1USN

CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN FIBROBLAST STROMELYSIN-1 INHIBITED WITH THIADIAZOLE INHIBITOR PNU-142372

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history. 

Literature

Structural characterizations of nonpeptidic thiadiazole inhibitors of matrix metalloproteinases reveal the basis for stromelysin selectivity.

Finzel, B.C., Baldwin, E.T., Bryant Jr., G.L., Hess, G.F., Wilks, J.W., Trepod, C.M., Mott, J.E., Marshall, V.P., Petzold, G.L., Poorman, R.A., O'Sullivan, T.J., Schostarez, H.J., Mitchell, M.A.

(1998) Protein Sci. 7: 2118-2126

  • DOI: 10.1002/pro.5560071008
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The binding of two 5-substituted-1,3,4-thiadiazole-2-thione inhibitors to the matrix metalloproteinase stromelysin (MMP-3) have been characterized by protein crystallography. Both inhibitors coordinate to the catalytic zinc cation via an exocyclic su ...

    The binding of two 5-substituted-1,3,4-thiadiazole-2-thione inhibitors to the matrix metalloproteinase stromelysin (MMP-3) have been characterized by protein crystallography. Both inhibitors coordinate to the catalytic zinc cation via an exocyclic sulfur and lay in an unusual position across the unprimed (P1-P3) side of the proteinase active site. Nitrogen atoms in the thiadiazole moiety make specific hydrogen bond interactions with enzyme structural elements that are conserved across all enzymes in the matrix metalloproteinase class. Strong hydrophobic interactions between the inhibitors and the side chain of tyrosine-155 appear to be responsible for the very high selectivity of these inhibitors for stromelysin. In these enzyme/inhibitor complexes, the S1' enzyme subsite is unoccupied. A conformational rearrangement of the catalytic domain occurs that reveals an inherent flexibility of the substrate binding region leading to speculation about a possible mechanism for modulation of stromelysin activity and selectivity.

    Organizational Affiliation: 

    Structural, Analytical & Medicinal Chemistry, Pharmacia and Upjohn, Kalamazoo, Michigan 49007, USA. Barry.C.Finzel@am.pnu.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
STROMELYSIN-1
A
165Homo sapiensMutation(s): 0 
Gene 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
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA
Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
IN9
Query on IN9
Download SDF File 
Download CCD File 
A
2-[3-(5-MERCAPTO-[1,3,4]THIADIAZOL-2YL)-UREIDO]-N-METHYL-3-PENTAFLUOROPHENYL-PROPIONAMIDE
PNU-142372
C13 H10 F5 N5 O2 S2
HZAXNPDJVFUGDS-BYPYZUCNSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IN9Ki: 18 nM (100) BINDINGDB
IN9Ki: 18 nM BINDINGMOAD
IN9Ki: 18 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.189 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 72.120α = 90.00
b = 72.120β = 90.00
c = 192.060γ = 120.00
Software Package:
Software NamePurpose
X-PLORphasing
XENGENdata reduction
X-PLORmodel building
XENGENdata scaling
PROFFTrefinement
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-12-23
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other
  • Version 1.4: 2018-03-07
    Type: Data collection