Structure of PDB 4y56 Chain A Binding Site BS01

Receptor Information

>4y56 Chain A (length=330) Species: 5116 (Cryphonectria parasitica)

STGSATTTPIDSLDDAYITPVQIGTPAQTLNLDFDTGSSDLWVFSSETTA
SEVDGQTIYTPSKSTTAKLLSGATWSISYGDGSSSSGDVYTDTVSVGGLT
VTGQAVESAKKVSSSFTEDSTIDGLLGLAFSTLNTVSPTQQKTFFDNAKA
SLDSPVFTADLGYHAPGTYNFGFIDTTAYTGSITYTAVSTKQGFWEWTST
GYAVGSGTFKSTSIDGIADTGTTLLYLPATVVSAYWAQVSGAKSSSSVGG
YVFPCSATLPSFTFGVGSARIVIPGDYIDFGPISTGSSSCFGGIQSSAGI
GINIFGDVALKAAFVVFNGATTPTLGFASK

Ligand information

• Ligand ID: 47J
• InChI: InChI=1S/C6H11N3/c1-5-3-6(4-7)9(2)8-5/h3H,4,7H2,1-2H3
• InChIKey: DAOWQCXPMWGSBW-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 1.9.2: Cc1cc(n(n1)C)CN
  CACTVS 3.385: Cn1nc(C)cc1CN
  ACDLabs 12.01: n1c(cc(n1C)CN)C
• Formula: C6 H11 N3
• Name: 1-(1,3-dimethyl-1H-pyrazol-5-yl)methanamine
• ChEMBL: CHEMBL4568622
• ZINC: ZINC000004298933
• PDB chain: 4y56 Chain A Residue 406

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4y56 A small nonrule of 3 compatible fragment library provides high hit rate of endothiapepsin crystal structures with various fragment chemotypes.
• Resolution: 1.63 Å
• Binding residue (original residue number in PDB): D33 Y79 D81 G221
• Binding residue (residue number reindexed from 1): D33 Y79 D81 G221
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): D35 S38 D40 W42 Y79 D219 T222
• Catalytic site (residue number reindexed from 1): D35 S38 D40 W42 Y79 D219 T222
• Enzyme Commision number: 3.4.23.22: endothiapepsin.

Gene Ontology

Molecular Function

• GO:0004190 aspartic-type endopeptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:4y56, PDBe:4y56, PDBj:4y56
• PDBsum: 4y56
• UniProt: P11838|CARP_CRYPA Endothiapepsin (Gene Name=EAPA)