Structure of PDB 2yj9 Chain A Binding Site BS01

Receptor Information

>2yj9 Chain A (length=216) Species: 9606 (Homo sapiens)

APRSVDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSE
QNLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEESCKY
NPKYSVANDTGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGI
YFEPDCSSEDMDHGVLVVGYGFEDNNKYWLVKNSWGEEWGMGGYVKMAKD
RRNHCGIASAASYPTV

Ligand information

• Ligand ID: YJ9
• InChI: InChI=1S/C26H25ClF3N3O4S/c27-19-3-1-2-4-21(19)38(36,37)18-13-20(22(34)32-24(15-31)9-10-24)33(14-18)23(35)25(11-12-25)16-5-7-17(8-6-16)26(28,29)30/h1-8,15,18,20,31H,9-14H2,(H,32,34)/b31-15+/t18-,20+/m1/s1
• InChIKey: ACNGWBKPMPBISI-UTGIELOBSA-N
• SMILES:
  OpenEye OEToolkits 1.7.2: c1ccc(c(c1)S(=O)(=O)C2CC(N(C2)C(=O)C3(CC3)c4ccc(cc4)C(F)(F)F)C(=O)NC5(CC5)C=N)Cl
  CACTVS 3.370: FC(F)(F)c1ccc(cc1)C2(CC2)C(=O)N3C[C@@H](C[C@H]3C(=O)NC4(CC4)C=N)[S](=O)(=O)c5ccccc5Cl
  CACTVS 3.370: FC(F)(F)c1ccc(cc1)C2(CC2)C(=O)N3C[CH](C[CH]3C(=O)NC4(CC4)C=N)[S](=O)(=O)c5ccccc5Cl
  OpenEye OEToolkits 1.7.2: c1ccc(c(c1)S(=O)(=O)[C@@H]2C[C@H](N(C2)C(=O)C3(CC3)c4ccc(cc4)C(F)(F)F)C(=O)NC5(CC5)C=N)Cl
  ACDLabs 12.01: O=S(=O)(c1ccccc1Cl)C5CC(C(=O)NC2(C=[N@H])CC2)N(C(=O)C4(c3ccc(cc3)C(F)(F)F)CC4)C5
• Formula: C26 H25 Cl F3 N3 O4 S
• Name: (2S,4R)-4-(2-chlorophenyl)sulfonyl-N-[1-(iminomethyl)cyclopropyl]-1-[1-[4-(trifluoromethyl)phenyl]cyclopropyl]carbonyl-pyrrolidine-2-carboxamide
• PDB chain: 2yj9 Chain A Residue 1221

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2yj9 Halogen Bonding at the Active Sites of Human Cathepsin L and Mek1 Kinase: Efficient Interactions in Different Environments.
• Resolution: 1.35 Å
• Binding residue (original residue number in PDB): G23 C25 G61 E63 G67 G68 L69 M70 A135 M161 D162 H163 A214
• Binding residue (residue number reindexed from 1): G23 C25 G61 E63 G67 G68 L69 M70 A135 M161 D162 H163 A210
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=7.02,IC50=0.095uM

Enzymatic activity

• Catalytic site (original residue number in PDB): Q19 C25 H163 N187
• Catalytic site (residue number reindexed from 1): Q19 C25 H163 N183
• Enzyme Commision number: 3.4.22.15: cathepsin L.

Gene Ontology

Molecular Function

• GO:0008234 cysteine-type peptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:2yj9, PDBe:2yj9, PDBj:2yj9
• PDBsum: 2yj9
• PubMed: 21898833
• UniProt: P07711|CATL1_HUMAN Procathepsin L (Gene Name=CTSL)