data_LEU
#
_chem_comp.id LEU
_chem_comp.name LEUCINE
_chem_comp.type 'L-PEPTIDE LINKING'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C6 H13 N O2'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_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 131.173
_chem_comp.one_letter_code L
_chem_comp.three_letter_code LEU
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code ?
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
_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
LEU N N N 0 1 N N N Y Y N 16.293 15.907 52.123 -1.661 0.627 -0.406 N LEU 1
LEU CA CA C 0 1 N N S Y N N 15.121 16.772 51.804 -0.205 0.441 -0.467 CA LEU 2
LEU C C C 0 1 N N N Y N Y 13.865 15.975 51.517 0.180 -0.055 -1.836 C LEU 3
LEU O O O 0 1 N N N Y N Y 12.808 16.576 51.643 -0.591 -0.731 -2.474 O LEU 4
LEU CB CB C 0 1 N N N N N N 15.395 17.657 50.575 0.221 -0.583 0.585 CB LEU 5
LEU CG CG C 0 1 N N N N N N 16.407 18.798 50.632 -0.170 -0.079 1.976 CG LEU 6
LEU CD1 CD1 C 0 1 N N N N N N 16.398 19.395 52.065 0.256 -1.104 3.029 CD1 LEU 7
LEU CD2 CD2 C 0 1 N N N N N N 17.792 18.247 50.210 0.526 1.254 2.250 CD2 LEU 8
LEU OXT OXT O 0 1 N Y N Y N Y 13.877 14.786 51.211 1.382 0.254 -2.348 OXT LEU 9
LEU H H H 0 1 N N N Y Y N 17.138 16.443 52.316 -2.077 -0.272 -0.592 H LEU 10
LEU H2 HN2 H 0 1 N Y N Y Y N 16.454 15.223 51.383 -1.884 0.858 0.550 H2 LEU 11
LEU HA HA H 0 1 N N N Y N N 14.962 17.396 52.714 0.291 1.391 -0.271 HA LEU 12
LEU HB2 1HB H 0 1 N N N N N N 15.673 16.990 49.725 1.301 -0.722 0.540 HB2 LEU 13
LEU HB3 2HB H 0 1 N N N N N N 14.421 18.076 50.228 -0.275 -1.534 0.390 HB3 LEU 14
LEU HG HG H 0 1 N N N N N N 16.148 19.623 49.927 -1.250 0.058 2.021 HG LEU 15
LEU HD11 1HD1 H 0 0 N N N N N N 17.137 20.228 52.106 -0.022 -0.745 4.019 HD11 LEU 16
LEU HD12 2HD1 H 0 0 N N N N N N 15.379 19.710 52.390 -0.240 -2.055 2.833 HD12 LEU 17
LEU HD13 3HD1 H 0 0 N N N N N N 16.577 18.624 52.850 1.336 -1.243 2.984 HD13 LEU 18
LEU HD21 1HD2 H 0 0 N N N N N N 18.531 19.080 50.251 1.606 1.115 2.205 HD21 LEU 19
LEU HD22 2HD2 H 0 0 N N N N N N 18.105 17.366 50.817 0.222 1.984 1.500 HD22 LEU 20
LEU HD23 3HD2 H 0 0 N N N N N N 17.768 17.745 49.214 0.247 1.613 3.241 HD23 LEU 21
LEU HXT HXT H 0 1 N Y N Y N Y 13.089 14.286 51.031 1.630 -0.064 -3.226 HXT LEU 22
#
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
LEU N CA SING N N 1
LEU N H SING N N 2
LEU N H2 SING N N 3
LEU CA C SING N N 4
LEU CA CB SING N N 5
LEU CA HA SING N N 6
LEU C O DOUB N N 7
LEU C OXT SING N N 8
LEU CB CG SING N N 9
LEU CB HB2 SING N N 10
LEU CB HB3 SING N N 11
LEU CG CD1 SING N N 12
LEU CG CD2 SING N N 13
LEU CG HG SING N N 14
LEU CD1 HD11 SING N N 15
LEU CD1 HD12 SING N N 16
LEU CD1 HD13 SING N N 17
LEU CD2 HD21 SING N N 18
LEU CD2 HD22 SING N N 19
LEU CD2 HD23 SING N N 20
LEU OXT HXT SING N N 21
#
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
LEU SMILES ACDLabs 10.04 'O=C(O)C(N)CC(C)C'
LEU SMILES_CANONICAL CACTVS 3.341 'CC(C)C[C@H](N)C(O)=O'
LEU SMILES CACTVS 3.341 'CC(C)C[CH](N)C(O)=O'
LEU SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'CC(C)C[C@@H](C(=O)O)N'
LEU SMILES 'OpenEye OEToolkits' 1.5.0 'CC(C)CC(C(=O)O)N'
LEU InChI InChI 1.03 'InChI=1S/C6H13NO2/c1-4(2)3-5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)/t5-/m0/s1'
