data_VAL
#
_chem_comp.id VAL
_chem_comp.name VALINE
_chem_comp.type "L-PEPTIDE LINKING"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C5 H11 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 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 117.146
_chem_comp.one_letter_code V
_chem_comp.three_letter_code VAL
_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 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
VAL N N N 0 1 N N N Y Y N 11.009 2.661 48.464 1.564 -0.642 0.454 N VAL 1
VAL CA CA C 0 1 N N S Y N N 10.415 3.985 48.550 0.145 -0.698 0.079 CA VAL 2
VAL C C C 0 1 N N N Y N Y 10.002 4.429 49.975 -0.037 -0.093 -1.288 C VAL 3
VAL O O O 0 1 N N N Y N Y 9.312 3.707 50.680 0.703 0.784 -1.664 O VAL 4
VAL CB CB C 0 1 N N N N N N 9.230 4.107 47.566 -0.682 0.086 1.098 CB VAL 5
VAL CG1 CG1 C 0 1 N N N N N N 8.585 5.457 47.708 -0.497 -0.528 2.487 CG1 VAL 6
VAL CG2 CG2 C 0 1 N N N N N N 9.689 3.877 46.132 -0.218 1.543 1.119 CG2 VAL 7
VAL OXT OXT O 0 1 N Y N Y N Y 10.377 5.639 50.362 -1.022 -0.529 -2.089 OXT VAL 8
VAL H H H 0 1 N N N Y Y N 11.281 2.368 47.525 1.825 0.332 0.455 H VAL 9
VAL H2 HN2 H 0 1 N Y N Y Y N 10.386 1.968 48.881 1.624 -0.959 1.410 H2 VAL 10
VAL HA HA H 0 1 N N N Y N N 11.226 4.692 48.259 -0.186 -1.736 0.064 HA VAL 11
VAL HB HB H 0 1 N N N N N N 8.478 3.321 47.813 -1.736 0.044 0.820 HB VAL 12
VAL HG11 1HG1 H 0 0 N N N N N N 7.729 5.545 46.997 -1.087 0.031 3.214 HG11 VAL 13
VAL HG12 2HG1 H 0 0 N N N N N N 8.279 5.666 48.759 -0.828 -1.566 2.472 HG12 VAL 14
VAL HG13 3HG1 H 0 0 N N N N N N 9.319 6.287 47.584 0.555 -0.486 2.765 HG13 VAL 15
VAL HG21 1HG2 H 0 0 N N N N N N 8.833 3.965 45.421 0.835 1.585 1.397 HG21 VAL 16
VAL HG22 2HG2 H 0 0 N N N N N N 10.527 4.557 45.853 -0.350 1.981 0.130 HG22 VAL 17
VAL HG23 3HG2 H 0 0 N N N N N N 10.218 2.902 46.020 -0.808 2.103 1.845 HG23 VAL 18
VAL HXT HXT H 0 1 N Y N Y N Y 10.123 5.911 51.236 -1.139 -0.140 -2.967 HXT VAL 19
#
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
VAL N CA SING N N 1
VAL N H SING N N 2
VAL N H2 SING N N 3
VAL CA C SING N N 4
VAL CA CB SING N N 5
VAL CA HA SING N N 6
VAL C O DOUB N N 7
VAL C OXT SING N N 8
VAL CB CG1 SING N N 9
VAL CB CG2 SING N N 10
VAL CB HB SING N N 11
VAL CG1 HG11 SING N N 12
VAL CG1 HG12 SING N N 13
VAL CG1 HG13 SING N N 14
VAL CG2 HG21 SING N N 15
VAL CG2 HG22 SING N N 16
VAL CG2 HG23 SING N N 17
VAL OXT HXT SING N N 18
#
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
VAL SMILES ACDLabs 10.04 O=C(O)C(N)C(C)C
VAL SMILES_CANONICAL CACTVS 3.341 CC(C)[C@H](N)C(O)=O
VAL SMILES CACTVS 3.341 CC(C)[CH](N)C(O)=O
VAL SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC(C)[C@@H](C(=O)O)N
VAL SMILES "OpenEye OEToolkits" 1.5.0 CC(C)C(C(=O)O)N
VAL InChI InChI 1.03 InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1
VAL InChIKey InChI 1.03 KZSNJWFQEVHDMF-BYPYZUCNSA-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
VAL "SYSTEMATIC NAME" ACDLabs 10.04 L-valine
VAL "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S)-2-amino-3-methyl-butanoic 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
VAL 'Create component' 1999-07-08 RCSB
VAL 'Modify descriptor' 2011-06-04 RCSB
VAL 'Modify backbone' 2023-11-03 PDBE
#
_pdbe_chem_comp_drugbank_details.comp_id VAL
_pdbe_chem_comp_drugbank_details.drugbank_id DB00161
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Valine
_pdbe_chem_comp_drugbank_details.description
'Valine is a branched-chain essential amino acid that has stimulant activity. It promotes muscle growth and tissue repair. It is a precursor in the penicillin biosynthetic pathway.'
