Structure of PDB 4dmx Chain A Binding Site BS01

Receptor Information
>4dmx 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 ID0LB
InChIInChI=1S/C22H27FN4O2/c23-16-5-7-17(8-6-16)26-11-13-27(14-12-26)21(29)19-4-2-1-3-18(19)20(28)25-22(15-24)9-10-22/h5-8,18-19H,1-4,9-14H2,(H,25,28)/t18-,19-/m1/s1
InChIKeyGHDIYQHGVKVLJX-RTBURBONSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1cc(ccc1N2CCN(CC2)C(=O)[C@@H]3CCCC[C@H]3C(=O)NC4(CC4)C#N)F
ACDLabs 12.01O=C(N2CCN(c1ccc(F)cc1)CC2)C4CCCCC4C(=O)NC3(C#N)CC3
CACTVS 3.370Fc1ccc(cc1)N2CCN(CC2)C(=O)[C@@H]3CCCC[C@H]3C(=O)NC4(CC4)C#N
OpenEye OEToolkits 1.7.6c1cc(ccc1N2CCN(CC2)C(=O)C3CCCCC3C(=O)NC4(CC4)C#N)F
CACTVS 3.370Fc1ccc(cc1)N2CCN(CC2)C(=O)[CH]3CCCC[CH]3C(=O)NC4(CC4)C#N
FormulaC22 H27 F N4 O2
Name(1R,2R)-N-(1-cyanocyclopropyl)-2-{[4-(4-fluorophenyl)piperazin-1-yl]carbonyl}cyclohexanecarboxamide
ChEMBLCHEMBL2070936
DrugBank
ZINCZINC000084689572
PDB chain4dmx Chain A Residue 301 [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]
PDB4dmx (1R,2R)-N-(1-cyanocyclopropyl)-2-(6-methoxy-1,3,4,5-tetrahydropyrido[4,3-b]indole-2-carbonyl)cyclohexanecarboxamide (AZD4996): a potent and highly selective cathepsin K inhibitor for the treatment of osteoarthritis.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		G23 C25 D61 G65 G66 Y67 N161
Binding residue
(residue number reindexed from 1)		G23 C25 D61 G65 G66 Y67 N161
Annotation score1
Binding affinityBindingDB: IC50=15nM
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:4dmx, PDBe:4dmx, PDBj:4dmx
PDBsum4dmx
PubMed22742641
UniProtP43235|CATK_HUMAN Cathepsin K (Gene Name=CTSK)

[Back to BioLiP]