1AU3

CRYSTAL STRUCTURE OF THE CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH A COVALENT PYRROLIDINONE INHIBITOR

• PDB DOI: https://doi.org/10.2210/pdb1AU3/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 1997-09-10 Released: 1998-10-14 
• Deposition Author(s): Zhao, B., Smith, W.W., Janson, C.A., Abdel-Meguid, S.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.353 
• R-Value Work: 0.193 
• R-Value Observed: 0.193 

Starting Model: experimental

Literature

Conformationally constrained 1,3-diamino ketones: a series of potent inhibitors of the cysteine protease cathepsin K.

Marquis, R.W., Yamashita, D.S., Ru, Y., LoCastro, S.M., Oh, H.J., Erhard, K.F., DesJarlais, R.L., Head, M.S., Smith, W.W., Zhao, B., Janson, C.A., Abdel-Meguid, S.S., Tomaszek, T.A., Levy, M.A., Veber, D.F.

(1998) J Med Chem 41: 3563-3567

• PubMed: 9733481 
• DOI: https://doi.org/10.1021/jm980295f
• Primary Citation of Related Structures:  
  1AU3, 1AU4

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Organizational Affiliation: 

Departments of Medicinal Chemistry, SmithKline Beecham Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 24.12 kDa 
• Atom Count: 1,742 
• Modelled 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  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
PCM	B [auth A]	1-[N[(PHENYLMETHOXY)CARBONYL]-L-LEUCYL-4-[[N/N-[(PHENYLMETHOXY)CARBONYL]-/NL-LEUCYL]AMINO]-3-PYRROLIDINONE/N C32 H42 N4 O7 GXENQLUSOCKXDN-GMQQYTKMSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.353 
• R-Value Work: 0.193 
• R-Value Observed: 0.193 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.84	α = 90
b = 50.99	β = 90
c = 103.58	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-10-14 
Deposition Author(s): Zhao, B., Smith, W.W., Janson, C.A., Abdel-Meguid, S.S.

Revision History  

• Version 1.0: 1998-10-14
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-03-07
  Changes: Data collection, Other
• Version 1.4: 2023-08-02
  Changes: Database references, Derived calculations, Refinement description