1I73

COMPLEX OF PRO-LEU-L-TRP PHOSPHONATE WITH THE CATALITIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (MET80 FORM)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.138 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Two crystal structures of human neutrophil collagenase, one complexed with a primed- and the other with an unprimed-side inhibitor: implications for drug design.

Gavuzzo, E.Pochetti, G.Mazza, F.Gallina, C.Gorini, B.D'Alessio, S.Pieper, M.Tschesche, H.Tucker, P.A.

(2000) J Med Chem 43: 3377-3385

  • DOI: 10.1021/jm9909589
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Two crystal structures of human neutrophil collagenase (HNC, MMP-8), one complexed with a primed- and the other with an unprimed-side inhibitor, were determined using synchrotron radiation at 100 K. Both inhibitors contain non-hydroxamate zinc-bindin ...

    Two crystal structures of human neutrophil collagenase (HNC, MMP-8), one complexed with a primed- and the other with an unprimed-side inhibitor, were determined using synchrotron radiation at 100 K. Both inhibitors contain non-hydroxamate zinc-binding functions. The Pro-Leu-L-Trp(P)(OH)(2) occupies the unprimed region of the active site, furnishes new structural information regarding interaction between the catalytic zinc ion and the phosphonate group, and is the only example of occupation of the S(1) subsite of MMP-8 by the bulky tryptophan side chain. The (R)-2-(biphenyl-4-ylsulfonyl)-1,2,3, 4-tetrahydroisochinolin-3-carboxylic acid, a conformationally constrained D-Tic derivative, accommodates its biphenyl substituent into the deep primary specificity S(1)' subsite, inducing a widening of the entrance to this pocket; this modification of the protein, mainly consisting in a shift of the segment centered at Pro217, is observed for the first time in MMP-8 complexes. Cation-aromatic interactions can stabilize the formation of both complexes, and the beneficial effect of aromatic substituents in proximity of the catalytic zinc ion is discussed. The phosphonate group bound to either a primed- or unprimed-side inhibitor maintains the same relative position with respect to the catalytic zinc ion, suggesting that this binding function can be exploited for the design of combined inhibitors assembled to interact with both primed and unprimed regions of the active cleft.


    Related Citations: 
    • X-RAY STRUCTURES OF HUMAN NEUTROPHIL COLLAGENASE COMPLEXED WITH PEPTIDE HYDROXAMATE AND PEPTIDE THIOL INHIBITORS. IMPLICATIONS FOR SUBSTRATE BINDING AND RATIONAL DRUG DESIGN
      Grams, F., Reinemer, P., Powers, J.C., Kleine, T., Pieper, M., Tschesche, H., Huber, R., Bode, W.
      (1995) Eur J Biochem 228: 830
    • Quantitative Structure-Activity Relationship of Human Neutrophil Collagenase (Mmp8-8) Inhibitors Using Comparative Molecular Field Analysis and X-Ray Structure Analysis
      Matter, H., Schwab, W., Barbier, D., Billen, G., Haase, B., Neises, B., Schudok, M., Thorwart, W., Schreuder, H., Brachvogel, V., Loenze, P., Weithmann, K.U.
      (1999) J Med Chem 42: 1908

    Organizational Affiliation

    Istituto di Strutturistica Chimica, CNR, C. P. n. 10, 00016 Monterotondo Stazione, Roma, Italy.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NEUTROPHIL COLLAGENASEA163Homo sapiensMutation(s): 0 
Gene Names: MMP8CLG1
EC: 3.4.24.34
Find proteins for P22894 (Homo sapiens)
Explore P22894 
Go to UniProtKB:  P22894
NIH Common Fund Data Resources
PHAROS  P22894
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
THREE RESIDUE PEPTIDE INHIBITORB3N/AMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PAT
Query on PAT
BL-PEPTIDE LINKINGC11 H13 N2 O5 PTRP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.138 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.983α = 90
b = 68.673β = 90
c = 70.486γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
SHELXLrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-03-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description