data_492
#
_chem_comp.id 492
_chem_comp.name "1-(2,2'-bithiophen-5-yl)methanamine"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C9 H9 N S2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms (5-thiophen-2-ylthiophen-2-yl)methylamine
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2009-01-20
_chem_comp.pdbx_modified_date 2021-03-01
_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 195.304
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 492
_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 3FU5
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
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
492 N18 N18 N 0 1 N N N N N N 34.377 1.471 1.684 -4.526 -0.209 -0.955 N18 492 1
492 C17 C17 C 0 1 N N N N N N 34.275 2.306 0.498 -3.948 -0.097 0.391 C17 492 2
492 C8 C8 C 0 1 Y N N N N N 33.011 1.975 -0.254 -2.469 0.169 0.282 C8 492 3
492 S7 S7 S 0 1 Y N N N N N 31.632 1.492 0.772 -1.221 -1.068 0.217 S7 492 4
492 C6 C6 C 0 1 Y N N N N N 30.610 1.258 -0.667 0.034 0.159 0.105 C6 492 5
492 C10 C10 C 0 1 Y N N N N N 31.301 1.549 -1.843 -0.533 1.384 0.122 C10 492 6
492 C9 C9 C 0 1 Y N N N N N 32.637 1.943 -1.603 -1.909 1.380 0.214 C9 492 7
492 C1 C1 C 0 1 Y N N N N N 29.178 0.823 -0.570 1.479 -0.109 0.008 C1 492 8
492 S2 S2 S 0 1 Y N N N N N 27.984 0.959 -1.872 2.735 1.118 -0.095 S2 492 9
492 C3 C3 C 0 1 Y N N N N N 26.688 0.260 -0.836 3.982 -0.119 -0.165 C3 492 10
492 C4 C4 C 0 1 Y N N N N N 27.253 -0.037 0.407 3.422 -1.331 -0.110 C4 492 11
492 C5 C5 C 0 1 Y N N N N N 28.611 0.265 0.566 2.046 -1.334 -0.009 C5 492 12
492 HN18 HN18 H 0 0 N N N N N N 34.400 0.509 1.414 -5.518 -0.388 -0.909 HN18 492 13
492 HN1A HN1A H 0 0 N N N N N N 35.215 1.698 2.180 -4.332 0.616 -1.502 HN1A 492 14
492 H17 H17 H 0 1 N N N N N N 34.254 3.364 0.798 -4.427 0.724 0.924 H17 492 15
492 H17A H17A H 0 0 N N N N N N 35.143 2.121 -0.152 -4.111 -1.027 0.935 H17A 492 16
492 H10 H10 H 0 1 N N N N N N 30.864 1.481 -2.828 0.045 2.295 0.064 H10 492 17
492 H9 H9 H 0 1 N N N N N N 33.318 2.200 -2.400 -2.491 2.290 0.238 H9 492 18
492 H3 H3 H 0 1 N N N N N N 25.659 0.099 -1.123 5.043 0.071 -0.242 H3 492 19
492 H4 H4 H 0 1 N N N N N N 26.672 -0.477 1.204 4.003 -2.240 -0.139 H4 492 20
492 H5 H5 H 0 1 N N N N N N 29.160 0.082 1.478 1.468 -2.245 0.049 H5 492 21
#
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
492 C17 N18 SING N N 1
492 N18 HN18 SING N N 2
492 N18 HN1A SING N N 3
492 C8 C17 SING N N 4
492 C17 H17 SING N N 5
492 C17 H17A SING N N 6
492 C9 C8 DOUB Y N 7
492 C8 S7 SING Y N 8
492 C6 S7 SING Y N 9
492 C10 C6 DOUB Y N 10
492 C6 C1 SING Y N 11
492 C10 C9 SING Y N 12
492 C10 H10 SING N N 13
492 C9 H9 SING N N 14
492 S2 C1 SING Y N 15
492 C1 C5 DOUB Y N 16
492 S2 C3 SING Y N 17
492 C3 C4 DOUB Y N 18
492 C3 H3 SING N N 19
492 C4 C5 SING Y N 20
492 C4 H4 SING N N 21
492 C5 H5 SING N N 22
#
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
492 SMILES ACDLabs 10.04 s2c(c1sc(cc1)CN)ccc2
492 SMILES_CANONICAL CACTVS 3.341 NCc1sc(cc1)c2sccc2
492 SMILES CACTVS 3.341 NCc1sc(cc1)c2sccc2
