966C

CRYSTAL STRUCTURE OF FIBROBLAST COLLAGENASE-1 COMPLEXED TO A DIPHENYL-ETHER SULPHONE BASED HYDROXAMIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.218 

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.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-1
A
157Homo sapiensMutation(s): 0 
Gene Names: MMP1 (CLG)
EC: 3.4.24.7
Find proteins for P03956 (Homo sapiens)
Go to Gene View: MMP1
Go to UniProtKB:  P03956
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RS2
Query on RS2

Download SDF File 
Download CCD File 
A
N-HYDROXY-2-[4-(4-PHENOXY-BENZENESULFONYL)-TETRAHYDRO-PYRAN-4-YL]-ACETAMIDE
C19 H21 N O6 S
ARIRIZBKMKMEBD-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RS2Ki: 23 nM (100) BINDINGDB
RS2Ki: 23 nM BINDINGMOAD
RS2Ki: 23 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 38.480α = 90.00
b = 56.520β = 90.00
c = 74.230γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
X-PLORmodel building
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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