1ZVX

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

PDB DOI: 10.2210/pdb1ZVX/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free: 0.244
R-Value Work: 0.208
R-Value Observed: 0.209

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

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 Search on PubMed
DOI: 10.1021/jm050787+
Primary Citation of Related Structures:
1ZS0, 1ZVX

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.

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

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

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

Organizational Affiliation:

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutrophil collagenase	A	163	Homo sapiens	Mutation(s): 0 Gene Names: MMP8, CLG1 EC: 3.4.24.34
UniProt & NIH Common Fund Data Resources
Find proteins for P22894 (Homo sapiens) Explore P22894 Go to UniProtKB: P22894
PHAROS: P22894
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22894
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FIN Query on FIN Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	(1R)-1-{[(4'-METHOXY-1,1'-BIPHENYL-4-YL)SULFONYL]AMINO}-2-METHYLPROPYLPHOSPHONIC ACID C₁₇ H₂₂ N O₆ P S BZVYQWLRCHLAGK-QGZVFWFLSA-N		Ligand Interaction
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Ligand Interaction

Binding Affinity Annotations
ID	Source	Binding Affinity
FIN	PDBBind: 1ZVX	Ki: 0.6 (nM) from 1 assay(s)
	BindingDB: 1ZVX	Ki: 0.6 (nM) from 1 assay(s)
	BindingDB: 1ZVX	IC50: 1.4 (nM) from 1 assay(s)
	Binding MOAD: 1ZVX	Ki: 0.6 (nM) from 1 assay(s)