Structure of PDB 4dmy Chain A Binding Site BS01

Receptor Information
>4dmy 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 ID0LC
InChIInChI=1S/C23H25FN4O2/c24-14-5-6-19-17(11-14)18-12-28(10-7-20(18)26-19)22(30)16-4-2-1-3-15(16)21(29)27-23(13-25)8-9-23/h5-6,11,15-16,26H,1-4,7-10,12H2,(H,27,29)/t15-,16-/m1/s1
InChIKeyHGJTURTZFKNELD-HZPDHXFCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1cc2c(cc1F)c3c([nH]2)CCN(C3)C(=O)C4CCCCC4C(=O)NC5(CC5)C#N
OpenEye OEToolkits 1.7.6c1cc2c(cc1F)c3c([nH]2)CCN(C3)C(=O)[C@@H]4CCCC[C@H]4C(=O)NC5(CC5)C#N
CACTVS 3.370Fc1ccc2[nH]c3CCN(Cc3c2c1)C(=O)[C@@H]4CCCC[C@H]4C(=O)NC5(CC5)C#N
CACTVS 3.370Fc1ccc2[nH]c3CCN(Cc3c2c1)C(=O)[CH]4CCCC[CH]4C(=O)NC5(CC5)C#N
ACDLabs 12.01N#CC5(NC(=O)C4CCCCC4C(=O)N2Cc1c3c(nc1CC2)ccc(F)c3)CC5
FormulaC23 H25 F N4 O2
Name(1R,2R)-N-(1-cyanocyclopropyl)-2-[(8-fluoro-1,3,4,5-tetrahydro-2H-pyrido[4,3-b]indol-2-yl)carbonyl]cyclohexanecarboxamide
ChEMBLCHEMBL2164678
DrugBank
ZINCZINC000095556465
PDB chain4dmy Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4dmy (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.
Resolution1.63 Å
Binding residue
(original residue number in PDB)		G23 C25 N60 G64 G65 G66 Y67 N161 H162
Binding residue
(residue number reindexed from 1)		G23 C25 N60 G64 G65 G66 Y67 N161 H162
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=9.00,IC50<0.001uM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:4dmy, PDBe:4dmy, PDBj:4dmy
PDBsum4dmy
PubMed22742641
UniProtP43235|CATK_HUMAN Cathepsin K (Gene Name=CTSK)

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