data_B1B
#
_chem_comp.id B1B
_chem_comp.name (2S)-2-[(2-chlorophenyl)methylcarbamoylamino]-4-methyl-N-oxidanyl-pentanamide
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C14 H20 Cl N3 O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2017-07-26
_chem_comp.pdbx_modified_date 2018-07-27
_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 313.780
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code B1B
_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 5Y1K
_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
B1B CL1 CL1 CL 0 0 N N N N N N 11.226 12.719 17.717 3.045 -2.003 -0.656 CL1 B1B 1
B1B CG1 C1 C 0 1 Y N N N N N 12.417 11.689 17.115 3.896 -0.531 -0.308 CG1 B1B 2
B1B CD1 C2 C 0 1 Y N N N N N 12.644 10.545 17.860 5.116 -0.278 -0.909 CD1 B1B 3
B1B C3 C3 C 0 1 Y N N N N N 13.585 9.623 17.476 5.793 0.894 -0.632 C3 B1B 4
B1B C4 C4 C 0 1 Y N N N N N 14.262 9.934 16.324 5.252 1.814 0.246 C4 B1B 5
B1B CG2 C5 C 0 1 Y N N N N N 14.008 11.089 15.609 4.033 1.562 0.848 CG2 B1B 6
B1B CB C6 C 0 1 Y N N N N N 13.072 12.058 15.959 3.352 0.393 0.566 CB B1B 7
B1B CA C7 C 0 1 N N N N N N 12.743 13.319 15.133 2.023 0.119 1.222 CA B1B 8
B1B N N1 N 0 1 N N N N N N 12.694 12.807 13.752 0.947 0.325 0.250 N B1B 9
B1B C8 C8 C 0 1 N N N N N N 13.680 13.013 12.783 -0.337 0.136 0.615 C8 B1B 10
B1B O O1 O 0 1 N N N N N N 14.572 13.875 12.844 -0.601 -0.205 1.752 O B1B 11
B1B N2 N2 N 0 1 N N N N N N 13.508 12.117 11.752 -1.327 0.326 -0.280 N2 B1B 12
B1B C9 C9 C 0 1 N N S N N N 14.431 11.859 10.692 -2.722 0.121 0.118 C9 B1B 13
B1B C10 C10 C 0 1 N N N N N N 14.856 10.509 11.146 -3.636 0.953 -0.784 C10 B1B 14
B1B C11 C11 C 0 1 N N N N N N 16.062 9.920 10.559 -3.364 2.441 -0.553 C11 B1B 15
B1B C12 C12 C 0 1 N N N N N N 17.101 10.973 10.488 -4.188 3.269 -1.541 C12 B1B 16
B1B C13 C13 C 0 1 N N N N N N 16.608 8.645 11.118 -3.757 2.815 0.878 C13 B1B 17
B1B C14 C14 C 0 1 N N N N N N 13.666 11.890 9.409 -3.074 -1.338 -0.019 C14 B1B 18
B1B O2 O2 O 0 1 N N N N N N 12.805 11.094 9.059 -2.241 -2.128 -0.410 O2 B1B 19
B1B N3 N3 N 0 1 N N N N N N 13.971 13.047 8.787 -4.314 -1.764 0.292 N3 B1B 20
B1B O3 O3 O 0 1 N N N N N N 13.232 13.287 7.624 -4.645 -3.135 0.164 O3 B1B 21
B1B H1 H1 H 0 1 N N N N N N 12.071 10.375 18.759 5.539 -0.997 -1.595 H1 B1B 22
B1B H2 H2 H 0 1 N N N N N N 13.778 8.721 18.038 6.746 1.091 -1.101 H2 B1B 23
B1B H3 H3 H 0 1 N N N N N N 15.019 9.253 15.964 5.782 2.730 0.463 H3 B1B 24
B1B H4 H4 H 0 1 N N N N N N 14.581 11.253 14.708 3.608 2.284 1.530 H4 B1B 25
B1B H5 H5 H 0 1 N N N N N N 13.529 14.081 15.245 1.999 -0.911 1.577 H5 B1B 26
B1B H6 H6 H 0 1 N N N N N N 11.774 13.745 15.431 1.886 0.797 2.065 H6 B1B 27
B1B H7 H7 H 0 1 N N N N N N 11.893 12.270 13.488 1.158 0.598 -0.657 H7 B1B 28
B1B H8 H8 H 0 1 N N N N N N 12.654 11.596 11.744 -1.116 0.599 -1.186 H8 B1B 29
B1B H9 H9 H 0 1 N N N N N N 15.272 12.568 10.680 -2.854 0.431 1.154 H9 B1B 30
B1B H10 H10 H 0 1 N N N N N N 14.024 9.820 10.938 -3.441 0.706 -1.827 H10 B1B 31
B1B H11 H11 H 0 1 N N N N N N 15.020 10.569 12.232 -4.678 0.733 -0.548 H11 B1B 32
B1B H12 H12 H 0 1 N N N N N N 15.803 9.692 9.514 -2.304 2.644 -0.703 H12 B1B 33
B1B H13 H13 H 0 1 N N N N N N 16.664 11.893 10.073 -3.994 4.329 -1.376 H13 B1B 34
B1B H14 H14 H 0 1 N N N N N N 17.489 11.174 11.498 -3.908 3.003 -2.560 H14 B1B 35
B1B H15 H15 H 0 1 N N N N N N 17.923 10.634 9.841 -5.248 3.066 -1.390 H15 B1B 36
B1B H16 H16 H 0 1 N N N N N N 15.810 7.889 11.155 -3.171 2.224 1.582 H16 B1B 37
B1B H17 H17 H 0 1 N N N N N N 17.425 8.284 10.476 -3.563 3.874 1.043 H17 B1B 38
B1B H18 H18 H 0 1 N N N N N N 16.991 8.824 12.134 -4.818 2.611 1.028 H18 B1B 39
B1B H19 H19 H 0 1 N N N N N N 14.666 13.680 9.128 -4.980 -1.132 0.605 H19 B1B 40
B1B H20 H20 H 0 1 N N N N N N 12.620 12.574 7.484 -5.556 -3.345 0.410 H20 B1B 41
#
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
B1B O3 N3 SING N N 1
B1B N3 C14 SING N N 2
B1B O2 C14 DOUB N N 3
B1B C14 C9 SING N N 4
B1B C12 C11 SING N N 5
B1B C11 C13 SING N N 6
B1B C11 C10 SING N N 7
B1B C9 C10 SING N N 8
B1B C9 N2 SING N N 9
B1B N2 C8 SING N N 10
B1B C8 O DOUB N N 11
B1B C8 N SING N N 12
B1B N CA SING N N 13
B1B CA CB SING N N 14
B1B CG2 CB DOUB Y N 15
B1B CG2 C4 SING Y N 16
B1B CB CG1 SING Y N 17
B1B C4 C3 DOUB Y N 18
B1B CG1 CL1 SING N N 19
B1B CG1 CD1 DOUB Y N 20
B1B C3 CD1 SING Y N 21
B1B CD1 H1 SING N N 22
B1B C3 H2 SING N N 23
B1B C4 H3 SING N N 24
B1B CG2 H4 SING N N 25
B1B CA H5 SING N N 26
B1B CA H6 SING N N 27
B1B N H7 SING N N 28
B1B N2 H8 SING N N 29
B1B C9 H9 SING N N 30
B1B C10 H10 SING N N 31
B1B C10 H11 SING N N 32
B1B C11 H12 SING N N 33
B1B C12 H13 SING N N 34
B1B C12 H14 SING N N 35
B1B C12 H15 SING N N 36
B1B C13 H16 SING N N 37
B1B C13 H17 SING N N 38
B1B C13 H18 SING N N 39
B1B N3 H19 SING N N 40
B1B O3 H20 SING N N 41
#
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
B1B InChI InChI 1.03 InChI=1S/C14H20ClN3O3/c1-9(2)7-12(13(19)18-21)17-14(20)16-8-10-5-3-4-6-11(10)15/h3-6,9,12,21H,7-8H2,1-2H3,(H,18,19)(H2,16,17,20)/t12-/m0/s1
B1B InChIKey InChI 1.03 GMYGHFKIKOTHED-LBPRGKRZSA-N
B1B SMILES_CANONICAL CACTVS 3.385 CC(C)C[C@H](NC(=O)NCc1ccccc1Cl)C(=O)NO
B1B SMILES CACTVS 3.385 CC(C)C[CH](NC(=O)NCc1ccccc1Cl)C(=O)NO
B1B SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 CC(C)C[C@@H](C(=O)NO)NC(=O)NCc1ccccc1Cl
B1B SMILES "OpenEye OEToolkits" 2.0.6 CC(C)CC(C(=O)NO)NC(=O)NCc1ccccc1Cl
#
_pdbx_chem_comp_identifier.comp_id B1B
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.6
_pdbx_chem_comp_identifier.identifier (2~{S})-2-[(2-chlorophenyl)methylcarbamoylamino]-4-methyl-~{N}-oxidanyl-pentanamide
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
B1B 'Create component' 2017-07-26 PDBJ
B1B 'Initial release' 2018-08-01 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
B1B CL1 Cl 3.000 -3.000 1
B1B CG1 C 4.299 -3.750 2
B1B CD1 C 4.299 -5.250 3
B1B C3 C 5.598 -6.000 4
B1B C4 C 6.897 -5.250 5
B1B CG2 C 6.897 -3.750 6
B1B CB C 5.598 -3.000 7
B1B CA C 5.598 -1.500 8
B1B N N 6.897 -0.750 9
B1B C8 C 6.897 0.750 10
B1B O O 5.598 1.500 11
B1B N2 N 8.196 1.500 12
B1B C9 C 8.196 3.000 13
B1B C10 C 6.897 3.750 14
B1B C11 C 6.897 5.250 15
B1B C12 C 5.598 6.000 16
B1B C13 C 8.196 6.000 17
B1B C14 C 9.495 3.750 18
B1B O2 O 9.495 5.250 19
B1B N3 N 10.794 3.000 20
B1B O3 O 12.093 3.750 21
#
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
B1B O3 N3 SINGLE NONE 1
B1B N3 C14 SINGLE NONE 2
B1B O2 C14 DOUBLE NONE 3
B1B C14 C9 SINGLE NONE 4
B1B C12 C11 SINGLE NONE 5
B1B C11 C13 SINGLE NONE 6
B1B C11 C10 SINGLE NONE 7
B1B C9 C10 SINGLE BEGINWEDGE 8
B1B C9 N2 SINGLE NONE 9
B1B N2 C8 SINGLE NONE 10
B1B C8 O DOUBLE NONE 11
B1B C8 N SINGLE NONE 12
B1B N CA SINGLE NONE 13
B1B CA CB SINGLE NONE 14
B1B CG2 CB SINGLE NONE 15
B1B CG2 C4 DOUBLE NONE 16
B1B CB CG1 DOUBLE NONE 17
B1B C4 C3 SINGLE NONE 18
B1B CG1 CL1 SINGLE NONE 19
B1B CG1 CD1 SINGLE NONE 20
B1B C3 CD1 DOUBLE NONE 21
#
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
B1B MurckoScaffold S1 scaffold c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
B1B amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
B1B peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
B1B phenyl F3 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-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
B1B CG1 S1 1
B1B CD1 S1 1
B1B C3 S1 1
B1B C4 S1 1
B1B CG2 S1 1
B1B CB S1 1
B1B N3 F1 1
B1B C14 F1 1
B1B O2 F1 1
B1B C9 F1 1
B1B O2 F2 1
B1B C14 F2 1
B1B C9 F2 1
B1B N2 F2 1
B1B CG1 F3 1
B1B CB F3 1
B1B CG2 F3 1
B1B C4 F3 1
B1B C3 F3 1
B1B CD1 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id B1B
_pdbe_chem_comp_rdkit_properties.exactmw 313.119
_pdbe_chem_comp_rdkit_properties.amw 313.785
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 9
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 21
_pdbe_chem_comp_rdkit_properties.NumAtoms 41
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 3
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.429
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 156.735
_pdbe_chem_comp_rdkit_properties.tpsa 90.460
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.005
_pdbe_chem_comp_rdkit_properties.CrippenMR 79.730
_pdbe_chem_comp_rdkit_properties.chi0v 10.700
_pdbe_chem_comp_rdkit_properties.chi1v 5.276
_pdbe_chem_comp_rdkit_properties.chi2v 1.925
_pdbe_chem_comp_rdkit_properties.chi3v 1.925
_pdbe_chem_comp_rdkit_properties.chi4v 1.026
_pdbe_chem_comp_rdkit_properties.chi0n 29.944
_pdbe_chem_comp_rdkit_properties.chi1n 14.648
_pdbe_chem_comp_rdkit_properties.chi2n 1.641
_pdbe_chem_comp_rdkit_properties.chi3n 1.641
_pdbe_chem_comp_rdkit_properties.chi4n 0.890
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.790
_pdbe_chem_comp_rdkit_properties.kappa1 4.143
_pdbe_chem_comp_rdkit_properties.kappa2 8.486
_pdbe_chem_comp_rdkit_properties.kappa3 6.013
_pdbe_chem_comp_rdkit_properties.Phi 1.674
#
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
B1B UniChem ChEMBL CHEMBL2332518
B1B UniChem PDBe B1B
B1B UniChem ZINC ZINC000095587041
B1B UniChem 'PubChem TPHARMA' 163636855
B1B UniChem PubChem 71584672
B1B UniChem BindingDb 50430632
#
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
B1B CL1 3.873 1.884 -0.937 ETKDGv3 1
B1B CG1 3.418 0.243 -0.489 ETKDGv3 2
B1B CD1 3.470 -0.790 -1.548 ETKDGv3 3
B1B C3 3.123 -2.054 -1.281 ETKDGv3 4
B1B C4 2.689 -2.427 0.077 ETKDGv3 5
B1B CG2 2.646 -1.505 1.044 ETKDGv3 6
B1B CB 3.026 -0.096 0.763 ETKDGv3 7
B1B CA 2.890 0.908 1.885 ETKDGv3 8
B1B N 1.479 1.088 2.215 ETKDGv3 9
B1B C8 0.564 1.706 1.303 ETKDGv3 10
B1B O 0.987 2.526 0.443 ETKDGv3 11
B1B N2 -0.825 1.355 1.343 ETKDGv3 12
B1B C9 -1.717 1.617 0.205 ETKDGv3 13
B1B C10 -1.342 0.735 -1.016 ETKDGv3 14
B1B C11 -1.013 -0.749 -0.706 ETKDGv3 15
B1B C12 -2.237 -1.525 -0.202 ETKDGv3 16
B1B C13 -0.449 -1.428 -1.962 ETKDGv3 17
B1B C14 -3.178 1.486 0.579 ETKDGv3 18
B1B O2 -3.520 1.014 1.698 ETKDGv3 19
B1B N3 -4.188 1.924 -0.334 ETKDGv3 20
B1B O3 -5.500 1.786 -0.028 ETKDGv3 21
B1B H1 3.784 -0.521 -2.549 ETKDGv3 22
B1B H2 3.156 -2.803 -2.061 ETKDGv3 23
B1B H3 2.403 -3.450 0.287 ETKDGv3 24
B1B H4 2.320 -1.789 2.037 ETKDGv3 25
B1B H5 3.423 0.511 2.776 ETKDGv3 26
B1B H6 3.350 1.890 1.656 ETKDGv3 27
B1B H7 1.098 0.591 3.052 ETKDGv3 28
B1B H8 -1.135 0.716 2.109 ETKDGv3 29
B1B H9 -1.584 2.679 -0.098 ETKDGv3 30
B1B H10 -2.142 0.787 -1.787 ETKDGv3 31
B1B H11 -0.442 1.193 -1.483 ETKDGv3 32
B1B H12 -0.221 -0.801 0.072 ETKDGv3 33
B1B H13 -3.102 -1.383 -0.885 ETKDGv3 34
B1B H14 -2.512 -1.192 0.817 ETKDGv3 35
B1B H15 -2.008 -2.610 -0.138 ETKDGv3 36
B1B H16 -1.205 -1.436 -2.776 ETKDGv3 37
B1B H17 -0.154 -2.475 -1.734 ETKDGv3 38
B1B H18 0.456 -0.891 -2.317 ETKDGv3 39
B1B H19 -3.922 2.379 -1.236 ETKDGv3 40
B1B H20 -5.758 0.906 -0.405 ETKDGv3 41
#