LEU InChIKey InChI 1.03 ROHFNLRQFUQHCH-YFKPBYRVSA-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
LEU 'SYSTEMATIC NAME' ACDLabs 10.04 L-leucine
LEU 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '(2S)-2-amino-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
LEU 'Create component' 1999-07-08 EBI
LEU 'Modify descriptor' 2011-06-04 RCSB
LEU 'Modify backbone' 2023-11-03 PDBE
LEU 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id LEU
_pdbx_chem_comp_pcm.modified_residue_id LYS
_pdbx_chem_comp_pcm.type Leucylation
_pdbx_chem_comp_pcm.category 'Amino acid'
_pdbx_chem_comp_pcm.position 'Amino-acid side chain'
_pdbx_chem_comp_pcm.polypeptide_position 'Any position'
_pdbx_chem_comp_pcm.comp_id_linking_atom C
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom NZ
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#
_pdbe_chem_comp_drugbank_details.comp_id LEU
_pdbe_chem_comp_drugbank_details.drugbank_id DB00149
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Leucine
_pdbe_chem_comp_drugbank_details.description 'An essential branched-chain amino acid important for hemoglobin formation.'
_pdbe_chem_comp_drugbank_details.cas_number 61-90-5
_pdbe_chem_comp_drugbank_details.mechanism_of_action
'This group of essential amino acids are identified as the branched-chain amino acids, BCAAs. Because this arrangement of carbon atoms cannot be made by humans, these amino acids are an essential element in the diet. The catabolism of all three compounds initiates in muscle and yields NADH and FADH2 which can be utilized for ATP generation. The catabolism of all three of these amino acids uses the same enzymes in the first two steps. The first step in each case is a transamination using a single BCAA aminotransferase, with a-ketoglutarate as amine acceptor. As a result, three different a-keto acids are produced and are oxidized using a common branched-chain a-keto acid dehydrogenase, yielding the three different CoA derivatives. Subsequently the metabolic pathways diverge, producing many intermediates. The principal product from valine is propionylCoA, the glucogenic precursor of succinyl-CoA. Isoleucine catabolism terminates with production of acetylCoA and propionylCoA; thus isoleucine is both glucogenic and ketogenic. Leucine gives rise to acetylCoA and acetoacetylCoA, and is thus classified as strictly ketogenic. There are a number of genetic diseases associated with faulty catabolism of the BCAAs. The most common defect is in the branched-chain a-keto acid dehydrogenase. Since there is only one dehydrogenase enzyme for all three amino acids, all three a-keto acids accumulate and are excreted in the urine. The disease is known as Maple syrup urine disease because of the characteristic odor of the urine in afflicted individuals. Mental retardation in these cases is extensive. Unfortunately, since these are essential amino acids, they cannot be heavily restricted in the diet; ultimately, the life of afflicted individuals is short and development is abnormal The main neurological problems are due to poor formation of myelin in the CNS.'
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
LEU '(2S)-2-Amino-4-methylpentanoic acid' DrugBank ?
LEU '(2S)-alpha-2-Amino-4-methylvaleric acid' DrugBank ?
LEU (2S)-alpha-Leucine DrugBank ?
LEU (S)-(+)-Leucine DrugBank ?
LEU (S)-Leucine DrugBank ?
LEU '2-Amino-4-methylvaleric acid' DrugBank ?
LEU L DrugBank ?
LEU L-Leucine DrugBank ?
LEU Leu DrugBank ?
LEU Leucine DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id LEU
_pdbe_chem_comp_drugbank_classification.drugbank_id DB00149
_pdbe_chem_comp_drugbank_classification.parent 'Leucine and derivatives'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Carboxylic acids and derivatives'
_pdbe_chem_comp_drugbank_classification.superclass 'Organic acids and derivatives'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as leucine and derivatives. These are compounds containing leucine or a derivative thereof resulting from reaction of leucine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
LEU DB00149 'Leucine--tRNA ligase, mitochondrial' Humans Q15031 unknown 1
LEU DB00149 'tRNA wybutosine-synthesizing protein 4' Humans O60294 unknown 2
LEU DB00149 'Leucine carboxyl methyltransferase 1' Humans Q9UIC8 unknown 3
LEU DB00149 'Leucine--tRNA ligase, cytoplasmic' Humans Q9P2J5 unknown 4
LEU DB00149 'Branched-chain-amino-acid aminotransferase, mitochondrial' Humans O15382 unknown 5
LEU DB00149 'Branched-chain-amino-acid aminotransferase, cytosolic' Humans P54687 unknown 6
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.09.6 'Core functionality.'
pdbeccdutils 0.8.6 '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
LEU N N 4.299 1.500 1
LEU CA C 5.598 0.750 2
LEU C C 6.897 1.500 3
LEU O O 8.196 0.750 4
LEU CB C 5.598 -0.750 5
LEU CG C 4.299 -1.500 6
LEU CD1 C 4.299 -3.000 7
LEU CD2 C 3.000 -0.750 8
LEU OXT O 6.897 3.000 9
#
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
LEU CA N SINGLE BEGINDASH 1
LEU CA C SINGLE NONE 2
LEU CA CB SINGLE NONE 3
LEU C O DOUBLE NONE 4
LEU C OXT SINGLE NONE 5
LEU CB CG SINGLE NONE 6
LEU CG CD1 SINGLE NONE 7
LEU CG CD2 SINGLE NONE 8
#
_pdbe_chem_comp_substructure.comp_id LEU
_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
LEU O F1 1
LEU C F1 1
LEU CA F1 1
LEU N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id LEU
_pdbe_chem_comp_rdkit_properties.exactmw 131.095
_pdbe_chem_comp_rdkit_properties.amw 131.175
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 9
_pdbe_chem_comp_rdkit_properties.NumAtoms 22
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.833
_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 73.327
_pdbe_chem_comp_rdkit_properties.tpsa 63.320
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.444
_pdbe_chem_comp_rdkit_properties.CrippenMR 35.066
_pdbe_chem_comp_rdkit_properties.chi0v 4.264
_pdbe_chem_comp_rdkit_properties.chi1v 1.882
_pdbe_chem_comp_rdkit_properties.chi2v 0.437
_pdbe_chem_comp_rdkit_properties.chi3v 0.437
_pdbe_chem_comp_rdkit_properties.chi4v 0.169
_pdbe_chem_comp_rdkit_properties.chi0n 17.264
_pdbe_chem_comp_rdkit_properties.chi1n 8.185
_pdbe_chem_comp_rdkit_properties.chi2n 0.437
_pdbe_chem_comp_rdkit_properties.chi3n 0.437
_pdbe_chem_comp_rdkit_properties.chi4n 0.169
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.570
_pdbe_chem_comp_rdkit_properties.kappa1 1.115
_pdbe_chem_comp_rdkit_properties.kappa2 3.455
_pdbe_chem_comp_rdkit_properties.kappa3 3.968
_pdbe_chem_comp_rdkit_properties.Phi 0.428
#
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
LEU UniChem ChEMBL CHEMBL291962
LEU UniChem DrugBank DB00149
LEU UniChem 'Guide to Pharmacology' 3312
LEU UniChem 'KEGG LIGAND' C00123
LEU UniChem ChEBI 15603
LEU UniChem ChEBI 57427
LEU UniChem ZINC ZINC000003645145
LEU UniChem eMolecules 514488
LEU UniChem fdasrs GMW67QNF9C
LEU UniChem SureChEMBL SCHEMBL3889
LEU UniChem HMDB HMDB0000687
LEU UniChem 'PubChem TPHARMA' 15146625
LEU UniChem NMRShiftDB 20026342
LEU UniChem ACTor 21675-61-6
LEU UniChem ACTor 25248-98-0
LEU UniChem ACTor 70-45-1
LEU UniChem Recon 'leu_L'
LEU UniChem DrugCentral 1557
LEU UniChem MetaboLights MTBLC15603
LEU UniChem MetaboLights MTBLC57427
LEU UniChem BRENDA 113715
LEU UniChem BRENDA 124073
LEU UniChem BRENDA 124800
LEU UniChem BRENDA 127
LEU UniChem BRENDA 145030
LEU UniChem BRENDA 145056
LEU UniChem BRENDA 145944
LEU UniChem BRENDA 145970
LEU UniChem BRENDA 229581
LEU UniChem BRENDA 260104
LEU UniChem BRENDA 421
LEU UniChem BRENDA 424
LEU UniChem BRENDA 46202
LEU UniChem BRENDA 641
LEU UniChem BRENDA 95409
LEU UniChem Rhea 57427
LEU UniChem ChemicalBook CB64796923
LEU UniChem ChemicalBook CB8742186
LEU UniChem DailyMed LEUCINE
LEU UniChem ClinicalTrials L-LEUCINE
LEU UniChem ClinicalTrials LEUCINE
LEU UniChem rxnorm LEUCINE
LEU UniChem MedChemExpress HY-N0486
LEU UniChem 'Probes And Drugs' PD008452
LEU UniChem CCDC LEUCIN
LEU UniChem 'PubChem TPHARMA' 15218991
LEU UniChem PubChem 6106
LEU UniChem PubChem 7045798
LEU UniChem Mcule MCULE-4930237913
LEU UniChem ACTor 71000-80-1
LEU UniChem Nikkaji J1.167C
LEU UniChem BindingDb 50219348
LEU UniChem 'EPA CompTox Dashboard' DTXSID9023203
#
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
LEU N -2.062 -1.121 1.471 ETKDGv3 1
LEU CA -1.195 -0.147 0.806 ETKDGv3 2
LEU C -2.004 0.652 -0.179 ETKDGv3 3
LEU O -2.700 0.067 -1.053 ETKDGv3 4
LEU CB -0.031 -0.881 0.103 ETKDGv3 5
LEU CG 0.969 0.051 -0.627 ETKDGv3 6
LEU CD1 1.722 0.967 0.350 ETKDGv3 7
LEU CD2 1.972 -0.788 -1.430 ETKDGv3 8
LEU OXT -1.965 2.042 -0.139 ETKDGv3 9
LEU H -1.504 -1.611 2.208 ETKDGv3 10
LEU H2 -2.813 -0.600 1.981 ETKDGv3 11
LEU HA -0.786 0.540 1.578 ETKDGv3 12
LEU HB2 -0.462 -1.598 -0.631 ETKDGv3 13
LEU HB3 0.523 -1.483 0.857 ETKDGv3 14
LEU HG 0.419 0.689 -1.352 ETKDGv3 15
LEU HD11 2.211 0.372 1.150 ETKDGv3 16
LEU HD12 2.501 1.547 -0.190 ETKDGv3 17
LEU HD13 1.029 1.701 0.811 ETKDGv3 18
LEU HD21 2.564 -1.444 -0.754 ETKDGv3 19
LEU HD22 1.438 -1.423 -2.169 ETKDGv3 20
LEU HD23 2.668 -0.127 -1.988 ETKDGv3 21
LEU HXT -2.495 2.596 -0.802 ETKDGv3 22
#