Structure of PDB 4y3y Chain A Binding Site BS01

Receptor Information

>4y3y Chain A (length=330) Species: 5116 (Cryphonectria parasitica)

STGSATTTPIDSLDDAYITPVQIGTPAQTLNLDFDTGSSDLWVFSSETTA
SEVDGQTIYTPSKSTTAKLLSGATWSISYGDGSSSSGDVYTDTVSVGGLT
VTGQAVESAKKVSSSFTEDSTIDGLLGLAFSTLNTVSPTQQKTFFDNAKA
SLDSPVFTADLGYHAPGTYNFGFIDTTAYTGSITYTAVSTKQGFWEWTST
GYAVGSGTFKSTSIDGIADTGTTLLYLPATVVSAYWAQVSGAKSSSSVGG
YVFPCSATLPSFTFGVGSARIVIPGDYIDFGPISTGSSSCFGGIQSSAGI
GINIFGDVALKAAFVVFNGATTPTLGFASK

Ligand information

• Ligand ID: DCL
• InChI: InChI=1S/C6H15NO/c1-5(2)3-6(7)4-8/h5-6,8H,3-4,7H2,1-2H3/t6-/m0/s1
• InChIKey: VPSSPAXIFBTOHY-LURJTMIESA-N
• SMILES:
  CACTVS 3.370: CC(C)C[CH](N)CO
  CACTVS 3.370: CC(C)C[C@H](N)CO
  OpenEye OEToolkits 1.7.2: CC(C)C[C@@H](CO)N
  OpenEye OEToolkits 1.7.2: CC(C)CC(CO)N
  ACDLabs 12.01: OCC(N)CC(C)C
• Formula: C6 H15 N O
• Name: 2-AMINO-4-METHYL-PENTAN-1-OL;
  LEUCINOL
• ChEMBL: CHEMBL1232141
• ZINC: ZINC000000391149
• PDB chain: 4y3y Chain A Residue 412

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4y3y Structures of endothiapepsin-fragment complexes from crystallographic fragment screening using a novel, diverse and affordable 96-compound fragment library.
• Resolution: 1.346 Å
• Binding residue (original residue number in PDB): D35 G37 Y79 G80 F194 D219
• Binding residue (residue number reindexed from 1): D35 G37 Y79 G80 F194 D219
• Annotation score: 1
• Binding affinity: MOAD: Kd=4.5mM
  PDBbind-CN: -logKd/Ki=2.35,Kd=4.5mM

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:4y3y, PDBe:4y3y, PDBj:4y3y
• PDBsum: 4y3y
• PubMed: 27139825
• UniProt: P11838|CARP_CRYPA Endothiapepsin (Gene Name=EAPA)