Structure of PDB 5qbz Chain A Binding Site BS01

Receptor Information
>5qbz Chain A (length=217) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LPDSVDWREKGCVTEVKYQGSCGASWAFSAVGALEAQLKLKTGKLVSLSA
QNLVDCSTEKYGNKGCNGGFMTTAFQYIIDNKGIDSDASYPYKAMDQKCQ
YDSKYRAATCSKYTELPYGREDVLKEAVANKGPVSVGVDARHPSFFLYRS
GVYYEPSCTQNVNHGVLVVGYGDLNGKEYWLVKNSWGHNFGEEGYIRMAR
NKGNHCGIASFPSYPEI
Ligand information
Ligand IDB8Y
InChIInChI=1S/C34H33Cl2FN6O3/c1-40-29-10-6-25(35)20-30(29)43(34(40)46)27-11-16-41(17-12-27)14-2-15-42-18-13-38-31(33(42)45)23-5-9-28(36)24(19-23)21-39-32(44)22-3-7-26(37)8-4-22/h3-10,13,18-20,27H,2,11-12,14-17,21H2,1H3,(H,39,44)
InChIKeyMNEPYBOQUOAGHK-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01C1C(CCN(C1)CCCN2C(C(=NC=C2)c4ccc(Cl)c(CNC(=O)c3ccc(cc3)F)c4)=O)N6C(=O)N(C)c5c6cc(cc5)Cl
OpenEye OEToolkits 2.0.6CN1c2ccc(cc2N(C1=O)C3CCN(CC3)CCCN4C=CN=C(C4=O)c5ccc(c(c5)CNC(=O)c6ccc(cc6)F)Cl)Cl
CACTVS 3.385CN1C(=O)N(C2CCN(CCCN3C=CN=C(C3=O)c4ccc(Cl)c(CNC(=O)c5ccc(F)cc5)c4)CC2)c6cc(Cl)ccc16
FormulaC34 H33 Cl2 F N6 O3
NameN-{[2-chloro-5-(4-{3-[4-(6-chloro-3-methyl-2-oxo-2,3-dihydro-1H-benzimidazol-1-yl)piperidin-1-yl]propyl}-3-oxo-3,4-dihydropyrazin-2-yl)phenyl]methyl}-4-fluorobenzamide
ChEMBLCHEMBL1171505
DrugBank
ZINCZINC000058660620
PDB chain5qbz Chain A Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5qbz Crystal structure of human Cathepsin-S with bound ligand
Resolution2.8 Å
Binding residue
(original residue number in PDB)		G62 K64 N67 G68 G69 F70 V162 N163 G165 F211
Binding residue
(residue number reindexed from 1)		G62 K64 N67 G68 G69 F70 V162 N163 G165 F211
Annotation score1
Binding affinityBindingDB: IC50=8000nM
Enzymatic activity
Catalytic site (original residue number in PDB) Q19 S25 H164 N184
Catalytic site (residue number reindexed from 1) Q19 S25 H164 N184
Enzyme Commision number 3.4.22.27: cathepsin S.
Gene Ontology
Molecular Function
GO:0008234 cysteine-type peptidase activity
Biological Process
GO:0006508 proteolysis

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5qbz, PDBe:5qbz, PDBj:5qbz
PDBsum5qbz
PubMed
UniProtP25774|CATS_HUMAN Cathepsin S (Gene Name=CTSS)

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