1D7X | pdb_00001d7x

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 (Depositor) 
  • R-Value Work: 
    0.262 (Depositor) 
  • R-Value Observed: 
    0.262 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1D7X

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 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.

Macromolecule Content 

  • Total Structure Weight: 40.03 kDa 
  • Atom Count: 2,947 
  • Modeled Residue Count: 342 
  • Deposited Residue Count: 346 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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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

Experimental Data & Validation

Experimental Data

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