data_0JY
#
_chem_comp.id 0JY
_chem_comp.name 4-methyl-L-leucine
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C7 H15 N O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2012-08-16
_chem_comp.pdbx_modified_date 2023-11-03
_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 145.200
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 0JY
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag Y
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 4G4L
_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
0JY O O O 0 1 N N N Y N Y -6.559 -0.949 10.477 -2.720 -0.648 -0.631 O 0JY 1
0JY C C C 0 1 N N N Y N Y -6.890 -0.480 11.578 -2.057 0.160 -0.025 C 0JY 2
0JY CA CA C 0 1 N N S Y N N -5.809 0.090 12.497 -0.653 -0.184 0.399 CA 0JY 3
0JY N N N 0 1 N N N Y Y N -6.276 1.258 13.245 -0.486 -1.643 0.403 N 0JY 4
0JY CB CB C 0 1 N N N N N N -5.188 -0.961 13.431 0.343 0.441 -0.581 CB 0JY 5
0JY CAI CAI C 0 1 N N N N N N -3.687 -0.735 13.747 1.769 0.194 -0.086 CAI 0JY 6
0JY CAB CAB C 0 1 N N N N N N -3.394 0.737 14.080 2.079 -1.303 -0.149 CAB 0JY 7
0JY CAC CAC C 0 1 N N N N N N -2.804 -1.110 12.540 2.756 0.957 -0.972 CAC 0JY 8
0JY CAA CAA C 0 1 N N N N N N -3.301 -1.636 14.926 1.899 0.681 1.359 CAA 0JY 9
0JY HA H2 H 0 1 N N N Y N N -4.996 0.433 11.840 -0.469 0.206 1.400 H2 0JY 10
0JY H2 H3 H 0 1 N Y N Y Y N -5.539 1.596 13.830 -0.173 -1.974 -0.498 H3 0JY 11
0JY H H4 H 0 1 N N N Y Y N -6.549 1.976 12.605 0.146 -1.933 1.134 H4 0JY 12
0JY H6 H6 H 0 1 N N N N N N -5.744 -0.949 14.380 0.216 -0.011 -1.565 H6 0JY 13
0JY H7 H7 H 0 1 N N N N N N -5.294 -1.948 12.956 0.162 1.513 -0.649 H7 0JY 14
0JY H8 H8 H 0 1 N N N N N N -4.006 1.048 14.940 1.670 -1.720 -1.070 H8 0JY 15
0JY H9 H9 H 0 1 N N N N N N -2.328 0.852 14.328 3.159 -1.452 -0.131 H9 0JY 16
0JY H10 H10 H 0 1 N N N N N N -3.638 1.365 13.210 1.629 -1.804 0.708 H10 0JY 17
0JY H11 H11 H 0 1 N N N N N N -1.747 -0.940 12.792 2.535 2.023 -0.927 H11 0JY 18
0JY H12 H12 H 0 1 N N N N N N -2.956 -2.171 12.290 3.772 0.781 -0.619 H12 0JY 19
0JY H13 H13 H 0 1 N N N N N N -3.080 -0.487 11.676 2.663 0.610 -2.001 H13 0JY 20
0JY H14 H14 H 0 1 N N N N N N -3.921 -1.384 15.799 1.196 0.137 1.990 H14 0JY 21
0JY H15 H15 H 0 1 N N N N N N -3.465 -2.689 14.652 2.915 0.505 1.711 H15 0JY 22
0JY H16 H16 H 0 1 N N N N N N -2.240 -1.482 15.173 1.678 1.747 1.404 H16 0JY 23
0JY OXT O1 O 0 1 N Y N Y N Y ? ? ? -2.570 1.366 0.267 O1 0JY 24
0JY HXT H1 H 0 1 N Y N Y N Y ? ? ? -3.474 1.542 -0.029 H1 0JY 25
#
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
0JY O C DOUB N N 1
0JY C CA SING N N 2
0JY CA N SING N N 3
0JY CA CB SING N N 4
0JY CAC CAI SING N N 5
0JY CB CAI SING N N 6
0JY CAI CAB SING N N 7
0JY CAI CAA SING N N 8
0JY CA HA SING N N 9
0JY N H2 SING N N 10
0JY N H SING N N 11
0JY CB H6 SING N N 12
0JY CB H7 SING N N 13
0JY CAB H8 SING N N 14
0JY CAB H9 SING N N 15
0JY CAB H10 SING N N 16
0JY CAC H11 SING N N 17
0JY CAC H12 SING N N 18
0JY CAC H13 SING N N 19
0JY CAA H14 SING N N 20
0JY CAA H15 SING N N 21
0JY CAA H16 SING N N 22
0JY C OXT SING N N 23
0JY OXT HXT SING N N 24
#
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
0JY SMILES ACDLabs 12.01 O=C(O)C(N)CC(C)(C)C
0JY InChI InChI 1.03 InChI=1S/C7H15NO2/c1-7(2,3)4-5(8)6(9)10/h5H,4,8H2,1-3H3,(H,9,10)/t5-/m0/s1
0JY InChIKey InChI 1.03 LPBSHGLDBQBSPI-YFKPBYRVSA-N
0JY SMILES_CANONICAL CACTVS 3.370 CC(C)(C)C[C@H](N)C(O)=O
0JY SMILES CACTVS 3.370 CC(C)(C)C[CH](N)C(O)=O
0JY SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 CC(C)(C)C[C@@H](C(=O)O)N
0JY SMILES "OpenEye OEToolkits" 1.7.6 CC(C)(C)CC(C(=O)O)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
0JY "SYSTEMATIC NAME" ACDLabs 12.01 4-methyl-L-leucine
0JY "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2S)-2-azanyl-4,4-dimethyl-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
0JY 'Create component' 2012-08-16 RCSB
0JY 'Initial release' 2012-10-26 RCSB
