Structure of PDB 5qby Chain B Binding Site BS01

Receptor Information
>5qby 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 IDN2A
InChIInChI=1S/C34H33Cl2FN6O3/c1-40-30-10-6-25(35)18-31(30)43(34(40)46)27-11-15-41(16-12-27)13-2-14-42-21-38-20-28(33(42)45)23-5-9-29(36)24(17-23)19-39-32(44)22-3-7-26(37)8-4-22/h3-10,17-18,20-21,27H,2,11-16,19H2,1H3,(H,39,44)
InChIKeyUUSUCXDJVSXCBL-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01Fc1ccc(cc1)C(=O)NCc2c(Cl)ccc(c2)C3=CN=CN(C3=O)CCCN6CCC(N5c4cc(Cl)ccc4N(C5=O)C)CC6
OpenEye OEToolkits 1.7.0CN1c2ccc(cc2N(C1=O)C3CCN(CC3)CCCN4C=NC=C(C4=O)c5ccc(c(c5)CNC(=O)c6ccc(cc6)F)Cl)Cl
CACTVS 3.370CN1C(=O)N(C2CCN(CCCN3C=NC=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-(1-{3-[4-(6-chloro-3-methyl-2-oxo-2,3-dihydro-1H-benzimidazol-1-yl)piperidin-1-yl]propyl}-6-oxo-1,6-dihydropyrimidin-5-yl)benzyl]-4-fluorobenzamide
ChEMBLCHEMBL1171504
DrugBank
ZINCZINC000058548709
PDB chain5qby 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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PDB5qby Diazinones as P2 replacements for pyrazole-based cathepsin S inhibitors
Resolution2.25 Å
Binding residue
(original residue number in PDB)		G62 K64 G68 G69 F70 M71 T73 E115 V162 G165 F211
Binding residue
(residue number reindexed from 1)		G63 K65 G69 G70 F71 M72 T74 E116 V163 G166 F212
Annotation score1
Binding affinityBindingDB: IC50=40nM
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
View graph for
Biological Process
External links
PDB RCSB:5qby, PDBe:5qby, PDBj:5qby
PDBsum5qby
PubMed20541404
UniProtP25774|CATS_HUMAN Cathepsin S (Gene Name=CTSS)

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