1MEM | pdb_00001mem

Crystal structure of Cathepsin K complexed with a potent vinyl sulfone inhibitor

• PDB DOI: https://doi.org/10.2210/pdb1MEM/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Komagataella phaffii GS115
• Mutation(s): No 


• Deposited: 1997-01-08 Released: 1998-01-14 
• Deposition Author(s): Mcgrath, M.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work: 
  0.175 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of human cathepsin K complexed with a potent inhibitor.

McGrath, M.E., Klaus, J.L., Barnes, M.G., Bromme, D.

(1997) Nat Struct Biol 4: 105-109

• PubMed: 9033587 
• DOI: https://doi.org/10.1038/nsb0297-105
• Primary Citation Related Structures: 
  1MEM

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 24.05 kDa 
• Atom Count: 1,790 
• Modeled Residue Count: 215 
• Deposited Residue Count: 215 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin K	A	215	Homo sapiens	Mutation(s): 0  Gene Names: CTSK, CTSO, CTSO2 EC: 3.4.22.38
UniProt & NIH Common Fund Data Resources
Find proteins for P43235 (Homo sapiens) Explore P43235  Go to UniProtKB:  P43235
PHAROS:  P43235 GTEx:  ENSG00000143387

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0D6	B [auth A]	N-{(1R)-3-phenyl-1-[2-(phenylsulfonyl)ethyl]propyl}-N~2~-(piperazin-1-ylcarbonyl)-L-leucinamide C28 H40 N4 O4 S GZQYXFWTRHRNKT-AHWVRZQESA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000234 (0D6)	B [auth A]	N-{(1R)-3-phenyl-1-[2-(phenylsulfonyl)ethyl]propyl}-N~2~-(piperazin-1-ylcarbonyl)-L-leucinamide	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work:  0.175 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.82	α = 90
b = 50.04	β = 90
c = 105.92	γ = 90

Software Package:

Software Name	Purpose
bioteX	data collection
MSC	data collection
bioteX	data reduction
MSC	data reduction
X-PLOR	model building
X-PLOR	refinement
bioteX	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-01-14 
Deposition Author(s): Mcgrath, M.E.

Revision History  

• Version 1.0: 1998-01-14
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2012-12-12
  Changes: Other
• Version 1.4: 2014-01-29
  Changes: Refinement description
• Version 1.5: 2024-04-03
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.6: 2024-11-06
  Changes: Structure summary