Macromolecule Content

• Total Structure Weight: 19.48 kDa 
• Atom Count: 1368 
• Modelled Residue Count: 168 
• Deposited Residue Count: 168 
• Unique protein chains: 1

3USN

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

• DOI: 10.2210/pdb3USN/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 1 
• Conformers Submitted: 1 

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

• PubMed: 9827994 
• 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. 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.

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Organizational Affiliation: 

Structural, Analytical & Medicinal Chemistry, Pharmacia & Upjohn, Kalamazoo, Michigan 49001, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
STROMELYSIN-1	A	168	Homo sapiens	Mutation(s): 0  Gene Names: MMP3, STMY1 EC: 3.4.24.17
Find proteins for P08254 (Homo sapiens) Explore P08254  Go to UniProtKB:  P08254
NIH Common Fund Data Resources
PHAROS:  P08254 GTEx:  ENSG00000149968

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATT	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
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ATT	Ki:  710   nM  BindingDB
ATT	Ki :  710   nM  PDBBind
ATT	Ki:  708   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 1 
• Conformers Submitted: 1 
• OLDERADO: 3USN Olderado

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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