_pdbe_chem_comp_drugbank_details.cas_number 72-18-4
_pdbe_chem_comp_drugbank_details.mechanism_of_action
'(Applies to Valine, Leucine and Isoleucine) 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
VAL '(2S)-2-Amino-3-methylbutanoic acid' DrugBank ?
VAL (S)-Valine DrugBank ?
VAL '2-Amino-3-methylbutyric acid' DrugBank ?
VAL 'L-(+)-alpha-Aminoisovaleric acid' DrugBank ?
VAL 'L-alpha-Amino-beta-methylbutyric acid' DrugBank ?
VAL L-valin DrugBank ?
VAL L-valine DrugBank ?
VAL Val DrugBank ?
VAL Valine DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id VAL
_pdbe_chem_comp_drugbank_classification.drugbank_id DB00161
_pdbe_chem_comp_drugbank_classification.parent 'Valine 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 valine and derivatives. These are compounds containing valine or a derivative thereof resulting from reaction of valine 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
VAL DB00161 'Propionyl-CoA carboxylase beta chain, mitochondrial' Humans P05166 unknown 1
VAL DB00161 'Branched-chain-amino-acid aminotransferase, cytosolic' Humans P54687 unknown 2
VAL DB00161 'Valine--tRNA ligase' Humans P26640 unknown 3
#
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
VAL N N 3.805 0.750 1
VAL CA C 5.104 0.000 2
VAL C C 5.104 -1.500 3
VAL O O 6.404 -2.250 4
VAL CB C 6.404 0.750 5
VAL CG1 C 7.702 0.000 6
VAL CG2 C 6.404 2.250 7
VAL OXT O 3.805 -2.250 8
#
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
VAL CA N SINGLE BEGINWEDGE 1
VAL CA C SINGLE NONE 2
VAL CA CB SINGLE NONE 3
VAL C O DOUBLE NONE 4
VAL C OXT SINGLE NONE 5
VAL CB CG1 SINGLE NONE 6
VAL CB CG2 SINGLE NONE 7
#
_pdbe_chem_comp_substructure.comp_id VAL
_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
VAL O F1 1
VAL C F1 1
VAL CA F1 1
VAL N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id VAL
_pdbe_chem_comp_rdkit_properties.exactmw 117.079
_pdbe_chem_comp_rdkit_properties.amw 117.148
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 8
_pdbe_chem_comp_rdkit_properties.NumAtoms 19
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.800
_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 64.152
_pdbe_chem_comp_rdkit_properties.tpsa 63.320
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.054
_pdbe_chem_comp_rdkit_properties.CrippenMR 30.449
_pdbe_chem_comp_rdkit_properties.chi0v 3.764
_pdbe_chem_comp_rdkit_properties.chi1v 1.632
_pdbe_chem_comp_rdkit_properties.chi2v 0.430
_pdbe_chem_comp_rdkit_properties.chi3v 0.430
_pdbe_chem_comp_rdkit_properties.chi4v 0.102
_pdbe_chem_comp_rdkit_properties.chi0n 14.764
_pdbe_chem_comp_rdkit_properties.chi1n 6.935
