Structure of PDB 3kwz Chain A Binding Site BS01

Receptor Information
>3kwz Chain A (length=215) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSP
QNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNP
TGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVY
YDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNK
NNACGIANLASFPKM
Ligand information
Ligand IDKWZ
InChIInChI=1S/C20H21F3N4/c21-20(22,23)16-7-4-6-15(12-16)18-13-17(25-19(14-24)26-18)8-5-11-27-9-2-1-3-10-27/h4,6-7,12-13H,1-3,5,8-11H2
InChIKeyXGXDWBUGQKHTSH-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.352FC(F)(F)c1cccc(c1)c2cc(CCCN3CCCCC3)nc(n2)C#N
OpenEye OEToolkits 1.7.0c1cc(cc(c1)C(F)(F)F)c2cc(nc(n2)C#N)CCCN3CCCCC3
FormulaC20 H21 F3 N4
Name4-(3-piperidin-1-ylpropyl)-6-[3-(trifluoromethyl)phenyl]pyrimidine-2-carbonitrile
ChEMBLCHEMBL1084400
DrugBank
ZINCZINC000049047453
PDB chain3kwz Chain A Residue 222 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3kwz Design and optimization of a series of novel 2-cyano-pyrimidines as cathepsin K inhibitors
Resolution1.49 Å
Binding residue
(original residue number in PDB)		G23 C25 G64 G65 A134 L160 N161 H162 A163
Binding residue
(residue number reindexed from 1)		G23 C25 G64 G65 A134 L160 N161 H162 A163
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.40,IC50=4nM
BindingDB: IC50=4nM
Enzymatic activity
Catalytic site (original residue number in PDB) Q19 C25 H162 N182
Catalytic site (residue number reindexed from 1) Q19 C25 H162 N182
Enzyme Commision number 3.4.22.38: cathepsin K.
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:3kwz, PDBe:3kwz, PDBj:3kwz
PDBsum3kwz
PubMed20149657
UniProtP43235|CATK_HUMAN Cathepsin K (Gene Name=CTSK)

[Back to BioLiP]