Structure of PDB 8jdz Chain A Binding Site BS03

Receptor Information
>8jdz Chain A (length=454) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LSQDFVEALKAVVGSPHVSTASAVREQHGHDESMHRCQPPDAVVWPQNVD
QVSRVASLCYNQGVPIIPFGTGTGVEGGVCAVQGGVCINLTHMDQITELN
TEDFSVVVEPGVTRKALNTHLRDSGLWFPVDPGADASLCGMAATGASGTN
AVRYGTMRDNVINLEVVLPDGRLLHTAGRGRHYRKSAAGYNLTGLFVGSE
GTLGIITSTTLRLHPAPEATVAATCAFPSVQAAVDSTVQILQAAVPVARI
EFLDDVMMDACNRHSLNCPVAPTLFLEFHGSQQTLAEQLQRTEAITQDNG
GSHFSWAAEKRNELWAARHNAWYAALALSPGSKAYSTDVCVPISRLPEIL
VETKEEIKASKLTGAIVGHVGDGNFHCILLVDPDAEEQRRVKAFAENLGR
RALALGGTCTGEHGIGLGKRQLLQEEVGPVGVETMRQLKNTLDPRGLMNP
GKVL
Ligand information
Ligand ID1QQ
InChIInChI=1S/C6H10O3/c1-3-4(2)5(7)6(8)9/h4H,3H2,1-2H3,(H,8,9)/t4-/m0/s1
InChIKeyJVQYSWDUAOAHFM-BYPYZUCNSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CC[C@H](C)C(=O)C(O)=O
OpenEye OEToolkits 1.7.0CCC(C)C(=O)C(=O)O
CACTVS 3.370CC[CH](C)C(=O)C(O)=O
OpenEye OEToolkits 1.7.0CC[C@H](C)C(=O)C(=O)O
ACDLabs 12.01O=C(C(=O)O)C(C)CC
FormulaC6 H10 O3
Name(3S)-3-methyl-2-oxopentanoic acid
ChEMBL
DrugBankDB15833
ZINCZINC000001532715
PDB chain8jdz Chain A Residue 503 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8jdz Lactate dehydrogenase D is a general dehydrogenase for D-2-hydroxyacids containing hydrophobic moieties and plays an important role in the pathogenesis of D-lactic acidosis
Resolution1.56 Å
Binding residue
(original residue number in PDB)		R347 W351 H398 H405 H443
Binding residue
(residue number reindexed from 1)		R318 W322 H369 H376 H413
Annotation score1
Enzymatic activity
Enzyme Commision number 1.1.2.4: D-lactate dehydrogenase (cytochrome).
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004458 D-lactate dehydrogenase (cytochrome) activity
GO:0005515 protein binding
GO:0008720 D-lactate dehydrogenase activity
GO:0016491 oxidoreductase activity
GO:0050660 flavin adenine dinucleotide binding
GO:0071949 FAD binding
Biological Process
GO:0006754 ATP biosynthetic process
GO:1903457 lactate catabolic process
Cellular Component
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8jdz, PDBe:8jdz, PDBj:8jdz
PDBsum8jdz
PubMed37863926
UniProtQ7TNG8|LDHD_MOUSE Probable D-lactate dehydrogenase, mitochondrial (Gene Name=Ldhd)

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