ISDA

Deposition Date 2005-05-16

Release Date 2005-12-06

Last Version Date 2023-08-23

Entry Detail

PDB ID:

1ZP5

Keywords:

HYDROLASE

Title:

Crystal structure of the complex between MMP-8 and a N-hydroxyurea inhibitor

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Escherichia coli BL21

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.80 Å

R-Value Free:

0.25

R-Value Work:

0.21

R-Value Observed:

0.21

Space Group:

P 21 21 21

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Neutrophil collagenase
Gene (Uniprot):MMP8
Chain IDs:A
Chain Length:163
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P22894 Pfam ID:PF00413 EC:3.4.24.34

Ligand Molecules

2NI

Primary Citation

N-Hydroxyurea as zinc binding group in matrix metalloproteinase inhibition: Mode of binding in a complex with MMP-8.

Campestre, C, Agamennone, M, Tortorella, P, Preziuso, S, Biasone, A, Gavuzzo, E, Pochetti, G, Mazza, F, Hiller, O, Tschesche, H, Consalvi, V, Gallina, C, Muri, E.M, Nieto, M.J, Sindelar, R.D, Williamson, J.S, Grams, F, Crimmin, M, Hinnes, L, Huxley, P, Pieper, M, Tschesche, H, Bode, W, Hajduck, P.J, Sheppard, G, Nettesheim, D.G, Olejniczak, E.T, Shuker, S.B, Meadows, R.P, Steinman, D.H, Carrera, G.M, Marcotte, P.A, Severin, J, Walter, K, Smith, H, Gubbins, E, Simmer, R, Holzman, T.F, Morgan, D.W, Davidsen, S.K, Summers, J.B, Fesik, S.W, Michaelides, M.R, Dellaria, J.F, Gong, J, Holms, J.H, Bouska, J.J, Stacey, J, Wada, C.K, Heyman, H.R, Curtin, M.L, Guo, Y, Goodfellow, C.L, Elmore, I.B, Albert, D.H, Magoc, T.J, Marcotte, P.A, Morgan, D.W, Davidsen, S.K.Show

Bioorg.Med.Chem.Lett. 16 20 24 (2006)

PMID: 16242329 DOI: 10.1016/j.bmcl.2005.09.057

Abstact

The first crystallographic structure of an N-hydroxyurea inhibitor bound into the active site of a matrix metalloproteinase is reported. The ligand and three other analogues were prepared and studied as inhibitors of MMP-2, MMP-3, and MMP-8. The crystal structure of the complex with MMP-8 shows that the N-hydroxyurea, contrary to the analogous hydroxamate, binds the catalytic zinc ion in a monodentate rather than bidentate mode and with high out-of-plane distortion of the amide bonds.

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Primary Citation of related structures