830C

COLLAGENASE-3 (MMP-13) COMPLEXED TO A SULPHONE-BASED HYDROXAMIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.Mol.Biol. 6: 217-221

  • DOI: 10.1038/6657
  • Primary Citation of Related Structures:  
  • Also Cited By: 3SHI

  • 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) inhibito ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MMP-13
A, B
168Homo sapiensMutation(s): 0 
Gene Names: MMP13
EC: 3.4.24.-
Find proteins for P45452 (Homo sapiens)
Go to Gene View: MMP13
Go to UniProtKB:  P45452
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
RS1
Query on RS1

Download SDF File 
Download CCD File 
A, B
4-[4-(4-CHLORO-PHENOXY)-BENZENESULFONYLMETHYL]-TETRAHYDRO-PYRAN-4-CARBOXYLIC ACID HYDROXYAMIDE
C19 H20 Cl N O6 S
ROSNVSQTEGHUKU-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RS1Ki: 0.3 - 0.6 nM (100) BINDINGDB
RS1IC50: 0 - 34 nM (100) BINDINGDB
RS1Ki: 0.52 nM BINDINGMOAD
RS1Ki: 0.52 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 136.072α = 90.00
b = 36.098β = 131.06
c = 96.368γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
CCP4data scaling
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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