3USN

STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN FIBROBLAST STROMELYSIN-1 INHIBITED WITH THE THIADIAZOLE INHIBITOR IPNU-107859, NMR, 1 STRUCTURE


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 
  • Conformers Submitted: 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Solution structures of stromelysin complexed to thiadiazole inhibitors.

Stockman, B.J.Waldon, D.J.Gates, J.A.Scahill, T.A.Kloosterman, D.A.Mizsak, S.A.Jacobsen, E.J.Belonga, K.L.Mitchell, M.A.Mao, B.Petke, J.D.Goodman, L.Powers, E.A.Ledbetter, S.R.Kaytes, P.S.Vogeli, G.Marshall, V.P.Petzold, G.L.Poorman, R.A.

(1998) Protein Sci 7: 2281-2286

  • DOI: 10.1002/pro.5560071105
  • Primary Citation of Related Structures:  
    3USN

  • PubMed Abstract: 
  • Unregulated or overexpressed matrix metalloproteinases (MMPs), including stromelysin, collagenase, and gelatinase. have been implicated in several pathological conditions including arthritis and cancer. Small-molecule MMP inhibitors may have therapeutic value in the treatment of these diseases ...

    Unregulated or overexpressed matrix metalloproteinases (MMPs), including stromelysin, collagenase, and gelatinase. have been implicated in several pathological conditions including arthritis and cancer. Small-molecule MMP inhibitors may have therapeutic value in the treatment of these diseases. In this regard, the solution structures of two stromelysin/ inhibitor complexes have been investigated using 1H, 13C, and 15N NMR spectroscopy. Both-inhibitors are members of a novel class of matrix metalloproteinase inhibitor that contain a thiadiazole group and that interact with stromelysin in a manner distinct from other classes of inhibitors. The inhibitors coordinate the catalytic zinc atom through their exocyclic sulfur atom, with the remainder of the ligand extending into the S1-S3 side of the active site. The binding of inhibitor containing a protonated or fluorinated aromatic ring was investigated using 1H and 19F NMR spectroscopy. The fluorinated ring was found to have a reduced ring-flip rate compared to the protonated version. A strong, coplanar interaction between the fluorinated ring of the inhibitor and the aromatic ring of Tyr155 is proposed to account for the reduced ring-flip rate and for the increase in binding affinity observed for the fluorinated inhibitor compared to the protonated inhibitor. Binding interactions observed for the thiadiazole class of ligands have implications for the design of matrix metalloproteinase inhibitors.


    Organizational Affiliation

    Structural, Analytical & Medicinal Chemistry, Pharmacia & Upjohn, Kalamazoo, Michigan 49001, USA. brian.j.stockman@am.pnu.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
STROMELYSIN-1 A168Homo sapiensMutation(s): 0 
Gene Names: MMP3STMY1
EC: 3.4.24.17
Find proteins for P08254 (Homo sapiens)
Explore P08254 
Go to UniProtKB:  P08254
NIH Common Fund Data Resources
PHAROS:  P08254
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATT
Query on ATT

Download Ideal Coordinates CCD File 
A
2-[3-(5-MERCAPTO-[1,3,4]THIADIAZOL-2-YL)-UREIDO]-N-METHYL-3-PHENYL-PROPIONAMIDE
C13 H15 N5 O2 S2
RKWXKADYTDWZIJ-VIFPVBQESA-N
 Ligand Interaction
ZN
Query on ZN

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

Download Ideal Coordinates CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ATTKi:  710   nM  BindingDB
ATTKi :  710   nM  PDBBind
ATTKi:  708   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 
  • Conformers Submitted: 
  • OLDERADO: 3USN Olderado

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 1998-06-18 
  • Released Date: 1999-01-20 
  • Deposition Author(s): Stockman, B.J.

Revision History  (Full details and data files)

  • Version 1.0: 1999-01-20
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance