1G4K

X-ray Structure of a Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.244 

wwPDB Validation   3D Report Full Report


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


Literature

X-ray structure of a novel matrix metalloproteinase inhibitor complexed to stromelysin.

Dunten, P., Kammlott, U., Crowther, R., Levin, W., Foley, L.H., Wang, P., Palermo, R.

(2001) Protein Sci 10: 923-926

  • DOI: 10.1110/ps.48401
  • Primary Citation of Related Structures:  
    1G4K

  • PubMed Abstract: 

    • A new class of matrix metalloproteinase (MMP) inhibitors has been identified by screening a collection of compounds against stromelysin. The inhibitors, 2,4,6-pyrimidine triones, have proven to be potent inhibitors of gelatinases A and B. An X-ray crysta ...

    A new class of matrix metalloproteinase (MMP) inhibitors has been identified by screening a collection of compounds against stromelysin. The inhibitors, 2,4,6-pyrimidine triones, have proven to be potent inhibitors of gelatinases A and B. An X-ray crystal structure of one representative compound bound to the catalytic domain of stromelysin shows that the compounds bind at the active site and ligand the active-site zinc. The pyrimidine triones mimic substrates in forming hydrogen bonds to key residues in the active site, and provide opportunities for placing appropriately chosen groups into the S1' specificity pocket of MMPS: A number of compounds have been synthesized and assayed against stromelysin, and the variations in potency are explained in terms of the binding mode revealed in the X-ray crystal structure.

    Organizational Affiliation: 

    Roche Research Center, Hoffmann-La Roche Inc., Nutley, New Jersey 07110, USA. pete.dunten@roche.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
STROMELYSIN-1 A, B, C168Homo sapiensMutation(s): 0 
Gene Names: MMP3, STMY1
EC: 3.4.24.17
Find proteins for P08254 (Homo sapiens)
Explore P08254 
Go to UniProtKB:  P08254
NIH Common Fund Data Resources
PHAROS:  P08254
GTEx:  ENSG00000149968
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HQQ
Query on HQQ
Download Ideal Coordinates CCD File 
A, B, C
5-METHYL-5-(4-PHENOXY-PHENYL)-PYRIMIDINE-2,4,6-TRIONE
C17 H14 N2 O4
RTBMLCLTYAPKIF-UHFFFAOYSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
A, B, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HQQIC50 :  2000   nM  PDBBind
HQQIC50:  2000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.244 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.8α = 90
b = 103.8β = 90
c = 147.49γ = 90
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-04-25
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2018-07-18
    Changes: Data collection, Database references