0JY 'Modify backbone' 2023-11-03 PDBE
#
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
0JY O O 9.495 -0.142 1
0JY C C 8.196 0.608 2
0JY CA C 6.897 -0.142 3
0JY N N 6.897 -1.643 4
0JY CB C 5.598 0.608 5
0JY CAI C 4.299 -0.142 6
0JY CAB C 3.549 1.157 7
0JY CAC C 3.000 -0.892 8
0JY CAA C 5.049 -1.442 9
0JY OXT O 8.196 2.107 10
#
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
0JY O C DOUBLE NONE 1
0JY C CA SINGLE NONE 2
0JY CA N SINGLE BEGINWEDGE 3
0JY CA CB SINGLE NONE 4
0JY CAC CAI SINGLE NONE 5
0JY CB CAI SINGLE NONE 6
0JY CAI CAB SINGLE NONE 7
0JY CAI CAA SINGLE NONE 8
0JY C OXT SINGLE NONE 9
#
_pdbe_chem_comp_substructure.comp_id 0JY
_pdbe_chem_comp_substructure.substructure_name peptide
_pdbe_chem_comp_substructure.id F1
_pdbe_chem_comp_substructure.substructure_type fragment
_pdbe_chem_comp_substructure.substructure_smiles NCC=O
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2
_pdbe_chem_comp_substructure.substructure_inchikeys LYIIBVSRGJSHAV-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
0JY O F1 1
0JY C F1 1
0JY CA F1 1
0JY N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 0JY
_pdbe_chem_comp_rdkit_properties.exactmw 145.110
_pdbe_chem_comp_rdkit_properties.amw 145.202
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 10
_pdbe_chem_comp_rdkit_properties.NumAtoms 25
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.857
_pdbe_chem_comp_rdkit_properties.NumRings 0
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_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 82.502
_pdbe_chem_comp_rdkit_properties.tpsa 63.320
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.834
_pdbe_chem_comp_rdkit_properties.CrippenMR 39.683
_pdbe_chem_comp_rdkit_properties.chi0v 4.764
_pdbe_chem_comp_rdkit_properties.chi1v 2.132
_pdbe_chem_comp_rdkit_properties.chi2v 0.499
_pdbe_chem_comp_rdkit_properties.chi3v 0.499
_pdbe_chem_comp_rdkit_properties.chi4v 0.229
_pdbe_chem_comp_rdkit_properties.chi0n 19.764
_pdbe_chem_comp_rdkit_properties.chi1n 9.435
_pdbe_chem_comp_rdkit_properties.chi2n 0.499
_pdbe_chem_comp_rdkit_properties.chi3n 0.499
_pdbe_chem_comp_rdkit_properties.chi4n 0.229
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.570
_pdbe_chem_comp_rdkit_properties.kappa1 1.221
_pdbe_chem_comp_rdkit_properties.kappa2 3.012
_pdbe_chem_comp_rdkit_properties.kappa3 4.323
_pdbe_chem_comp_rdkit_properties.Phi 0.368
#
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
0JY UniChem PDBe 0JY
0JY UniChem ZINC ZINC000000391810
0JY UniChem eMolecules 529834
0JY UniChem SureChEMBL SCHEMBL196695
0JY UniChem ACTor 57224-50-7
0JY UniChem Nikkaji J265.403B
0JY UniChem BindingDb 18148
0JY UniChem 'EPA CompTox Dashboard' DTXSID50205846
0JY UniChem BRENDA 203573
0JY UniChem BRENDA 215063
0JY UniChem ChemicalBook CB6176701
0JY UniChem 'PubChem TPHARMA' 16044322
0JY UniChem PubChem 194032
0JY UniChem PubChem 6950506
#
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
0JY O 3.263 0.464 0.999 ETKDGv3 1
0JY C 2.741 -0.228 0.083 ETKDGv3 2
0JY CA 1.294 -0.641 0.171 ETKDGv3 3
0JY N 1.086 -1.506 1.335 ETKDGv3 4
0JY CB 0.381 0.610 0.241 ETKDGv3 5
0JY CAI -1.127 0.391 -0.103 ETKDGv3 6
0JY CAB -1.868 1.726 0.129 ETKDGv3 7
0JY CAC -1.306 -0.009 -1.585 ETKDGv3 8
0JY CAA -1.769 -0.683 0.799 ETKDGv3 9
0JY HA 1.060 -1.221 -0.745 ETKDGv3 10
0JY H2 1.394 -1.010 2.204 ETKDGv3 11
0JY H 1.683 -2.359 1.231 ETKDGv3 12
0JY H6 0.466 1.051 1.260 ETKDGv3 13
0JY H7 0.781 1.378 -0.460 ETKDGv3 14
0JY H8 -1.440 2.528 -0.511 ETKDGv3 15
0JY H9 -2.948 1.629 -0.115 ETKDGv3 16
0JY H10 -1.782 2.043 1.190 ETKDGv3 17
0JY H11 -0.788 0.713 -2.252 ETKDGv3 18
0JY H12 -2.383 -0.022 -1.858 ETKDGv3 19
0JY H13 -0.907 -1.025 -1.785 ETKDGv3 20
0JY H14 -1.371 -1.692 0.565 ETKDGv3 21
0JY H15 -2.868 -0.720 0.642 ETKDGv3 22
0JY H16 -1.577 -0.459 1.871 ETKDGv3 23
0JY OXT 3.505 -0.614 -1.013 ETKDGv3 24
0JY HXT 4.479 -0.346 -1.088 ETKDGv3 25
#