Structure of PDB 3kwb Chain X Binding Site BS01

Receptor Information
>3kwb Chain X (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 IDORH
InChIInChI=1S/C19H20F3N5O2/c20-19(21,22)14-6-4-7-15(12-14)27-18(29)26(17(28)16(13-23)24-27)11-5-10-25-8-2-1-3-9-25/h4,6-7,12H,1-3,5,8-11H2
InChIKeyHKAVWQNLXOMWLR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.352FC(F)(F)c1cccc(c1)N2N=C(C#N)C(=O)N(CCCN3CCCCC3)C2=O
OpenEye OEToolkits 1.7.0c1cc(cc(c1)N2C(=O)N(C(=O)C(=N2)C#N)CCCN3CCCCC3)C(F)(F)F
FormulaC19 H20 F3 N5 O2
Name3,5-dioxo-4-(3-piperidin-1-ylpropyl)-2-[3-(trifluoromethyl)phenyl]-2,3,4,5-tetrahydro-1,2,4-triazine-6-carbonitrile
ChEMBLCHEMBL1084114
DrugBank
ZINCZINC000049046145
PDB chain3kwb Chain X Residue 1216 [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]
PDB3kwb Dioxo-triazines as a novel series of cathepsin K inhibitors
Resolution2.02 Å
Binding residue
(original residue number in PDB)		G1023 C1025 Y1067 A1134 A1137 S1138 L1160 N1161 L1209
Binding residue
(residue number reindexed from 1)		G23 C25 Y67 A134 A137 S138 L160 N161 L209
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.77,IC50=17nM
BindingDB: IC50=17nM
Enzymatic activity
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:3kwb, PDBe:3kwb, PDBj:3kwb
PDBsum3kwb
PubMed20153187
UniProtP43235|CATK_HUMAN Cathepsin K (Gene Name=CTSK)

[Back to BioLiP]