Structure of PDB 5qbv Chain B Binding Site BS01

Receptor Information
>5qbv Chain B (length=219) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ILPDSVDWREKGCVTEVKYQGSCGASWAFSAVGALEAQLKLKTGKLVSLS
AQNLVDCSTEKYGNKGCNGGFMTTAFQYIIDNKGIDSDASYPYKAMDQKC
QYDSKYRAATCSKYTELPYGREDVLKEAVANKGPVSVGVDARHPSFFLYR
SGVYYEPSCTQNVNHGVLVVGYGDLNGKEYWLVKNSWGHNFGEEGYIRMA
RNKGNHCGIASFPSYPEIL
Ligand information
Ligand IDN2D
InChIInChI=1S/C34H34Cl2N6O3/c1-39-30-12-9-26(35)21-31(30)42(34(39)45)27-14-18-40(19-15-27)16-5-17-41-32(43)13-11-29(38-41)24-8-10-28(36)25(20-24)22-37-33(44)23-6-3-2-4-7-23/h2-4,6-13,20-21,27H,5,14-19,22H2,1H3,(H,37,44)
InChIKeyZJXORVFCSQEKCZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CN1c2ccc(cc2N(C1=O)C3CCN(CC3)CCCN4C(=O)C=CC(=N4)c5ccc(c(c5)CNC(=O)c6ccccc6)Cl)Cl
CACTVS 3.370CN1C(=O)N(C2CCN(CCCN3N=C(C=CC3=O)c4ccc(Cl)c(CNC(=O)c5ccccc5)c4)CC2)c6cc(Cl)ccc16
ACDLabs 12.01Clc1ccc2c(c1)N(C(=O)N2C)C6CCN(CCCN3N=C(C=CC3=O)c4ccc(Cl)c(c4)CNC(=O)c5ccccc5)CC6
FormulaC34 H34 Cl2 N6 O3
NameN-[2-chloro-5-(1-{3-[4-(6-chloro-3-methyl-2-oxo-2,3-dihydro-1H-benzimidazol-1-yl)piperidin-1-yl]propyl}-6-oxo-1,6-dihydropyridazin-3-yl)benzyl]benzamide
ChEMBLCHEMBL1171314
DrugBank
ZINCZINC000058547796
PDB chain5qbv Chain B 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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PDB5qbv Diazinones as P2 replacements for pyrazole-based cathepsin S inhibitors
Resolution1.796 Å
Binding residue
(original residue number in PDB)		G62 G68 G69 F70 T73 V162 G165 F211
Binding residue
(residue number reindexed from 1)		G63 G69 G70 F71 T74 V163 G166 F212
Annotation score1
Binding affinityBindingDB: IC50=430nM
Enzymatic activity
Catalytic site (original residue number in PDB) Q19 S25 H164 N184
Catalytic site (residue number reindexed from 1) Q20 S26 H165 N185
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
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Biological Process
External links
PDB RCSB:5qbv, PDBe:5qbv, PDBj:5qbv
PDBsum5qbv
PubMed20541404
UniProtP25774|CATS_HUMAN Cathepsin S (Gene Name=CTSS)

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