1D8M

CRYSTAL STRUCTURE OF MMP3 COMPLEXED WITH A HETEROCYCLE-BASED INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.277 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Heterocycle-based MMP inhibitors with P2' substituents.

Pikul, S.Dunham, K.M.Almstead, N.G.De, B.Natchus, M.G.Taiwo, Y.O.Williams, L.E.Hynd, B.A.Hsieh, L.C.Janusz, M.J.Gu, F.Mieling, G.E.

(2001) Bioorg.Med.Chem.Lett. 11: 1009-1013

  • Primary Citation of Related Structures:  1G05

  • PubMed Abstract: 
  • Potent and selective inhibition of matrix metalloproteinases was demonstrated for a series of sulfonamide-based hydroxamic acids. The design of the heterocyclic sulfonamides incorporates a six- or seven-member central ring with a P2' substituent that ...

    Potent and selective inhibition of matrix metalloproteinases was demonstrated for a series of sulfonamide-based hydroxamic acids. The design of the heterocyclic sulfonamides incorporates a six- or seven-member central ring with a P2' substituent that can be modified. Binding interactions of this substituent at the S2' site are believed to contribute to high inhibitory potency against stromelysin, collagenase-3 and gelatinases A and B, and to provide selectivity against collagenase-1 and matrilysin. An X-ray structure of a stromelysin inhibitor complex was obtained to provide insights into the SAR and selectivity trends observed for the series.


    Organizational Affiliation

    Procter and Gamble Pharmaceuticals, Health Care Research Center, Mason, OH 45040, USA. spikul@avalonrx.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
STROMELYSIN-1 PRECURSOR
A, B
173Homo sapiensGene Names: MMP3 (STMY1)
EC: 3.4.24.17
Find proteins for P08254 (Homo sapiens)
Go to Gene View: MMP3
Go to UniProtKB:  P08254
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
BBH
Query on BBH

Download SDF File 
Download CCD File 
B
1-BENZYL-3-(4-METHOXY-BENZENESULFONYL)-6-OXO-HEXAHYDRO-PYRIMIDINE-4-CARBOXYLIC ACID HYDROXYAMIDE
C19 H21 N3 O6 S
SUSMVCKSLVPRCL-QGZVFWFLSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BBHIC50: 3.1 nM (100) BINDINGDB
BBHIC50: 3.1 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.277 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.960α = 90.00
b = 78.590β = 90.00
c = 105.930γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
X-PLORmodel building
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-10-25
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance