data_S0R
#
_chem_comp.id S0R
_chem_comp.name '(2S)-2-benzamido-4-methyl-pentanoic acid'
_chem_comp.type 'L-peptide linking'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C13 H17 N O3'
_chem_comp.mon_nstd_parent_comp_id LEU
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2023-04-07
_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 235.279
_chem_comp.one_letter_code L
_chem_comp.three_letter_code S0R
_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 6IW7
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
_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
S0R CA C1 C 0 1 N N S Y N N 232.143 -3.495 420.624 1.663 0.451 0.106 CA S0R 1
S0R CB C2 C 0 1 N N N N N N 231.667 -3.169 419.216 2.650 -0.536 -0.521 CB S0R 2
S0R CG C3 C 0 1 N N N N N N 231.852 -4.324 418.242 2.447 -1.922 0.094 CG S0R 3
S0R O1 O1 O 0 1 N N N N N N 233.042 -5.611 422.155 -0.527 1.074 1.550 O1 S0R 4
S0R C5 C4 C 0 1 Y N N N N N 230.493 -8.059 424.374 -3.646 -1.071 -1.297 C5 S0R 5
S0R C6 C5 C 0 1 Y N N N N N 231.347 -7.166 423.749 -2.355 -0.708 -0.971 C6 S0R 6
S0R C2 C6 C 0 1 Y N N N N N 229.644 -6.655 422.152 -3.183 0.413 1.000 C2 S0R 7
S0R C4 C7 C 0 1 Y N N N N N 229.218 -8.254 423.886 -4.701 -0.693 -0.486 C4 S0R 8
S0R C C8 C 0 1 N N N N N N 231.848 -5.500 421.968 -0.734 0.428 0.542 C S0R 9
S0R C1 C9 C 0 1 Y N N N N N 230.923 -6.460 422.638 -2.115 0.039 0.183 C1 S0R 10
S0R C3 C10 C 0 1 Y N N N N N 228.796 -7.551 422.775 -4.469 0.047 0.660 C3 S0R 11
S0R N N1 N 0 1 N N N Y Y N 231.341 -4.559 421.185 0.295 0.065 -0.249 N S0R 12
S0R C7 C11 C 0 1 N N N Y N Y 232.010 -2.245 421.434 1.944 1.839 -0.409 C7 S0R 13
S0R O O2 O 0 1 N N N Y N Y 230.925 -1.862 421.803 1.089 2.444 -1.012 O S0R 14
S0R CD1 C12 C 0 1 N N N N N N 233.086 -5.117 418.609 3.345 -2.934 -0.619 CD1 S0R 15
S0R CD2 C13 C 0 1 N N N N N N 230.641 -5.243 418.194 2.808 -1.878 1.580 CD2 S0R 16
S0R H1 H1 H 0 1 N N N Y N N 233.200 -3.797 420.586 1.774 0.436 1.190 H1 S0R 17
S0R H2 H2 H 0 1 N N N N N N 232.236 -2.304 418.845 2.478 -0.587 -1.597 H2 S0R 18
S0R H3 H3 H 0 1 N N N N N N 230.598 -2.914 419.258 3.669 -0.200 -0.332 H3 S0R 19
S0R H4 H4 H 0 1 N N N N N N 232.001 -3.902 417.237 1.404 -2.220 -0.017 H4 S0R 20
S0R H5 H5 H 0 1 N N N N N N 230.826 -8.604 425.245 -3.833 -1.649 -2.190 H5 S0R 21
S0R H6 H6 H 0 1 N N N N N N 232.347 -7.020 424.130 -1.533 -1.000 -1.607 H6 S0R 22
S0R H7 H7 H 0 1 N N N N N N 229.307 -6.107 421.285 -3.003 0.987 1.897 H7 S0R 23
S0R H8 H8 H 0 1 N N N N N N 228.553 -8.953 424.371 -5.709 -0.977 -0.748 H8 S0R 24
S0R H9 H9 H 0 1 N N N N N N 227.798 -7.702 422.391 -5.296 0.336 1.291 H9 S0R 25
S0R H10 H10 H 0 1 N N N Y Y N 230.364 -4.586 420.974 0.130 -0.450 -1.054 H10 S0R 26
S0R O2 O3 O 0 1 N Y N Y N Y 232.854 -1.705 421.682 3.144 2.402 -0.199 O2 S0R 27
S0R H12 H12 H 0 1 N N N N N N 233.957 -4.446 418.642 4.388 -2.636 -0.508 H12 S0R 28
S0R H13 H13 H 0 1 N N N N N N 232.943 -5.581 419.596 3.200 -3.921 -0.181 H13 S0R 29
S0R H14 H14 H 0 1 N N N N N N 233.255 -5.901 417.856 3.088 -2.965 -1.678 H14 S0R 30
S0R H15 H15 H 0 1 N N N N N N 229.748 -4.660 417.927 3.851 -1.580 1.692 H15 S0R 31
S0R H16 H16 H 0 1 N N N N N N 230.806 -6.027 417.440 2.168 -1.157 2.089 H16 S0R 32
S0R H17 H17 H 0 1 N N N N N N 230.494 -5.707 419.180 2.663 -2.865 2.019 H17 S0R 33
S0R H18 H18 H 0 1 N Y N Y N Y 232.605 -0.946 422.196 3.277 3.294 -0.549 H18 S0R 34
