Structure of PDB 5tdi Chain A Binding Site BS01

Receptor Information
>5tdi 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]
APDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLAP
QNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNP
TGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVY
YDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNK
NNACGIANLASFPKM
Ligand information
Ligand ID7AS
InChIInChI=1S/C25H29F4N3O3S/c1-23(2,26)14-20(22(33)32-24(15-30)12-13-24)31-21(25(27,28)29)18-6-4-16(5-7-18)17-8-10-19(11-9-17)36(3,34)35/h4-11,15,20-21,30-31H,12-14H2,1-3H3,(H,32,33)/b30-15-/t20-,21-/m0/s1
InChIKeyZVRLJSQZXQQABF-OLOBTLGRSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)(F)C[C@H](N[C@@H](c1ccc(cc1)c2ccc(cc2)[S](C)(=O)=O)C(F)(F)F)C(=O)NC3(CC3)C=N
OpenEye OEToolkits 2.0.6[H]/N=C\C1(CC1)NC(=O)[C@H](CC(C)(C)F)N[C@@H](c2ccc(cc2)c3ccc(cc3)S(=O)(=O)C)C(F)(F)F
ACDLabs 12.01c2cc(c1ccc(S(=O)(C)=O)cc1)ccc2C(NC(CC(C)(C)F)C(=O)NC3(CC3)[C@H]=N)C(F)(F)F
OpenEye OEToolkits 2.0.6CC(C)(CC(C(=O)NC1(CC1)C=N)NC(c2ccc(cc2)c3ccc(cc3)S(=O)(=O)C)C(F)(F)F)F
CACTVS 3.385CC(C)(F)C[CH](N[CH](c1ccc(cc1)c2ccc(cc2)[S](C)(=O)=O)C(F)(F)F)C(=O)NC3(CC3)C=N
FormulaC25 H29 F4 N3 O3 S
Name4-fluoro-N-{1-[(Z)-iminomethyl]cyclopropyl}-N~2~-{(1S)-2,2,2-trifluoro-1-[4'-(methylsulfonyl)[1,1'-biphenyl]-4-yl]ethyl }-L-leucinamide;
covalently linked Odanacatib
ChEMBL
DrugBank
ZINC
PDB chain5tdi 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

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PDB5tdi Identification of mouse cathepsin K structural elements that regulate the potency of odanacatib.
Resolution1.4 Å
Binding residue
(original residue number in PDB)
G23 C25 E59 N60 D61 G64 G65 G66 Y67 A134 L160 N161 H162 A163
Binding residue
(residue number reindexed from 1)
G23 C25 E59 N60 D61 G64 G65 G66 Y67 A134 L160 N161 H162 A163
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=9.74,Ki=0.18nM
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

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Biological Process
External links
PDB RCSB:5tdi, PDBe:5tdi, PDBj:5tdi
PDBsum5tdi
PubMed28049758
UniProtP43235|CATK_HUMAN Cathepsin K (Gene Name=CTSK)

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