Structure of PDB 6lpt Chain A Binding Site BS02

Receptor Information
>6lpt Chain A (length=466) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VRRLPFSTVSKQDLAAFERIVPGGVVTDPEALQAPNVDWLRTLRGCSKVL
LRPRTSEEVSHILRHCHERNLAVNPQGGNTGMVGGSVPVFDEIILSTARM
NRVLSFHSVSGILVCQAGCVLEELSRYVEERDFIMPLDLGAKGSCHIGGN
VATNAGGLRFLRYGSLHGTVLGLEVVLADGTVLDCLTSLRKDNTGYDLKQ
LFIGSEGTLGIITTVSILCPPKPRAVNVAFLGCPGFAEVLQTFSTCKGML
GEILSAFEFMDAVCMQLVGRHLHLASPVQESPFYVLIETSGSNAGHDAEK
LGHFLEHALGSGLVTDGTMATDQRKVKMLWALRERITEALSRDGYVYKYD
LSLPVERLYDIVTDLRARLGPHAKHVVGYGHLGDGNLHLNVTAEAFSPSL
LAALEPHVYEWTAGQQGSVSAEHGVGFRKRDVLGYSKPPGALQLMQQLKA
LLDPKGILNPYKTLPS
Ligand information
Ligand IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain6lpt Chain A Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6lpt Structure, substrate specificity, and catalytic mechanism of human D-2-HGDH and insights into pathogenicity of disease-associated mutations.
Resolution2.621 Å
Binding residue
(original residue number in PDB)		H434 H441 E475
Binding residue
(residue number reindexed from 1)		H381 H388 E422
Annotation score1
Enzymatic activity
Enzyme Commision number 1.1.99.39: D-2-hydroxyglutarate dehydrogenase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0008270 zinc ion binding
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0050660 flavin adenine dinucleotide binding
GO:0051990 (R)-2-hydroxyglutarate dehydrogenase activity
GO:0071949 FAD binding
Biological Process
GO:0006103 2-oxoglutarate metabolic process
GO:0006108 malate metabolic process
GO:0010042 response to manganese ion
GO:0010043 response to zinc ion
GO:0019538 protein metabolic process
GO:0032025 response to cobalt ion
GO:0032026 response to magnesium ion
GO:0051592 response to calcium ion
Cellular Component
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6lpt, PDBe:6lpt, PDBj:6lpt
PDBsum6lpt
PubMed33431826
UniProtQ8N465|D2HDH_HUMAN D-2-hydroxyglutarate dehydrogenase, mitochondrial (Gene Name=D2HGDH)

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