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 1.3 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: https://doi.org/10.1021/jm9904699
  • Primary Citation of Related Structures:  
    1D7X

  • 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-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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
STROMELYSIN-1 PRECURSOR
A, B
173Homo sapiensMutation(s): 0 
EC: 3.4.24.17
UniProt & NIH Common Fund Data Resources
Find proteins for P08254 (Homo sapiens)
Explore P08254 
Go to UniProtKB:  P08254
PHAROS:  P08254
GTEx:  ENSG00000149968 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08254
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SPC
Query on SPC

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

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
I [auth B],
J [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
K [auth B]
L [auth B]
E [auth A],
F [auth A],
G [auth A],
K [auth B],
L [auth B],
M [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
SPC PDBBind:  1D7X IC50: 3 (nM) from 1 assay(s)
BindingDB:  1D7X IC50: 19 (nM) from 1 assay(s)
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  (Full details and data files)

  • 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
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations