFS 29
#
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
JFS C08 N07 DOUB Y N 1
JFS C08 N09 SING Y N 2
JFS C15 C14 DOUB Y N 3
JFS C15 C10 SING Y N 4
JFS N07 C05 SING Y N 5
JFS C14 C13 SING Y N 6
JFS O17 C16 SING N N 7
JFS N09 C10 SING N N 8
JFS N09 C04 SING Y N 9
JFS C10 C11 DOUB Y N 10
JFS C05 C04 DOUB Y N 11
JFS C05 C06 SING Y N 12
JFS C13 C16 SING N N 13
JFS C13 C12 DOUB Y N 14
JFS C04 C03 SING Y N 15
JFS C06 C01 DOUB Y N 16
JFS C11 C12 SING Y N 17
JFS C03 C02 DOUB Y N 18
JFS C01 C02 SING Y N 19
JFS C15 H151 SING N N 20
JFS C01 H011 SING N N 21
JFS C02 H021 SING N N 22
JFS C03 H031 SING N N 23
JFS C06 H061 SING N N 24
JFS C08 H081 SING N N 25
JFS C11 H111 SING N N 26
JFS C12 H121 SING N N 27
JFS C14 H141 SING N N 28
JFS C16 H162 SING N N 29
JFS C16 H161 SING N N 30
JFS O17 H171 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
JFS SMILES ACDLabs 12.01 'c1(ccc(CO)cc1)n3c2ccccc2nc3'
JFS InChI InChI 1.03 'InChI=1S/C14H12N2O/c17-9-11-5-7-12(8-6-11)16-10-15-13-3-1-2-4-14(13)16/h1-8,10,17H,9H2'
JFS InChIKey InChI 1.03 IRZKUEWQJPIBJF-UHFFFAOYSA-N
JFS SMILES_CANONICAL CACTVS 3.385 'OCc1ccc(cc1)n2cnc3ccccc23'
JFS SMILES CACTVS 3.385 'OCc1ccc(cc1)n2cnc3ccccc23'
JFS SMILES_CANONICAL 'OpenEye OEToolkits' 2.0.6 'c1ccc2c(c1)ncn2c3ccc(cc3)CO'
JFS SMILES 'OpenEye OEToolkits' 2.0.6 'c1ccc2c(c1)ncn2c3ccc(cc3)CO'
#
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
JFS 'SYSTEMATIC NAME' ACDLabs 12.01 '[4-(1H-benzimidazol-1-yl)phenyl]methanol'
JFS 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 2.0.6 '[4-(benzimidazol-1-yl)phenyl]methanol'
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
JFS 'Create component' 2018-09-10 RCSB
JFS 'Initial release' 2018-10-10 RCSB
JFS 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id JFS
_pdbx_chem_comp_pcm.modified_residue_id LYS
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category 'Covalent chemical modification'
_pdbx_chem_comp_pcm.position 'Amino-acid side chain'
_pdbx_chem_comp_pcm.polypeptide_position 'Any position'
_pdbx_chem_comp_pcm.comp_id_linking_atom C16
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom NZ
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#
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
JFS C10 C 7.483 -0.669 1
JFS C13 C 8.415 2.183 2
JFS C15 C 8.951 -0.359 3
JFS C01 C 3.000 -4.052 4
JFS C02 C 3.000 -2.552 5
JFS C03 C 4.299 -1.802 6
JFS C04 C 5.598 -2.552 7
JFS C05 C 5.598 -4.052 8
JFS C06 C 4.299 -4.802 9
JFS N07 N 7.018 -4.509 10
JFS C08 C 7.893 -3.302 11
JFS N09 N 7.018 -2.095 12
JFS C11 C 6.482 0.448 13
JFS C12 C 6.948 1.873 14
JFS C14 C 9.417 1.066 15
JFS C16 C 8.881 3.608 16
JFS O17 O 10.349 3.918 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
JFS C08 N07 DOUBLE NONE 1
JFS C08 N09 SINGLE NONE 2
JFS C15 C14 SINGLE NONE 3
JFS C15 C10 DOUBLE NONE 4
JFS N07 C05 SINGLE NONE 5
JFS C14 C13 DOUBLE NONE 6
JFS O17 C16 SINGLE NONE 7
JFS N09 C10 SINGLE NONE 8
JFS N09 C04 SINGLE NONE 9
JFS C10 C11 SINGLE NONE 10
JFS C05 C04 DOUBLE NONE 11
JFS C05 C06 SINGLE NONE 12
JFS C13 C16 SINGLE NONE 13
JFS C13 C12 SINGLE NONE 14
JFS C04 C03 SINGLE NONE 15
JFS C06 C01 DOUBLE NONE 16
JFS C11 C12 DOUBLE NONE 17
JFS C03 C02 DOUBLE NONE 18
JFS C01 C02 SINGLE NONE 19
#
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
JFS MurckoScaffold S1 scaffold c1ccc(-n2cnc3ccccc32)cc1 InChI=1S/C13H10N2/c1-2-6-11(7-3-1)15-10-14-12-8-4-5-9-13(12)15/h1-10H XNCMQRWVMWLODV-UHFFFAOYSA-N
JFS benzimidazole F1 fragment 'c1ccc2[nH]cnc2c1' InChI=1S/C7H6N2/c1-2-4-7-6(3-1)8-5-9-7/h1-5H,(H,8,9) HYZJCKYKOHLVJF-UHFFFAOYSA-N
JFS imidazole F2 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
JFS phenyl F3 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
