1BGO

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Use of X-Ray Co-Crystal Structures and Molecular Modeling to Design Potent and Selective Non-Peptide Inhibitors of Cathepsin K

Desjarlais, R.L., Yamashita, D.S., Oh, H.J., Uzinskas, I.N., Erhard, K.F., Allen, A.C., Haltiwanger, R.C., Zhao, B.G., Smith, W.W., Abdel-Meguid, S.S., Dalessio, K., Janson, C.A., Mcqueney, M.S., Tomaszek, T.A., Levy, M.A., Veber, D.F.

(1998) J Am Chem Soc 120: 9114


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CATHEPSIN K215Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43235
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
I10
Query on I10
Download Ideal Coordinates CCD File 
B [auth A]1-[2-(3-BIPHENYL)-4-METHYLVALERYL)]AMINO-3-(2-PYRIDYLSULFONYL)AMINO-2-PROPANONE
C26 H31 N3 O4 S
YCDHZDINQZLSRR-DNQXCXABSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
I10 PDBBind:  1BGO Ki: 3.5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.240 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.55α = 90
b = 71.55β = 90
c = 55.09γ = 90
Software Package:
Software NamePurpose
XENGENdata collection
CCP4data reduction
X-PLORmodel building
X-PLORrefinement
XENGENdata reduction
CCP4data scaling
X-PLORphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-06-08
    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