Structure of PDB 5dnd Chain A Binding Site BS01

Receptor Information

>5dnd Chain A (length=353) Species: 10141 (Cavia porcellus)

ERHLLLIYTGGTLGMQSKGGVLVPGPGLVTLLRTLPMFHDKEFAQAQGLP
DHALALPPASHGPRVLYTVLECQPLLDSSDMTIDDWIRIAKIIERHYEQY
QGFVVIHGADTMASGASMLSFMLENLHKPVILTGAQVPIRVLWNDARENL
LGALLVAGQYIIPEVCLFMNSQLFRGNRVTKVDSQKFEAFCSPLSPLATV
GADVTIAWDLVRKVKWKDPLVVHSNMEHDVALLRLYPGIPASLVRAFLQP
PLKGVVLETFGSGNGPSKPDLLQELRAAAQRGLIMVNCSQCLRGSVTPGY
ATSLAGANIVSGLDMTSEAALAKLSYVLGLPELSLERRQELLAKDLRGEM
TLP

Ligand information

• Ligand ID: ASN
• InChI: InChI=1S/C4H8N2O3/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H2,6,7)(H,8,9)/t2-/m0/s1
• InChIKey: DCXYFEDJOCDNAF-REOHCLBHSA-N
• SMILES:
  CACTVS 3.370: N[C@@H](CC(N)=O)C(O)=O
  ACDLabs 12.01: O=C(N)CC(N)C(=O)O
  CACTVS 3.370: N[CH](CC(N)=O)C(O)=O
  OpenEye OEToolkits 1.7.2: C(C(C(=O)O)N)C(=O)N
  OpenEye OEToolkits 1.7.2: C([C@@H](C(=O)O)N)C(=O)N
• Formula: C4 H8 N2 O3
• Name: ASPARAGINE
• ChEMBL: CHEMBL58832
• DrugBank: DB00174
• ZINC: ZINC000001532556
• PDB chain: 5dnd Chain A Residue 700

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5dnd Experimental Data in Support of a Direct Displacement Mechanism for Type I/II l-Asparaginases.
• Resolution: 2.29 Å
• Binding residue (original residue number in PDB): T19 D84 S85 G115 A116 D117 A142
• Binding residue (residue number reindexed from 1): T12 D77 S78 G108 A109 D110 A135
• Annotation score: 5

Enzymatic activity

• Catalytic site (original residue number in PDB): T19 V28 A116 D117 K188
• Catalytic site (residue number reindexed from 1): T12 V21 A109 D110 K181
• Enzyme Commision number: 3.5.1.1: asparaginase.

Gene Ontology

Molecular Function

• GO:0004067 asparaginase activity

Biological Process

• GO:0009066 aspartate family amino acid metabolic process

External links

• PDB: RCSB:5dnd, PDBe:5dnd, PDBj:5dnd
• PDBsum: 5dnd
• PubMed: 26733195
• UniProt: H0W0T5