JFS Z235449082 F4 fragment OCc1ccc(-n2cnc3ccccc32)cc1 InChI=1S/C14H12N2O/c17-9-11-5-7-12(8-6-11)16-10-15-13-3-1-2-4-14(13)16/h1-8,10,17H,9H2 IRZKUEWQJPIBJF-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
JFS C10 S1 1
JFS C13 S1 1
JFS C15 S1 1
JFS C01 S1 1
JFS C02 S1 1
JFS C03 S1 1
JFS C04 S1 1
JFS C05 S1 1
JFS C06 S1 1
JFS N07 S1 1
JFS C08 S1 1
JFS N09 S1 1
JFS C11 S1 1
JFS C12 S1 1
JFS C14 S1 1
JFS C04 F1 1
JFS N09 F1 1
JFS C08 F1 1
JFS N07 F1 1
JFS C05 F1 1
JFS C06 F1 1
JFS C01 F1 1
JFS C02 F1 1
JFS C03 F1 1
JFS C04 F2 1
JFS C05 F2 1
JFS N07 F2 1
JFS C08 F2 1
JFS N09 F2 1
JFS C10 F3 1
JFS C15 F3 1
JFS C14 F3 1
JFS C13 F3 1
JFS C12 F3 1
JFS C11 F3 1
JFS C01 F3 2
JFS C06 F3 2
JFS C05 F3 2
JFS C04 F3 2
JFS C03 F3 2
JFS C02 F3 2
JFS O17 F4 1
JFS C16 F4 1
JFS C13 F4 1
JFS C14 F4 1
JFS C15 F4 1
JFS C10 F4 1
JFS C11 F4 1
JFS C12 F4 1
JFS N09 F4 1
JFS C08 F4 1
JFS N07 F4 1
JFS C05 F4 1
JFS C06 F4 1
JFS C01 F4 1
JFS C02 F4 1
JFS C03 F4 1
JFS C04 F4 1
#
_pdbe_chem_comp_rdkit_properties.comp_id JFS
_pdbe_chem_comp_rdkit_properties.exactmw 224.095
_pdbe_chem_comp_rdkit_properties.amw 224.263
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_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 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 17
_pdbe_chem_comp_rdkit_properties.NumAtoms 29
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.071
_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 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_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 115.914
_pdbe_chem_comp_rdkit_properties.tpsa 38.050
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.845
_pdbe_chem_comp_rdkit_properties.CrippenMR 63.860
_pdbe_chem_comp_rdkit_properties.chi0v 8.303
_pdbe_chem_comp_rdkit_properties.chi1v 4.572
_pdbe_chem_comp_rdkit_properties.chi2v 2.071
_pdbe_chem_comp_rdkit_properties.chi3v 2.071
_pdbe_chem_comp_rdkit_properties.chi4v 1.323
_pdbe_chem_comp_rdkit_properties.chi0n 20.303
_pdbe_chem_comp_rdkit_properties.chi1n 10.480
_pdbe_chem_comp_rdkit_properties.chi2n 2.071
_pdbe_chem_comp_rdkit_properties.chi3n 2.071
_pdbe_chem_comp_rdkit_properties.chi4n 1.323
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.130
_pdbe_chem_comp_rdkit_properties.kappa1 3.432
_pdbe_chem_comp_rdkit_properties.kappa2 4.032
_pdbe_chem_comp_rdkit_properties.kappa3 1.704
_pdbe_chem_comp_rdkit_properties.Phi 0.814
#
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
JFS UniChem ZINC ZINC000000168836
JFS UniChem eMolecules 4851873
JFS UniChem SureChEMBL SCHEMBL12970574
JFS UniChem PubChem 2763828
JFS UniChem Mcule MCULE-7703200627
#
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
JFS C10 0.422 -0.282 -0.646 ETKDGv3 1
JFS C13 3.047 0.762 -0.381 ETKDGv3 2
JFS C15 0.611 1.018 -0.360 ETKDGv3 3
JFS C01 -4.708 -0.314 0.865 ETKDGv3 4
JFS C02 -3.592 0.432 1.518 ETKDGv3 5
JFS C03 -2.341 0.352 1.029 ETKDGv3 6
JFS C04 -2.118 -0.472 -0.175 ETKDGv3 7
JFS C05 -3.096 -1.156 -0.728 ETKDGv3 8
JFS C06 -4.472 -1.088 -0.210 ETKDGv3 9
JFS N07 -2.606 -1.997 -1.768 ETKDGv3 10
JFS C08 -1.325 -1.777 -1.789 ETKDGv3 11
JFS N09 -0.899 -0.818 -0.816 ETKDGv3 12
JFS C11 1.602 -1.162 -0.830 ETKDGv3 13
JFS C12 2.840 -0.671 -0.698 ETKDGv3 14
JFS C14 1.978 1.558 -0.206 ETKDGv3 15
JFS C16 4.437 1.294 -0.190 ETKDGv3 16
JFS O17 4.786 1.205 1.162 ETKDGv3 17
JFS H151 -0.228 1.694 -0.270 ETKDGv3 18
JFS H011 -5.708 -0.244 1.271 ETKDGv3 19
JFS H021 -3.790 1.025 2.401 ETKDGv3 20
JFS H031 -1.526 0.861 1.525 ETKDGv3 21
JFS H061 -5.270 -1.649 -0.679 ETKDGv3 22
JFS H081 -0.659 -2.263 -2.489 ETKDGv3 23
JFS H111 1.465 -2.211 -1.058 ETKDGv3 24
JFS H121 3.692 -1.327 -0.824 ETKDGv3 25
JFS H141 2.103 2.604 0.046 ETKDGv3 26
JFS H162 5.153 0.704 -0.804 ETKDGv3 27
JFS H161 4.492 2.355 -0.527 ETKDGv3 28
JFS H171 5.707 1.566 1.233 ETKDGv3 29
#