Structure of PDB 3pmy Chain A Binding Site BS01

Receptor Information
>3pmy Chain A (length=330) Species: 5116 (Cryphonectria parasitica) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
STGSATTTPIDSLDDAYITPVQIGTPAQTLNLDFDTGSSDLWVFSSETTA
SEVDGQTIYTPSKSTTAKLLSGATWSISYGDGSSSSGDVYTDTVSVGGLT
VTGQAVESAKKVSSSFTEDSTIDGLLGLAFSTLNTVSPTQQKTFFDNAKA
SLDSPVFTADLGYHAPGTYNFGFIDTTAYTGSITYTAVSTKQGFWEWTST
GYAVGSGTFKSTSIDGIADTGTTLLYLPATVVSAYWAQVSGAKSSSSVGG
YVFPCSATLPSFTFGVGSARIVIPGDYIDFGPISTGSSSCFGGIQSSAGI
GINIFGDVALKAAFVVFNGATTPTLGFASK
Ligand information
Ligand ID41L
InChIInChI=1S/C15H13N3O/c19-15(10-12-6-2-1-3-7-12)17-18-11-16-13-8-4-5-9-14(13)18/h1-9,11H,10H2,(H,17,19)
InChIKeyLGOMVYVBROQGHX-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1ccc(cc1)CC(=O)Nn2cnc3c2cccc3
ACDLabs 12.01O=C(Nn1c2ccccc2nc1)Cc3ccccc3
CACTVS 3.370O=C(Cc1ccccc1)Nn2cnc3ccccc23
FormulaC15 H13 N3 O
NameN-(1H-benzimidazol-1-yl)-2-phenylacetamide
ChEMBLCHEMBL1560712
DrugBank
ZINCZINC000003187033
PDB chain3pmy Chain A Residue 2001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3pmy A small nonrule of 3 compatible fragment library provides high hit rate of endothiapepsin crystal structures with various fragment chemotypes.
Resolution1.38 Å
Binding residue
(original residue number in PDB)		D35 Y79 G80 D81 G221 T222 Y226
Binding residue
(residue number reindexed from 1)		D35 Y79 G80 D81 G221 T222 Y226
Annotation score1
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

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Molecular Function
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Biological Process
External links
PDB RCSB:3pmy, PDBe:3pmy, PDBj:3pmy
PDBsum3pmy
PubMed21972967
UniProtP11838|CARP_CRYPA Endothiapepsin (Gene Name=EAPA)

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