_pdbe_chem_comp_rdkit_properties.chi2n 0.430
_pdbe_chem_comp_rdkit_properties.chi3n 0.430
_pdbe_chem_comp_rdkit_properties.chi4n 0.102
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.570
_pdbe_chem_comp_rdkit_properties.kappa1 1.011
_pdbe_chem_comp_rdkit_properties.kappa2 2.668
_pdbe_chem_comp_rdkit_properties.kappa3 1.930
_pdbe_chem_comp_rdkit_properties.Phi 0.337
#
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
VAL UniChem ChEMBL CHEMBL43068
VAL UniChem DrugBank DB00161
VAL UniChem 'Guide to Pharmacology' 4794
VAL UniChem 'KEGG LIGAND' C00183
VAL UniChem ChEBI 16414
VAL UniChem ChEBI 57762
VAL UniChem ZINC ZINC000000895099
VAL UniChem fdasrs HG18B9YRS7
VAL UniChem PharmGKB PA451843
VAL UniChem HMDB HMDB0000883
VAL UniChem 'PubChem TPHARMA' 15119814
VAL UniChem Recon 'val_L'
VAL UniChem DrugCentral 4128
VAL UniChem MetaboLights MTBLC16414
VAL UniChem MetaboLights MTBLC57762
VAL UniChem BRENDA 1079
VAL UniChem BRENDA 1210
VAL UniChem BRENDA 171028
VAL UniChem BRENDA 229599
VAL UniChem BRENDA 246
VAL UniChem BRENDA 260102
VAL UniChem BRENDA 835
VAL UniChem Rhea 57762
VAL UniChem ChemicalBook CB3381690
VAL UniChem ChemicalBook CB4875617
VAL UniChem DailyMed VALINE
VAL UniChem ClinicalTrials L-VALINE
VAL UniChem ClinicalTrials VALINE
VAL UniChem rxnorm VALINE
VAL UniChem MedChemExpress HY-N0717
VAL UniChem 'Probes And Drugs' PD010194
VAL UniChem CCDC LVALIN
VAL UniChem eMolecules 514495
VAL UniChem SureChEMBL SCHEMBL8516
VAL UniChem 'PubChem TPHARMA' 15218854
VAL UniChem PubChem 6287
VAL UniChem PubChem 6971018
VAL UniChem PubChem 88733505
VAL UniChem Mcule MCULE-2507309072
VAL UniChem Mcule MCULE-9143825935
VAL UniChem NMRShiftDB 20026335
VAL UniChem ACTor 16872-32-5
VAL UniChem Nikkaji J9.179K
VAL UniChem BindingDb 50463208
VAL UniChem 'EPA CompTox Dashboard' DTXSID40883233
VAL UniChem BRENDA 171029
#
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
VAL N 1.136 -1.607 -0.917 ETKDGv3 1
VAL CA 0.701 -0.232 -0.649 ETKDGv3 2
VAL C 1.487 0.386 0.484 ETKDGv3 3
VAL O 1.754 -0.278 1.522 ETKDGv3 4
VAL CB -0.836 -0.170 -0.430 ETKDGv3 5
VAL CG1 -1.306 -0.887 0.847 ETKDGv3 6
VAL CG2 -1.344 1.280 -0.438 ETKDGv3 7
VAL OXT 1.895 1.714 0.393 ETKDGv3 8
VAL H 1.108 -2.175 -0.040 ETKDGv3 9
VAL H2 2.133 -1.584 -1.232 ETKDGv3 10
VAL HA 0.924 0.361 -1.565 ETKDGv3 11
VAL HB -1.316 -0.684 -1.293 ETKDGv3 12
VAL HG11 -1.008 -1.955 0.835 ETKDGv3 13
VAL HG12 -0.891 -0.401 1.755 ETKDGv3 14
VAL HG13 -2.415 -0.853 0.913 ETKDGv3 15
VAL HG21 -2.454 1.297 -0.389 ETKDGv3 16
VAL HG22 -0.944 1.844 0.432 ETKDGv3 17
VAL HG23 -1.035 1.793 -1.373 ETKDGv3 18
VAL HXT 2.411 2.152 1.146 ETKDGv3 19
#