data_JPB
#
_chem_comp.id JPB
_chem_comp.name ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-2,4,6-tris(chloranyl)benzamide
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H7 Cl3 N2 O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2019-03-14
_chem_comp.pdbx_modified_date 2019-08-02
_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 321.544
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code JPB
_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 6R1K
_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
JPB C4 C1 C 0 1 N N S N N N 24.258 18.067 -7.044 -2.754 0.572 0.366 C4 JPB 1
JPB C5 C2 C 0 1 N N N N N N 25.892 19.840 -7.163 -0.383 0.250 0.829 C5 JPB 2
JPB C6 C3 C 0 1 Y N N N N N 26.265 21.159 -7.762 1.016 0.106 0.382 C6 JPB 3
JPB C11 C4 C 0 1 Y N N N N N 26.375 22.280 -6.939 1.535 -1.160 0.094 C11 JPB 4
JPB C7 C5 C 0 1 Y N N N N N 26.597 21.283 -9.112 1.828 1.235 0.241 C7 JPB 5
JPB C8 C6 C 0 1 Y N N N N N 26.990 22.497 -9.651 3.136 1.093 -0.178 C8 JPB 6
JPB C9 C7 C 0 1 Y N N N N N 27.070 23.586 -8.808 3.644 -0.165 -0.457 C9 JPB 7
JPB C10 C8 C 0 1 Y N N N N N 26.758 23.505 -7.463 2.844 -1.287 -0.323 C10 JPB 8
JPB N1 N1 N 0 1 N N N N N N 23.387 16.378 -8.366 -4.473 -0.778 -0.431 N1 JPB 9
JPB N2 N2 N 0 1 N N N N N N 24.707 19.341 -7.488 -1.365 0.429 -0.077 N2 JPB 10
JPB C3 C9 C 0 1 N N N N N N 22.734 18.033 -6.854 -3.578 1.356 -0.676 C3 JPB 11
JPB O1 O1 O 0 1 N N N N N N 25.573 16.994 -8.791 -3.108 -1.705 1.124 O1 JPB 12
JPB C1 C10 C 0 1 N N N N N N 24.530 17.087 -8.152 -3.440 -0.775 0.421 C1 JPB 13
JPB C2 C11 C 0 1 N N N N N N 22.305 16.835 -7.655 -4.643 0.369 -1.100 C2 JPB 14
JPB O2 O2 O 0 1 N N N N N N 21.218 16.290 -7.658 -5.513 0.583 -1.918 O2 JPB 15
JPB O3 O3 O 0 1 N N N N N N 26.640 19.261 -6.376 -0.651 0.208 2.014 O3 JPB 16
JPB CL1 CL1 CL 0 0 N N N N N N 26.500 19.925 -10.196 1.193 2.813 0.589 CL1 JPB 17
JPB CL2 CL2 CL 0 0 N N N N N N 27.582 25.107 -9.466 5.289 -0.334 -0.984 CL2 JPB 18
JPB CL3 CL3 CL 0 0 N N N N N N 25.971 22.179 -5.235 0.534 -2.568 0.261 CL3 JPB 19
JPB H1 H1 H 0 1 N N N N N N 24.763 17.755 -6.118 -2.796 1.064 1.338 H1 JPB 20
JPB H2 H2 H 0 1 N N N N N N 27.227 22.588 -10.701 3.764 1.964 -0.288 H2 JPB 21
JPB H3 H3 H 0 1 N N N N N N 26.812 24.380 -6.832 3.247 -2.265 -0.543 H3 JPB 22
JPB H4 H4 H 0 1 N N N N N N 23.340 15.595 -8.986 -5.051 -1.548 -0.553 H4 JPB 23
JPB H5 H5 H 0 1 N N N N N N 24.103 19.884 -8.071 -1.151 0.463 -1.023 H5 JPB 24
JPB H6 H6 H 0 1 N N N N N N 22.269 18.952 -7.242 -4.030 2.237 -0.222 H6 JPB 25
JPB H7 H7 H 0 1 N N N N N N 22.473 17.910 -5.793 -2.954 1.639 -1.524 H7 JPB 26
#
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
JPB CL1 C7 SING N N 1
JPB C8 C7 DOUB Y N 2
JPB C8 C9 SING Y N 3
JPB CL2 C9 SING N N 4
JPB C7 C6 SING Y N 5
JPB C9 C10 DOUB Y N 6
JPB O1 C1 DOUB N N 7
JPB N1 C1 SING N N 8
JPB N1 C2 SING N N 9
JPB C1 C4 SING N N 10
JPB C6 C5 SING N N 11
JPB C6 C11 DOUB Y N 12
JPB O2 C2 DOUB N N 13
JPB C2 C3 SING N N 14
JPB N2 C5 SING N N 15
JPB N2 C4 SING N N 16
JPB C10 C11 SING Y N 17
JPB C5 O3 DOUB N N 18
JPB C4 C3 SING N N 19
JPB C11 CL3 SING N N 20
JPB C4 H1 SING N N 21
JPB C8 H2 SING N N 22
JPB C10 H3 SING N N 23
JPB N1 H4 SING N N 24
JPB N2 H5 SING N N 25
JPB C3 H6 SING N N 26
JPB C3 H7 SING N N 27
#
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
JPB InChI InChI 1.03 InChI=1S/C11H7Cl3N2O3/c12-4-1-5(13)9(6(14)2-4)11(19)15-7-3-8(17)16-10(7)18/h1-2,7H,3H2,(H,15,19)(H,16,17,18)/t7-/m0/s1
JPB InChIKey InChI 1.03 LBWIBZYKUVIBKH-ZETCQYMHSA-N
JPB SMILES_CANONICAL CACTVS 3.385 Clc1cc(Cl)c(C(=O)N[C@H]2CC(=O)NC2=O)c(Cl)c1
JPB SMILES CACTVS 3.385 Clc1cc(Cl)c(C(=O)N[CH]2CC(=O)NC2=O)c(Cl)c1
JPB SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1c(cc(c(c1Cl)C(=O)N[C@H]2CC(=O)NC2=O)Cl)Cl
JPB SMILES "OpenEye OEToolkits" 2.0.7 c1c(cc(c(c1Cl)C(=O)NC2CC(=O)NC2=O)Cl)Cl
#
_pdbx_chem_comp_identifier.comp_id JPB
_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 ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-2,4,6-tris(chloranyl)benzamide
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
JPB 'Create component' 2019-03-14 RCSB
JPB 'Initial release' 2019-08-07 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
JPB C4 C 6.897 2.364 1
JPB C5 C 5.598 0.114 2
JPB C6 C 5.598 -1.386 3
JPB C11 C 4.299 -2.136 4
JPB C7 C 6.897 -2.136 5
JPB C8 C 6.897 -3.636 6
JPB C9 C 5.598 -4.386 7
JPB C10 C 4.299 -3.636 8
JPB N1 N 6.147 4.672 9
JPB N2 N 6.897 0.864 10
JPB C3 C 8.111 3.246 11
JPB O1 O 4.257 2.782 12
JPB C1 C 5.684 3.246 13
JPB C2 C 7.647 4.672 14
JPB O2 O 8.529 5.886 15
JPB O3 O 4.299 0.864 16
JPB CL1 Cl 8.196 -1.386 17
JPB CL2 Cl 5.598 -5.886 18
JPB CL3 Cl 3.000 -1.386 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
JPB CL1 C7 SINGLE NONE 1
JPB C8 C7 DOUBLE NONE 2
JPB C8 C9 SINGLE NONE 3
JPB CL2 C9 SINGLE NONE 4
JPB C7 C6 SINGLE NONE 5
JPB C9 C10 DOUBLE NONE 6
JPB O1 C1 DOUBLE NONE 7
JPB N1 C1 SINGLE NONE 8
JPB N1 C2 SINGLE NONE 9
JPB C1 C4 SINGLE NONE 10
JPB C6 C5 SINGLE NONE 11
JPB C6 C11 DOUBLE NONE 12
JPB O2 C2 DOUBLE NONE 13
JPB C2 C3 SINGLE NONE 14
JPB N2 C5 SINGLE NONE 15
JPB C4 N2 SINGLE BEGINDASH 16
JPB C10 C11 SINGLE NONE 17
JPB C5 O3 DOUBLE NONE 18
JPB C4 C3 SINGLE NONE 19
JPB C11 CL3 SINGLE 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
JPB MurckoScaffold S1 scaffold 'O=C1C[C@H](NC(=O)c2ccccc2)C(=O)N1' InChI=1S/C11H10N2O3/c14-9-6-8(11(16)13-9)12-10(15)7-4-2-1-3-5-7/h1-5,8H,6H2,(H,12,15)(H,13,14,16)/t8-/m0/s1 YXRORANDLJEXTG-QMMMGPOBSA-N
JPB amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
JPB barbiturates F2 fragment NC1CC(=O)NC1=O InChI=1S/C4H6N2O2/c5-2-1-3(7)6-4(2)8/h2H,1,5H2,(H,6,7,8) YDNMHDRXNOHCJH-UHFFFAOYSA-N
JPB peptide F3 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
JPB phenyl F4 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
JPB succinimide F5 fragment O=C1CCC(=O)N1 InChI=1S/C4H5NO2/c6-3-1-2-4(7)5-3/h1-2H2,(H,5,6,7) KZNICNPSHKQLFF-UHFFFAOYSA-N
JPB Z1827898537 F6 fragment c1ccc(CNC2CCNC2)cc1 InChI=1S/C11H16N2/c1-2-4-10(5-3-1)8-13-11-6-7-12-9-11/h1-5,11-13H,6-9H2 NFLXIAUKMQBTMN-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
JPB C4 S1 1
JPB C5 S1 1
JPB C6 S1 1
JPB C11 S1 1
JPB C7 S1 1
JPB C8 S1 1
JPB C9 S1 1
JPB C10 S1 1
JPB N1 S1 1
