1CIZ

X-RAY STRUCTURE OF HUMAN STROMELYSIN CATALYTIC DOMAIN COMPLEXES WITH NON-PEPTIDE INHIBITORS: IMPLICATION FOR INHIBITOR SELECTIVITY

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.209 

wwPDB Validation   3D Report Full Report


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


Literature

X-ray structure of human stromelysin catalytic domain complexed with nonpeptide inhibitors: implications for inhibitor selectivity.

Pavlovsky, A.G., Williams, M.G., Ye, Q.Z., Ortwine, D.F., Purchase II, C.F., White, A.D., Dhanaraj, V., Roth, B.D., Johnson, L.L., Hupe, D., Humblet, C., Blundell, T.L.

(1999) Protein Sci 8: 1455-1462

  • DOI: 10.1110/ps.8.7.1455
  • Primary Citation of Related Structures:  
    1QIC, 1QIA, 1B8Y, 1CAQ, 1CIZ

  • PubMed Abstract: 

    • Effective inhibitors of matrix metalloproteinases (MMPs), a family of connective tissue-degrading enzymes, could be useful for the treatment of diseases such as cancer, multiple sclerosis, and arthritis. Many of the known MMP inhibitors are derived from ...

    Effective inhibitors of matrix metalloproteinases (MMPs), a family of connective tissue-degrading enzymes, could be useful for the treatment of diseases such as cancer, multiple sclerosis, and arthritis. Many of the known MMP inhibitors are derived from peptide substrates, with high potency in vitro but little selectivity among MMPs and poor bioavailability. We have discovered nonpeptidic MMP inhibitors with improved properties, and report here the crystal structures of human stromelysin-1 catalytic domain (SCD) complexed with four of these inhibitors. The structures were determined and refined at resolutions ranging from 1.64 to 2.0 A. Each inhibitor binds in the active site of SCD such that a bulky diphenyl piperidine moiety penetrates a deep, predominantly hydrophobic S'1 pocket. The active site structure of the SCD is similar in all four inhibitor complexes, but differs substantially from the peptide hydroxamate complex, which has a smaller side chain bound in the S'1 pocket. The largest differences occur in the loop forming the "top" of this pocket. The occupation of these nonpeptidic inhibitors in the S'1 pocket provides a structural basis to explain their selectivity among MMPs. An analysis of the unique binding mode predicts structural modifications to design improved MMP inhibitors.

    Organizational Affiliation: 

    Department of Chemistry, Parke-Davis Pharmaceutical Research, Division of Warner-Lambert Company, Ann Arbor, Michigan 48105, USA. Alexander.Pavlovsky@wl.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (STROMELYSIN-1) A168Homo sapiensMutation(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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DPS
Query on DPS
Download Ideal Coordinates CCD File 
A
3-(1H-INDOL-3-YL)-2-[4-(4-PHENYL-PIPERIDIN-1-YL)-BENZENESULFONYLAMINO]-PROPIONIC ACID
C28 H29 N3 O4 S
ULOTXPTWJAUGGE-MHZLTWQESA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 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 %)
DPSKi:  36   nM  Binding MOAD
DPSKi :  36   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.209 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.37α = 90
b = 69.37β = 90
c = 74.4γ = 90
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-09-01
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2018-01-24
    Changes: Database references
  • Version 1.4: 2018-01-31
    Changes: Database references