492 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1cc(sc1)c2ccc(s2)CN
492 SMILES "OpenEye OEToolkits" 1.5.0 c1cc(sc1)c2ccc(s2)CN
492 InChI InChI 1.03 InChI=1S/C9H9NS2/c10-6-7-3-4-9(12-7)8-2-1-5-11-8/h1-5H,6,10H2
492 InChIKey InChI 1.03 FHYTVXBZSXZMGD-UHFFFAOYSA-N
#
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
492 "SYSTEMATIC NAME" ACDLabs 10.04 "1-(2,2'-bithiophen-5-yl)methanamine"
492 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 (5-thiophen-2-ylthiophen-2-yl)methanamine
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
492 'Create component' 2009-01-20 RCSB
492 'Modify aromatic_flag' 2011-06-04 RCSB
492 'Modify descriptor' 2011-06-04 RCSB
492 'Modify synonyms' 2021-03-01 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id 492
_pdbx_chem_comp_synonyms.name (5-thiophen-2-ylthiophen-2-yl)methylamine
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_details.comp_id 492
_pdbe_chem_comp_drugbank_details.drugbank_id DB07094
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name "1-(2,2'-bithiophen-5-yl)methanamine"
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number ?
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_synonyms.comp_id 492
_pdbe_chem_comp_synonyms.name (5-thiophen-2-ylthiophen-2-yl)methylamine
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_classification.comp_id 492
_pdbe_chem_comp_drugbank_classification.drugbank_id DB07094
_pdbe_chem_comp_drugbank_classification.parent 'Bi- and oligothiophenes'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Bi- and oligothiophenes'
_pdbe_chem_comp_drugbank_classification.superclass 'Organoheterocyclic compounds'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as bi- and oligothiophenes. These are organic compounds containing two or more linked thiophene rings. Thiophene is a five-member aromatic ring with one sulfur and four carbon atoms.'
#
_pdbe_chem_comp_drugbank_targets.comp_id 492
_pdbe_chem_comp_drugbank_targets.drugbank_id DB07094
_pdbe_chem_comp_drugbank_targets.name 'Leukotriene A-4 hydrolase'
_pdbe_chem_comp_drugbank_targets.organism Humans
_pdbe_chem_comp_drugbank_targets.uniprot_id P09960
_pdbe_chem_comp_drugbank_targets.pharmacologically_active unknown
_pdbe_chem_comp_drugbank_targets.ordinal 1
#
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
492 N18 N 3.884 0.760 1
492 C17 C 4.999 -0.243 2
492 C8 C 6.426 0.220 3
492 S7 S 7.639 -0.661 4
492 C6 C 8.853 0.220 5
492 C10 C 8.389 1.647 6
492 C9 C 6.889 1.647 7
492 C1 C 10.280 -0.243 8
492 S2 S 10.743 -1.670 9
492 C3 C 12.243 -1.670 10
492 C4 C 12.707 -0.243 11
492 C5 C 11.493 0.638 12
#
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
492 C17 N18 SINGLE NONE 1
492 C8 C17 SINGLE NONE 2
492 C9 C8 DOUBLE NONE 3
492 C8 S7 SINGLE NONE 4
492 C6 S7 SINGLE NONE 5
492 C10 C6 DOUBLE NONE 6
492 C6 C1 SINGLE NONE 7
492 C10 C9 SINGLE NONE 8
492 S2 C1 SINGLE NONE 9
492 C1 C5 DOUBLE NONE 10
492 S2 C3 SINGLE NONE 11
492 C3 C4 DOUBLE NONE 12
492 C4 C5 SINGLE NONE 13
#
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
492 MurckoScaffold S1 scaffold c1csc(-c2cccs2)c1 InChI=1S/C8H6S2/c1-3-7(9-5-1)8-4-2-6-10-8/h1-6H OHZAHWOAMVVGEL-UHFFFAOYSA-N
492 thiophen F1 fragment c1ccsc1 InChI=1S/C4H4S/c1-2-4-5-3-1/h1-4H YTPLMLYBLZKORZ-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
492 C8 S1 1
492 S7 S1 1
492 C6 S1 1
492 C10 S1 1
492 C9 S1 1
492 C1 S1 1
492 S2 S1 1
492 C3 S1 1
492 C4 S1 1
492 C5 S1 1
492 C8 F1 1
492 C9 F1 1
492 C10 F1 1
492 C6 F1 1
492 S7 F1 1
492 C1 F1 2
492 C5 F1 2
492 C4 F1 2
492 C3 F1 2
492 S2 F1 2
#
_pdbe_chem_comp_rdkit_properties.comp_id 492
_pdbe_chem_comp_rdkit_properties.exactmw 195.018
_pdbe_chem_comp_rdkit_properties.amw 195.312
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 1
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_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 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 21
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.111
_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 92.235
_pdbe_chem_comp_rdkit_properties.tpsa 26.020
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.501
_pdbe_chem_comp_rdkit_properties.CrippenMR 53.935
_pdbe_chem_comp_rdkit_properties.chi0v 7.397
_pdbe_chem_comp_rdkit_properties.chi1v 4.673
_pdbe_chem_comp_rdkit_properties.chi2v 2.933
_pdbe_chem_comp_rdkit_properties.chi3v 2.933
_pdbe_chem_comp_rdkit_properties.chi4v 2.006
_pdbe_chem_comp_rdkit_properties.chi0n 14.764
_pdbe_chem_comp_rdkit_properties.chi1n 7.435
_pdbe_chem_comp_rdkit_properties.chi2n 1.182
_pdbe_chem_comp_rdkit_properties.chi3n 1.182
_pdbe_chem_comp_rdkit_properties.chi4n 0.708
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.640
_pdbe_chem_comp_rdkit_properties.kappa1 2.672
_pdbe_chem_comp_rdkit_properties.kappa2 3.391
_pdbe_chem_comp_rdkit_properties.kappa3 1.434
_pdbe_chem_comp_rdkit_properties.Phi 0.755
#
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
492 UniChem ChEMBL CHEMBL538940
492 UniChem DrugBank DB07094
492 UniChem PDBe 492
492 UniChem ZINC ZINC000000158800
492 UniChem eMolecules 720366
492 UniChem SureChEMBL SCHEMBL2690127
492 UniChem BindingDb 50294164
492 UniChem 'EPA CompTox Dashboard' DTXSID50380066
492 UniChem BRENDA 158843
492 UniChem 'Probes And Drugs' PD006111
492 UniChem PubChem 2776424
#
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
492 N18 -4.175 0.349 -0.612 ETKDGv3 1
492 C17 -3.557 0.071 0.682 ETKDGv3 2
492 C8 -2.078 -0.139 0.539 ETKDGv3 3
492 S7 -0.860 1.154 0.600 ETKDGv3 4
492 C6 0.467 0.020 0.241 ETKDGv3 5
492 C10 -0.026 -1.213 0.087 ETKDGv3 6
492 C9 -1.494 -1.301 0.248 ETKDGv3 7
492 C1 1.884 0.412 0.133 ETKDGv3 8
492 S2 2.484 2.075 0.344 ETKDGv3 9
492 C3 4.171 1.595 0.053 ETKDGv3 10
492 C4 4.224 0.286 -0.178 ETKDGv3 11
492 C5 2.913 -0.398 -0.133 ETKDGv3 12
492 HN18 -3.993 -0.458 -1.252 ETKDGv3 13
492 HN1A -3.719 1.194 -1.029 ETKDGv3 14
492 H17 -3.740 0.926 1.367 ETKDGv3 15
492 H17A -4.028 -0.830 1.131 ETKDGv3 16
492 H10 0.580 -2.078 -0.143 ETKDGv3 17
492 H9 -2.044 -2.225 0.127 ETKDGv3 18
492 H3 5.028 2.255 0.060 ETKDGv3 19
492 H4 5.151 -0.233 -0.382 ETKDGv3 20
492 H5 2.812 -1.461 -0.303 ETKDGv3 21
#