Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18722.12 
• Atom Count: 1312 
• Residue Count: 163 
• Unique protein chains: 1

1ZVX

Crystal structure of the complex between MMP-8 and a phosphonate inhibitor (R-enantiomer)

• DOI: 10.2210/pdb1ZVX/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21


• Deposited: 2005-06-03 Released: 2006-05-16 
• Deposition Author(s): Pochetti, G., Gavuzzo, E., Campestre, C., Agamennone, M., Tortorella, P., Consalvi, V., Gallina, C., Hiller, O., Tschesche, H., Tucker, P.A., Mazza, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.244 
• R-Value Work: 0.208 

Literature

Structural insight into the stereoselective inhibition of MMP-8 by enantiomeric sulfonamide phosphonates.

Pochetti, G., Gavuzzo, E., Campestre, C., Agamennone, M., Tortorella, P., Consalvi, V., Gallina, C., Hiller, O., Tschesche, H., Tucker, P.A., Mazza, F.

(2006) J.Med.Chem. 49: 923-931

• PubMed: 16451058 
• DOI: 10.1021/jm050787+
• Primary Citation of Related Structures:  
  1ZS0


• PubMed Abstract: 
  

Potent and selective inhibitors of matrix metalloproteinases (MMPs), a family of zinc proteases that can degrade all the components of the extracellular matrix, could be useful for treatment of diseases such as cancer and arthritis. The most potent MMP inhibitors are based on hydroxamate as zinc-binding group (ZBG). alpha-Arylsulfonylamino phosphonates incorporate a particularly favorable combination of phosphonate as ZBG and arylsulfonylamino backbone so that their affinity exceptionally attains the nanomolar strength frequently observed for hydroxamate analogues. The detailed mode of binding of [1-(4'-methoxybiphenyl-4-sulfonylamino)-2-methylpropyl]phosphonate has been clarified by the crystal structures of the complexes that the R- and S-enantiomers respectively form with MMP-8. The reasons for the preferential MMP-8 inhibition by the R-phosphonate are underlined and the differences in the mode of binding of analogous alpha-arylsulfonylamino hydroxamates and carboxylates are discussed.

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Related Citations: 

• 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
• X-ray structuresof 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
• 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




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Organizational Affiliation: 

Istituto di Cristallografia, C.N.R., Monterotondo Stazione, Rome, Italy.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Neutrophil collagenase	A	163	Homo sapiens	Mutation(s): 0  Gene Names: MMP8 (CLG1) EC: 3.4.24.34
Find proteins for P22894 (Homo sapiens) Go to Gene View: MMP8 Go to UniProtKB:  P22894

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
FIN	A	(1R)-1-{[(4'-METHOXY-1,1'-BIPHENYL-4-YL)SULFONYL]AMINO}-2-METHYLPROPYLPHOSPHONIC ACID C17 H22 N O6 P S BZVYQWLRCHLAGK-QGZVFWFLSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
FIN	Ki: 0.6 nM (100) BINDINGDB
FIN	IC50: 1.4 nM (100) BINDINGDB
FIN	Ki: 0.6 nM BINDINGMOAD
FIN	Ki: 0.6 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.244 
• R-Value Work: 0.208 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 32.706	α = 90.00
b = 54.754	β = 90.00
c = 68.413	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
SCALEPACK	data scaling
AMoRE	phasing
MAR345	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-06-03 
• Released Date: 2006-05-16 
• Deposition Author(s): Pochetti, G., Gavuzzo, E., Campestre, C., Agamennone, M., Tortorella, P., Consalvi, V., Gallina, C., Hiller, O., Tschesche, H., Tucker, P.A., Mazza, F.

Revision History 

• Version 1.0: 2006-05-16
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-10-11
  Type: Advisory, Refinement description
• Version 1.4: 2018-01-24
  Type: Database references