data_556
#
_chem_comp.id 556
_chem_comp.name 3-(thiophen-2-yl)-6,7-dihydro-5H-pyrrolo[1,2-a]imidazole
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H10 N2 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2013-12-12
_chem_comp.pdbx_modified_date 2013-12-20
_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 190.265
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 556
_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 4NVO
_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
556 CAF CAF C 0 1 N N N N N N -16.440 1.923 3.080 3.582 -0.244 -0.108 CAF 556 1
556 CAE CAE C 0 1 N N N N N N -17.451 1.903 1.962 3.051 -1.653 0.239 CAE 556 2
556 CAG CAG C 0 1 N N N N N N -18.715 2.340 2.628 1.566 -1.544 -0.171 CAG 556 3
556 NAM NAM N 0 1 Y N N N N N -18.275 2.940 3.899 1.234 -0.116 -0.072 NAM 556 4
556 CAK CAK C 0 1 Y N N N N N -16.983 2.684 4.118 2.356 0.645 -0.037 CAK 556 5
556 NAH NAH N 0 1 Y N N N N N -16.653 3.251 5.280 2.008 1.905 0.046 NAH 556 6
556 CAD CAD C 0 1 Y N N N N N -17.720 3.857 5.786 0.675 2.004 0.073 CAD 556 7
556 CAL CAL C 0 1 Y N N N N N -18.708 3.656 4.928 0.159 0.746 0.000 CAL 556 8
556 CAJ CAJ C 0 1 Y N N N N N -19.956 4.105 5.072 -1.268 0.377 -0.001 CAJ 556 9
556 SAI SAI S 0 1 Y N N N N N -20.702 4.511 6.497 -1.893 -1.267 0.029 SAI 556 10
556 CAB CAB C 0 1 Y N N N N N -22.139 4.937 5.800 -3.547 -0.673 0.007 CAB 556 11
556 CAA CAA C 0 1 Y N N N N N -22.014 4.753 4.479 -3.548 0.663 -0.020 CAA 556 12
556 CAC CAC C 0 1 Y N N N N N -20.817 4.293 4.070 -2.299 1.249 -0.020 CAC 556 13
556 H1 H1 H 0 1 N N N N N N -16.243 0.898 3.428 4.325 0.073 0.623 H1 556 14
556 H2 H2 H 0 1 N N N N N N -15.502 2.378 2.731 4.005 -0.231 -1.112 H2 556 15
556 H3 H3 H 0 1 N N N N N N -17.556 0.891 1.545 3.562 -2.418 -0.347 H3 556 16
556 H4 H4 H 0 1 N N N N N N -17.166 2.602 1.162 3.146 -1.854 1.306 H4 556 17
556 H5 H5 H 0 1 N N N N N N -19.243 3.081 2.011 1.432 -1.891 -1.196 H5 556 18
556 H6 H6 H 0 1 N N N N N N -19.375 1.479 2.812 0.943 -2.124 0.509 H6 556 19
556 H7 H7 H 0 1 N N N N N N -17.772 4.406 6.715 0.108 2.920 0.139 H7 556 20
556 H8 H8 H 0 1 N N N N N N -23.017 5.297 6.315 -4.431 -1.294 0.015 H8 556 21
556 H9 H9 H 0 1 N N N N N N -22.819 4.960 3.789 -4.459 1.242 -0.038 H9 556 22
556 H10 H10 H 0 1 N N N N N N -20.578 4.096 3.035 -2.157 2.319 -0.040 H10 556 23
#
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
556 CAE CAG SING N N 1
556 CAE CAF SING N N 2
556 CAG NAM SING N N 3
556 CAF CAK SING N N 4
556 NAM CAK SING Y N 5
556 NAM CAL SING Y N 6
556 CAC CAA SING Y N 7
556 CAC CAJ DOUB Y N 8
556 CAK NAH DOUB Y N 9
556 CAA CAB DOUB Y N 10
556 CAL CAJ SING N N 11
556 CAL CAD DOUB Y N 12
556 CAJ SAI SING Y N 13
556 NAH CAD SING Y N 14
556 CAB SAI SING Y N 15
556 CAF H1 SING N N 16
556 CAF H2 SING N N 17
556 CAE H3 SING N N 18
556 CAE H4 SING N N 19
556 CAG H5 SING N N 20
556 CAG H6 SING N N 21
556 CAD H7 SING N N 22
556 CAB H8 SING N N 23
556 CAA H9 SING N N 24
556 CAC H10 SING N N 25
#
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
556 SMILES ACDLabs 12.01 n1cc(n2c1CCC2)c3sccc3
556 InChI InChI 1.03 InChI=1S/C10H10N2S/c1-4-10-11-7-8(12(10)5-1)9-3-2-6-13-9/h2-3,6-7H,1,4-5H2
556 InChIKey InChI 1.03 LYZIBEKPTIUDDV-UHFFFAOYSA-N
556 SMILES_CANONICAL CACTVS 3.385 C1Cn2c(C1)ncc2c3sccc3
556 SMILES CACTVS 3.385 C1Cn2c(C1)ncc2c3sccc3
556 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 c1cc(sc1)c2cnc3n2CCC3
556 SMILES "OpenEye OEToolkits" 1.7.6 c1cc(sc1)c2cnc3n2CCC3
#
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
556 "SYSTEMATIC NAME" ACDLabs 12.01 3-(thiophen-2-yl)-6,7-dihydro-5H-pyrrolo[1,2-a]imidazole
556 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 3-thiophen-2-yl-6,7-dihydro-5H-pyrrolo[1,2-a]imidazole
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
556 'Create component' 2013-12-12 RCSB
556 'Initial release' 2013-12-25 RCSB
#
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
556 CAF C 3.875 -3.134 1
556 CAE C 3.000 -1.927 2
556 CAG C 3.875 -0.720 3
