1D7X

CRYSTAL STRUCTURE OF MMP3 COMPLEXED WITH A MODIFIED PROLINE SCAFFOLD BASED INHIBITOR.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.262 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Design, synthesis, and biological evaluation of matrix metalloproteinase inhibitors derived from a modified proline scaffold.

Cheng, M.De, B.Almstead, N.G.Pikul, S.Dowty, M.E.Dietsch, C.R.Dunaway, C.M.Gu, F.Hsieh, L.C.Janusz, M.J.Taiwo, Y.O.Natchus, M.G.Hudlicky, T.Mandel, M.

(1999) J Med Chem 42: 5426-5436

  • DOI: 10.1021/jm9904699
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The synthesis and structure-activity relationship (SAR) studies of a series of proline-based matrix metalloproteinase inhibitors are described. The data reveal a remarkable potency enhancement in those compounds that contain an sp(2) center at the C- ...

    The synthesis and structure-activity relationship (SAR) studies of a series of proline-based matrix metalloproteinase inhibitors are described. The data reveal a remarkable potency enhancement in those compounds that contain an sp(2) center at the C-4 carbon of the ring relative to similar, saturated compounds. This effect was noted in compounds that contained a functionalized oxime moiety or an exomethylene at C-4, and the potencies were typically <10 nM for MMP-3 and <100 nM for MMP-1. Comparisons were then made against compounds with similar functionality where the C-4 carbon was reduced to sp(3) hybridization and the effect was typically an order of magnitude loss in potency. A comparison of compounds 14 and 34 exemplifies this observation. An X-ray structure was obtained for a stromelysin-inhibitor complex which provided insights into the SAR and selectivity trends observed within the series. In vitro intestinal permeability data for many compounds was also accumulated.


    Organizational Affiliation

    Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
STROMELYSIN-1 PRECURSOR
A, B
173Homo sapiensMutation(s): 0 
Gene Names: MMP3STMY1
EC: 3.4.24.17
Find proteins for P08254 (Homo sapiens)
Go to UniProtKB:  P08254
NIH Common Fund Data Resources
PHAROS  P08254
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPC
Query on SPC

Download CCD File 
A, B
N-HYDROXY 1N(4-METHOXYPHENYL)SULFONYL-4-(Z,E-N-METHOXYIMINO)PYRROLIDINE-2R-CARBOXAMIDE
C13 H19 N3 O6 S
OJLWCTMBGWSVFC-JOYOIKCWSA-N
 Ligand Interaction
ZN
Query on ZN

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

Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SPCIC50:  19   nM  BindingDB
SPCIC50 :  3   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.262 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.85α = 90
b = 78.22β = 90
c = 104.74γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
SMARTdata reduction
SAINTdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-10-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance