1D5J | pdb_00001d5j

CRYSTAL STRUCTURE OF MMP3 COMPLEXED WITH A THIAZEPINE BASED INHIBITOR.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.257 (Depositor) 
  • R-Value Work: 
    0.237 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1D5J

This is version 1.4 of the entry. See complete history

Literature

Design, synthesis, and biological evaluation of potent thiazine- and thiazepine-based matrix metalloproteinase inhibitors.

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

(1999) J Med Chem 42: 4547-4562

  • DOI: https://doi.org/10.1021/jm990330y
  • Primary Citation Related Structures: 
    1D5J

  • PubMed Abstract: 

    The synthesis and enzyme inhibition data for a series of thiazine- and thiazepine-based matrix metalloproteinase (MMP) inhibitors are described. The thiazine- and thiazepine-based inhibitors were discovered by optimization of hetererocyclic sulfonamide-based inhibitors. The most potent series of inhibitors was obtained by modification of the amino acid D-penicillamine. This amino acid provides a gem-dimethyl group on the thiazine or thiazepine ring which has a dramatic effect on the in vitro potency of this series. In particular, the sulfide 4a and the sulfone 5a were potent, broad-spectrum inhibitors of the MMPs with IC(50)'s against MMP-1 of 0.8 and 1.9 nM, respectively. The binding mode of this novel thiazepine-based series of MMP inhibitors was established based on X-ray crystallography of the complex of stromelysin and 4a.


  • Organizational Affiliation
    • Procter and Gamble Pharmaceuticals, Health Care Research Center, 8700 Mason-Montgomery Road, Mason, Ohio 45040, USA.

Macromolecule Content 

  • Total Structure Weight: 40.08 kDa 
  • Atom Count: 2,869 
  • 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
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
MM3

Query on MM3



Download:Ideal Coordinates CCD File
H [auth A],
N [auth B]
N-HYDROXY-4-[(4-METHOXYLPHENYL)SULFONYL]-2,2-DIMETHYL-HEXAHYDRO-1,4-THIAZEPINE-3(S)-CARBOXAMIDE
C15 H22 N2 O5 S2
CYYCSKFJEOSZTF-CYBMUJFWSA-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: 2.60 Å
  • R-Value Free:  0.257 (Depositor) 
  • R-Value Work:  0.237 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.78α = 90
b = 78.54β = 90
c = 105.27γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-10-09
    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: 2018-10-03
    Changes: Advisory, Data collection, Source and taxonomy, Structure summary
  • Version 1.4: 2024-02-07
    Changes: Advisory, Data collection, Database references, Derived calculations