#
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
S0R CD2 CG SING N N 1
S0R CG CD1 SING N N 2
S0R CG CB SING N N 3
S0R CB CA SING N N 4
S0R CA N SING N N 5
S0R CA C7 SING N N 6
S0R N C SING N N 7
S0R C7 O DOUB N N 8
S0R C O1 DOUB N N 9
S0R C C1 SING N N 10
S0R C2 C1 DOUB Y N 11
S0R C2 C3 SING Y N 12
S0R C1 C6 SING Y N 13
S0R C3 C4 DOUB Y N 14
S0R C6 C5 DOUB Y N 15
S0R C4 C5 SING Y N 16
S0R CA H1 SING N N 17
S0R CB H2 SING N N 18
S0R CB H3 SING N N 19
S0R CG H4 SING N N 20
S0R C5 H5 SING N N 21
S0R C6 H6 SING N N 22
S0R C2 H7 SING N N 23
S0R C4 H8 SING N N 24
S0R C3 H9 SING N N 25
S0R N H10 SING N N 26
S0R C7 O2 SING N N 27
S0R CD1 H12 SING N N 28
S0R CD1 H13 SING N N 29
S0R CD1 H14 SING N N 30
S0R CD2 H15 SING N N 31
S0R CD2 H16 SING N N 32
S0R CD2 H17 SING N N 33
S0R O2 H18 SING N N 34
#
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
S0R InChI InChI 1.06 'InChI=1S/C13H17NO3/c1-9(2)8-11(13(16)17)14-12(15)10-6-4-3-5-7-10/h3-7,9,11H,8H2,1-2H3,(H,14,15)(H,16,17)/t11-/m0/s1'
S0R InChIKey InChI 1.06 POLGZPYHEPOBFG-NSHDSACASA-N
S0R SMILES_CANONICAL CACTVS 3.385 'CC(C)C[C@H](NC(=O)c1ccccc1)C(O)=O'
S0R SMILES CACTVS 3.385 'CC(C)C[CH](NC(=O)c1ccccc1)C(O)=O'
S0R SMILES_CANONICAL 'OpenEye OEToolkits' 2.0.7 'CC(C)C[C@@H](C(=O)O)NC(=O)c1ccccc1'
S0R SMILES 'OpenEye OEToolkits' 2.0.7 'CC(C)CC(C(=O)O)NC(=O)c1ccccc1'
#
_pdbx_chem_comp_identifier.comp_id S0R
_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 '(2~{S})-2-benzamido-4-methyl-pentanoic acid'
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
S0R 'Create component' 2023-04-07 PDBJ
S0R 'Initial release' 2023-04-19 RCSB
S0R 'Modify backbone' 2024-09-26 PDBE
S0R 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id S0R
_pdbx_chem_comp_pcm.modified_residue_id LEU
_pdbx_chem_comp_pcm.type Benzoylation
_pdbx_chem_comp_pcm.category 'Named protein modification'
_pdbx_chem_comp_pcm.position 'Amino-acid backbone'
_pdbx_chem_comp_pcm.polypeptide_position N-terminal
_pdbx_chem_comp_pcm.comp_id_linking_atom ?
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom ?
_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
S0R CA C 5.598 1.875 1
S0R CB C 4.299 2.625 2
S0R CG C 4.299 4.125 3
S0R O1 O 3.000 0.375 4
S0R C5 C 5.598 -4.125 5
S0R C6 C 5.598 -2.625 6
S0R C2 C 3.000 -2.625 7
S0R C4 C 4.299 -4.875 8
S0R C C 4.299 -0.375 9
S0R C1 C 4.299 -1.875 10
S0R C3 C 3.000 -4.125 11
S0R N N 5.598 0.375 12
S0R C7 C 6.897 2.625 13
S0R O O 6.897 4.125 14
S0R CD1 C 5.598 4.875 15
S0R CD2 C 3.000 4.875 16
S0R O2 O 8.196 1.875 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
S0R CD2 CG SINGLE NONE 1
S0R CG CD1 SINGLE NONE 2
S0R CG CB SINGLE NONE 3
S0R CA CB SINGLE BEGINWEDGE 4
S0R CA N SINGLE NONE 5
S0R CA C7 SINGLE NONE 6
S0R N C SINGLE NONE 7
S0R C7 O DOUBLE NONE 8
S0R C O1 DOUBLE NONE 9
S0R C C1 SINGLE NONE 10
S0R C2 C1 DOUBLE NONE 11
S0R C2 C3 SINGLE NONE 12
S0R C1 C6 SINGLE NONE 13
S0R C3 C4 DOUBLE NONE 14
S0R C6 C5 DOUBLE NONE 15
S0R C4 C5 SINGLE NONE 16
S0R C7 O2 SINGLE NONE 17
#
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
S0R MurckoScaffold S1 scaffold c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
S0R amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
S0R peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
S0R 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
S0R C5 S1 1
S0R C6 S1 1
S0R C2 S1 1
S0R C4 S1 1
S0R C1 S1 1
S0R C3 S1 1
S0R N F1 1
S0R C F1 1
S0R O1 F1 1
S0R C1 F1 1
S0R O F2 1
S0R C7 F2 1
S0R CA F2 1
S0R N F2 1
S0R C5 F3 1
S0R C6 F3 1
S0R C1 F3 1
S0R C2 F3 1
S0R C3 F3 1
S0R C4 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id S0R
_pdbe_chem_comp_rdkit_properties.exactmw 235.121
_pdbe_chem_comp_rdkit_properties.amw 235.283
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 17
_pdbe_chem_comp_rdkit_properties.NumAtoms 34
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.385
_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 124.682
_pdbe_chem_comp_rdkit_properties.tpsa 66.400
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.861
_pdbe_chem_comp_rdkit_properties.CrippenMR 64.521
_pdbe_chem_comp_rdkit_properties.chi0v 8.172
_pdbe_chem_comp_rdkit_properties.chi1v 4.060
_pdbe_chem_comp_rdkit_properties.chi2v 1.364
_pdbe_chem_comp_rdkit_properties.chi3v 1.364
_pdbe_chem_comp_rdkit_properties.chi4v 0.757
_pdbe_chem_comp_rdkit_properties.chi0n 25.172
_pdbe_chem_comp_rdkit_properties.chi1n 12.415
_pdbe_chem_comp_rdkit_properties.chi2n 1.364
_pdbe_chem_comp_rdkit_properties.chi3n 1.364
_pdbe_chem_comp_rdkit_properties.chi4n 0.757
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.840
_pdbe_chem_comp_rdkit_properties.kappa1 2.939
_pdbe_chem_comp_rdkit_properties.kappa2 6.034
_pdbe_chem_comp_rdkit_properties.kappa3 4.264
_pdbe_chem_comp_rdkit_properties.Phi 1.043
#
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
S0R UniChem ZINC ZINC000000399556
S0R UniChem eMolecules 530268
S0R UniChem BRENDA 100192
S0R UniChem BRENDA 102512
S0R UniChem BRENDA 171178
S0R UniChem BRENDA 31697
S0R UniChem BRENDA 37941
S0R UniChem BRENDA 43814
S0R UniChem ChemicalBook CB8180685
S0R UniChem Nikkaji J231.987J
S0R UniChem SureChEMBL SCHEMBL2158900
S0R UniChem 'PubChem TPHARMA' 15961015
S0R UniChem PubChem 853887
S0R UniChem Mcule MCULE-9850346606
S0R UniChem ACTor 17966-67-5
#
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
S0R CA -1.153 -1.402 -0.352 ETKDGv3 1
S0R CB -2.409 -0.522 -0.542 ETKDGv3 2
S0R CG -2.773 0.326 0.702 ETKDGv3 3
S0R O1 1.353 -2.023 0.857 ETKDGv3 4
S0R C5 4.853 0.274 0.564 ETKDGv3 5
S0R C6 3.792 -0.543 0.544 ETKDGv3 6
S0R C2 2.296 1.305 -0.014 ETKDGv3 7
S0R C4 4.685 1.712 0.281 ETKDGv3 8
S0R C 1.275 -0.931 0.232 ETKDGv3 9
S0R C1 2.438 -0.013 0.232 ETKDGv3 10
S0R C3 3.471 2.202 0.008 ETKDGv3 11
S0R N 0.070 -0.605 -0.482 ETKDGv3 12
S0R C7 -1.130 -2.505 -1.371 ETKDGv3 13
S0R O -0.983 -2.237 -2.594 ETKDGv3 14
S0R CD1 -4.144 0.986 0.500 ETKDGv3 15
S0R CD2 -1.720 1.402 1.008 ETKDGv3 16
S0R H1 -1.198 -1.863 0.660 ETKDGv3 17
S0R H2 -2.287 0.136 -1.432 ETKDGv3 18
S0R H3 -3.272 -1.194 -0.755 ETKDGv3 19
S0R H4 -2.852 -0.346 1.585 ETKDGv3 20
S0R H5 5.837 -0.118 0.788 ETKDGv3 21
S0R H6 3.932 -1.597 0.751 ETKDGv3 22
S0R H7 1.325 1.742 -0.206 ETKDGv3 23
S0R H8 5.545 2.369 0.298 ETKDGv3 24
S0R H9 3.345 3.258 -0.195 ETKDGv3 25
S0R H10 0.111 0.118 -1.236 ETKDGv3 26
S0R O2 -1.286 -3.826 -0.965 ETKDGv3 27
S0R H12 -4.121 1.677 -0.370 ETKDGv3 28
S0R H13 -4.922 0.213 0.324 ETKDGv3 29
S0R H14 -4.433 1.559 1.407 ETKDGv3 30
S0R H15 -0.786 0.937 1.384 ETKDGv3 31
S0R H16 -1.495 2.004 0.101 ETKDGv3 32
S0R H17 -2.083 2.084 1.806 ETKDGv3 33
S0R H18 -1.277 -4.582 -1.639 ETKDGv3 34
#