456C

CRYSTAL STRUCTURE OF COLLAGENASE-3 (MMP-13) COMPLEXED TO A DIPHENYL-ETHER SULPHONE BASED HYDROXAMIC ACID

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.338 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Crystal structures of MMP-1 and -13 reveal the structural basis for selectivity of collagenase inhibitors.

Lovejoy, B., Welch, A.R., Carr, S., Luong, C., Broka, C., Hendricks, R.T., Campbell, J.A., Walker, K.A., Martin, R., Van Wart, H., Browner, M.F.

(1999) Nat Struct Biol 6: 217-221

  • DOI: 10.1038/6657
  • Primary Citation of Related Structures:  
    456C, 830C, 966C

  • PubMed Abstract: 

    • The X-ray crystal structures of the catalytic domain of human collagenase-3 (MMP-13) and collagenase-1 (MMP-1) with bound inhibitors provides a basis for understanding the selectivity profile of a novel series of matrix metalloprotease (MMP) inhibitors. ...

    The X-ray crystal structures of the catalytic domain of human collagenase-3 (MMP-13) and collagenase-1 (MMP-1) with bound inhibitors provides a basis for understanding the selectivity profile of a novel series of matrix metalloprotease (MMP) inhibitors. Differences in the relative size and shape of the MMP S1' pockets suggest that this pocket is a critical determinant of MMP inhibitor selectivity. The collagenase-3 S1' pocket is long and open, easily accommodating large P1' groups, such as diphenylether. In contrast, the collagenase-1 S1' pocket must undergo a conformational change to accommodate comparable P1' groups. The selectivity of the diphenylether series of inhibitors for collagenase-3 is largely determined by their affinity for the preformed S1' pocket of collagenase-3, as compared to the induced fit in collagenase-1.

    Organizational Affiliation: 

    Inflammatory Diseases Unit, Roche Bioscience, Palo Alto, California 94304, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MMP-13 A, B168Homo sapiensMutation(s): 0 
Gene Names: MMP13
EC: 3.4.24
Find proteins for P45452 (Homo sapiens)
Explore P45452 
Go to UniProtKB:  P45452
NIH Common Fund Data Resources
PHAROS:  P45452
GTEx:  ENSG00000137745
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
345Ki :  0.17000000178813934   nM  PDBBind
CBPKi:  0.17000000178813934   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.338 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.004α = 90
b = 35.622β = 131.19
c = 94.875γ = 90
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-08-06
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-03-07
    Changes: Data collection