556 NAM N 5.295 -1.177 4
556 CAK C 5.295 -2.677 5
556 NAH N 6.721 -3.140 6
556 CAD C 7.603 -1.927 7
556 CAL C 6.721 -0.713 8
556 CAJ C 7.185 0.713 9
556 SAI S 6.303 1.927 10
556 CAB C 7.185 3.140 11
556 CAA C 8.611 2.677 12
556 CAC C 8.611 1.177 13
#
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
556 CAE CAG SINGLE NONE 1
556 CAE CAF SINGLE NONE 2
556 CAG NAM SINGLE NONE 3
556 CAF CAK SINGLE NONE 4
556 NAM CAK SINGLE NONE 5
556 NAM CAL SINGLE NONE 6
556 CAC CAA SINGLE NONE 7
556 CAC CAJ DOUBLE NONE 8
556 CAK NAH DOUBLE NONE 9
556 CAA CAB DOUBLE NONE 10
556 CAL CAJ SINGLE NONE 11
556 CAL CAD DOUBLE NONE 12
556 CAJ SAI SINGLE NONE 13
556 NAH CAD SINGLE NONE 14
556 CAB SAI SINGLE NONE 15
#
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
556 MurckoScaffold S1 scaffold c1csc(-c2cnc3n2CCC3)c1 InChI=1S/C10H10N2S/c1-4-10-11-7-8(12(10)5-1)9-3-2-6-13-9/h2-3,6-7H,1,4-5H2 LYZIBEKPTIUDDV-UHFFFAOYSA-N
556 imidazole F1 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
556 thiophen F2 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
556 CAF S1 1
556 CAE S1 1
556 CAG S1 1
556 NAM S1 1
556 CAK S1 1
556 NAH S1 1
556 CAD S1 1
556 CAL S1 1
556 CAJ S1 1
556 SAI S1 1
556 CAB S1 1
556 CAA S1 1
556 CAC S1 1
556 CAD F1 1
556 CAL F1 1
556 NAM F1 1
556 CAK F1 1
556 NAH F1 1
556 CAJ F2 1
556 CAC F2 1
556 CAA F2 1
556 CAB F2 1
556 SAI F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 556
_pdbe_chem_comp_rdkit_properties.exactmw 190.056
_pdbe_chem_comp_rdkit_properties.amw 190.271
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 2
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 0
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 1
_pdbe_chem_comp_rdkit_properties.NumHBD 0
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 13
_pdbe_chem_comp_rdkit_properties.NumAtoms 23
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.300
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_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 94.906
_pdbe_chem_comp_rdkit_properties.tpsa 17.820
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.123
_pdbe_chem_comp_rdkit_properties.CrippenMR 52.273
_pdbe_chem_comp_rdkit_properties.chi0v 7.119
_pdbe_chem_comp_rdkit_properties.chi1v 4.343
_pdbe_chem_comp_rdkit_properties.chi2v 2.344
_pdbe_chem_comp_rdkit_properties.chi3v 2.344
_pdbe_chem_comp_rdkit_properties.chi4v 1.628
_pdbe_chem_comp_rdkit_properties.chi0n 16.303
_pdbe_chem_comp_rdkit_properties.chi1n 8.526
_pdbe_chem_comp_rdkit_properties.chi2n 1.640
_pdbe_chem_comp_rdkit_properties.chi3n 1.640
_pdbe_chem_comp_rdkit_properties.chi4n 1.088
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.090
_pdbe_chem_comp_rdkit_properties.kappa1 2.480
_pdbe_chem_comp_rdkit_properties.kappa2 2.703
_pdbe_chem_comp_rdkit_properties.kappa3 1.036
_pdbe_chem_comp_rdkit_properties.Phi 0.516
#
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
556 UniChem PDBe 556
556 UniChem ZINC ZINC000000388812
556 UniChem eMolecules 6818514
556 UniChem PubChem 853036
556 UniChem Mcule MCULE-1385228060
#
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
556 CAF -3.137 -0.663 -0.418 ETKDGv3 1
556 CAE -2.930 0.867 -0.488 ETKDGv3 2
556 CAG -1.424 1.138 -0.255 ETKDGv3 3
556 NAM -0.902 -0.105 0.275 ETKDGv3 4
556 CAK -1.809 -1.137 0.015 ETKDGv3 5
556 NAH -1.266 -2.261 -0.326 ETKDGv3 6
556 CAD 0.138 -2.011 -0.245 ETKDGv3 7
556 CAL 0.352 -0.729 0.039 ETKDGv3 8
556 CAJ 1.657 -0.047 0.130 ETKDGv3 9
556 SAI 1.879 1.648 0.623 ETKDGv3 10
556 CAB 3.645 1.557 0.447 ETKDGv3 11
556 CAA 3.987 0.334 0.049 ETKDGv3 12
556 CAC 2.847 -0.592 -0.133 ETKDGv3 13
556 H1 -3.389 -1.071 -1.420 ETKDGv3 14
556 H2 -3.913 -0.938 0.328 ETKDGv3 15
556 H3 -3.525 1.360 0.311 ETKDGv3 16
556 H4 -3.253 1.266 -1.474 ETKDGv3 17
556 H5 -1.267 1.963 0.471 ETKDGv3 18
556 H6 -0.926 1.378 -1.220 ETKDGv3 19
556 H7 0.896 -2.749 -0.469 ETKDGv3 20
556 H8 4.343 2.363 0.631 ETKDGv3 21
556 H9 5.015 0.044 -0.125 ETKDGv3 22
556 H10 2.981 -1.616 -0.454 ETKDGv3 23
#