1EUB

SOLUTION STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN COLLAGENASE-3 (MMP-13) COMPLEXED TO A POTENT NON-PEPTIDIC SULFONAMIDE INHIBITOR


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 
  • Selection Criteria: BACK CALCULATED DATA AGREE WITH EXPERIMENTAL NOESY SPECTRUM, STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH FAVORABLE NON-BOND ENERGY,TARGET FUNCTION 

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This is version 1.2 of the entry. See complete history


Literature

Solution structure of the catalytic domain of human collagenase-3 (MMP-13) complexed to a potent non-peptidic sulfonamide inhibitor: binding comparison with stromelysin-1 and collagenase-1.

Zhang, X.Gonnella, N.C.Koehn, J.Pathak, N.Ganu, V.Melton, R.Parker, D.Hu, S.I.Nam, K.Y.

(2000) J Mol Biol 301: 513-524

  • DOI: 10.1006/jmbi.2000.3988
  • Primary Citation of Related Structures:  
    1EUB

  • PubMed Abstract: 
  • The full three-dimensional structure of the catalytic domain of human collagenase-3 (MMP-13) complexed to a potent, sulfonamide hydroxamic acid inhibitor (CGS 27023) has been determined by NMR spectroscopy. The results reveal a core domain for the pr ...

    The full three-dimensional structure of the catalytic domain of human collagenase-3 (MMP-13) complexed to a potent, sulfonamide hydroxamic acid inhibitor (CGS 27023) has been determined by NMR spectroscopy. The results reveal a core domain for the protein consisting of three alpha-helices and five beta-sheet strands with an overall tertiary fold similar to the catalytic domains of other matrix metalloproteinase family members. The S1' pocket, which is the major site of hydrophobic binding interaction, was found to be a wide cleft spanning the length of the protein and presenting facile opportunity for inhibitor extension deep into the pocket. Comparison with the reported X-ray structure of collagenase-3 showed evidence of flexibility for the loop region flanking the S1' pocket in both NMR and X-ray data. This flexibility was corroborated by NMR dynamics studies. Inhibitor binding placed the methoxy phenyl ring in the S1' pocket with the remainder of the molecule primarily solvent-exposed. The binding mode for this inhibitor was found to be similar with respect to stromelysin-1 and collagenase-1; however, subtle comparative differences in the interactions between inhibitor and enzyme were observed for the three MMPs that were consistent with their respective binding potencies.


    Organizational Affiliation

    Novartis Institute for Biomedical Research, 556 Morris Ave., Summit, NJ 07901, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
COLLAGENASE 3A171Homo sapiensMutation(s): 0 
Gene Names: MMP13
EC: 3.4.24
Find proteins for P45452 (Homo sapiens)
Explore P45452 
Go to UniProtKB:  P45452
NIH Common Fund Data Resources
PHAROS  P45452
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MSB
Query on MSB

Download Ideal Coordinates CCD File 
A
1-METHYLOXY-4-SULFONE-BENZENE
C7 H8 O3 S
XUNSZADDFLWFOL-UHFFFAOYSA-N
 Ligand Interaction
HAV
Query on HAV

Download Ideal Coordinates CCD File 
A
HYDROXYAMINOVALINE
C5 H12 N2 O2
USSBBYRBOWZYSB-SCSAIBSYSA-N
 Ligand Interaction
3MP
Query on 3MP

Download Ideal Coordinates CCD File 
A
3-METHYLPYRIDINE
C6 H7 N
ITQTTZVARXURQS-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 
  • Selection Criteria: BACK CALCULATED DATA AGREE WITH EXPERIMENTAL NOESY SPECTRUM, STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH FAVORABLE NON-BOND ENERGY,TARGET FUNCTION 
  • OLDERADO: 1EUB Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-04-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance