Structure of PDB 2nyr Chain A Binding Site BS01

Receptor Information

>2nyr Chain A (length=259) Species: 9606 (Homo sapiens)

PSSSMADFRKFFAKAKHIVIISGAGVSAESGVPTFRGAGGYWRKWQAQDL
ATPLAFAHNPSRVWEFYHYRREVMGSKEPNAGHRAIAECETRLGKQGRRV
VVITQNIDELHRKAGTKNLLEIHGSLFKTRCTSCGVVAENYKSPICPALS
GKGAPEPGTQDASIPVEKLPRCEEAGCGGLLRPHVVWFGENLDPAILEEV
DRELAHCDLCLVVGTSSVVYPAAMFAPQVAARGVPVAEFNTERFHFQGPC
GTTLPEALA

Ligand information

• Ligand ID: ZN
• InChI: InChI=1S/Zn/q+2
• InChIKey: PTFCDOFLOPIGGS-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Zn++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Zn+2]
• Formula: Zn
• Name: ZINC ION
• ChEMBL: CHEMBL1236970
• DrugBank: DB14532
• PDB chain: 2nyr Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2nyr Structural basis of inhibition of the human NAD+-dependent deacetylase SIRT5 by suramin.
• Resolution: 2.06 Å
• Binding residue (original residue number in PDB): C166 C169 C207 C212
• Binding residue (residue number reindexed from 1): C131 C134 C172 C177
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): P68 T69 F70 R71 N141 D143 H158
• Catalytic site (residue number reindexed from 1): P33 T34 F35 R36 N106 D108 H123
• Enzyme Commision number: 2.3.1.-

Gene Ontology

Molecular Function

• GO:0036054 protein-malonyllysine demalonylase activity
• GO:0036055 protein-succinyllysine desuccinylase activity
• GO:0070403 NAD+ binding

External links

• PDB: RCSB:2nyr, PDBe:2nyr, PDBj:2nyr
• PDBsum: 2nyr
• PubMed: 17355872
• UniProt: Q9NXA8|SIR5_HUMAN NAD-dependent protein deacylase sirtuin-5, mitochondrial (Gene Name=SIRT5)