JPB N2 S1 1
JPB C3 S1 1
JPB O1 S1 1
JPB C1 S1 1
JPB C2 S1 1
JPB O2 S1 1
JPB O3 S1 1
JPB N1 F1 1
JPB C1 F1 1
JPB O1 F1 1
JPB C4 F1 1
JPB N1 F1 2
JPB C2 F1 2
JPB O2 F1 2
JPB C3 F1 2
JPB N2 F1 3
JPB C5 F1 3
JPB O3 F1 3
JPB C6 F1 3
JPB C3 F2 1
JPB C2 F2 1
JPB O2 F2 1
JPB N1 F2 1
JPB C1 F2 1
JPB O1 F2 1
JPB C4 F2 1
JPB N2 F2 1
JPB O1 F3 1
JPB C1 F3 1
JPB C4 F3 1
JPB N2 F3 1
JPB C6 F4 1
JPB C7 F4 1
JPB C8 F4 1
JPB C9 F4 1
JPB C10 F4 1
JPB C11 F4 1
JPB C4 F5 1
JPB C1 F5 1
JPB O1 F5 1
JPB N1 F5 1
JPB C2 F5 1
JPB O2 F5 1
JPB C3 F5 1
JPB C5 F6 1
JPB N2 F6 1
JPB C4 F6 1
JPB C3 F6 1
JPB C2 F6 1
JPB N1 F6 1
JPB C1 F6 1
JPB C6 F6 1
JPB C7 F6 1
JPB C8 F6 1
JPB C9 F6 1
JPB C10 F6 1
JPB C11 F6 1
#
_pdbe_chem_comp_rdkit_properties.comp_id JPB
_pdbe_chem_comp_rdkit_properties.exactmw 319.952
_pdbe_chem_comp_rdkit_properties.amw 321.547
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 19
_pdbe_chem_comp_rdkit_properties.NumAtoms 26
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 3
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.182
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 132.695
_pdbe_chem_comp_rdkit_properties.tpsa 75.270
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.737
_pdbe_chem_comp_rdkit_properties.CrippenMR 70.227
_pdbe_chem_comp_rdkit_properties.chi0v 11.021
_pdbe_chem_comp_rdkit_properties.chi1v 5.708
_pdbe_chem_comp_rdkit_properties.chi2v 2.692
_pdbe_chem_comp_rdkit_properties.chi3v 2.692
_pdbe_chem_comp_rdkit_properties.chi4v 2.068
_pdbe_chem_comp_rdkit_properties.chi0n 15.753
_pdbe_chem_comp_rdkit_properties.chi1n 7.968
_pdbe_chem_comp_rdkit_properties.chi2n 1.936
_pdbe_chem_comp_rdkit_properties.chi3n 1.936
_pdbe_chem_comp_rdkit_properties.chi4n 1.194
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.300
_pdbe_chem_comp_rdkit_properties.kappa1 7.474
_pdbe_chem_comp_rdkit_properties.kappa2 5.365
_pdbe_chem_comp_rdkit_properties.kappa3 2.997
_pdbe_chem_comp_rdkit_properties.Phi 2.110
#
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
JPB UniChem PDBe JPB
JPB UniChem PubChem 138756825
#
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
JPB C4 -2.143 -0.306 -0.703 ETKDGv3 1
JPB C5 0.339 -0.803 -0.598 ETKDGv3 2
JPB C6 1.719 -0.342 -0.336 ETKDGv3 3
JPB C11 2.722 -0.612 -1.204 ETKDGv3 4
JPB C7 2.020 0.435 0.903 ETKDGv3 5
JPB C8 3.265 0.874 1.134 ETKDGv3 6
JPB C9 4.347 0.588 0.174 ETKDGv3 7
JPB C10 4.090 -0.122 -0.930 ETKDGv3 8
JPB N1 -4.013 0.944 0.221 ETKDGv3 9
JPB N2 -0.751 0.130 -0.571 ETKDGv3 10
JPB C3 -2.630 -1.020 0.581 ETKDGv3 11
JPB O1 -3.020 1.707 -1.761 ETKDGv3 12
JPB C1 -3.064 0.869 -0.822 ETKDGv3 13
JPB C2 -3.764 -0.171 1.052 ETKDGv3 14
JPB O2 -4.441 -0.413 2.085 ETKDGv3 15
JPB O3 0.124 -2.020 -0.847 ETKDGv3 16
JPB CL1 0.784 0.736 2.121 ETKDGv3 17
JPB CL2 5.971 1.171 0.492 ETKDGv3 18
JPB CL3 2.455 -1.485 -2.711 ETKDGv3 19
JPB H1 -2.262 -0.959 -1.596 ETKDGv3 20
JPB H2 3.489 1.427 2.038 ETKDGv3 21
JPB H3 4.885 -0.334 -1.634 ETKDGv3 22
JPB H4 -4.756 1.667 0.345 ETKDGv3 23
JPB H5 -0.533 1.148 -0.477 ETKDGv3 24
JPB H6 -1.842 -1.064 1.363 ETKDGv3 25
JPB H7 -2.993 -2.044 0.348 ETKDGv3 26
#