Structure of PDB 6lpp Chain A Binding Site BS03

Receptor Information
>6lpp 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 ID2HG
InChIInChI=1S/C5H8O5/c6-3(5(9)10)1-2-4(7)8/h3,6H,1-2H2,(H,7,8)(H,9,10)/t3-/m1/s1
InChIKeyHWXBTNAVRSUOJR-GSVOUGTGSA-N
SMILES
SoftwareSMILES
CACTVS 3.370O[CH](CCC(O)=O)C(O)=O
ACDLabs 12.01O=C(O)CCC(O)C(=O)O
OpenEye OEToolkits 1.7.0C(CC(=O)O)C(C(=O)O)O
OpenEye OEToolkits 1.7.0C(CC(=O)O)[C@H](C(=O)O)O
CACTVS 3.370O[C@H](CCC(O)=O)C(O)=O
FormulaC5 H8 O5
Name(2R)-2-hydroxypentanedioic acid
ChEMBLCHEMBL1614745
DrugBank
ZINCZINC000000402968
PDB chain6lpp Chain A Residue 603 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6lpp Structure, substrate specificity, and catalytic mechanism of human D-2-HGDH and insights into pathogenicity of disease-associated mutations.
Resolution2.65 Å
Binding residue
(original residue number in PDB)		R386 T390 K401 Y432 H434 H441 N443 H476
Binding residue
(residue number reindexed from 1)		R333 T337 K348 Y379 H381 H388 N390 H423
Annotation score5
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:6lpp, PDBe:6lpp, PDBj:6lpp
PDBsum6lpp
PubMed33431826
UniProtQ8N465|D2HDH_HUMAN D-2-hydroxyglutarate dehydrogenase, mitochondrial (Gene Name=D2HGDH)

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