1ZP5 | pdb_00001zp5

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

• PDB DOI: https://doi.org/10.2210/pdb1ZP5/pdb

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


• Deposited: 2005-05-16 Released: 2005-12-06 
• Deposition Author(s): Campestre, C., Agamennone, M., Tortorella, P., Preziuso, S., Biasone, A., Gavuzzo, E., Pochetti, G., Mazza, F., Tschesche, H., Gallina, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.251 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

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.

(2006) Bioorg Med Chem Lett 16: 20-24

• PubMed: 16242329 
• DOI: https://doi.org/10.1016/j.bmcl.2005.09.057
• Primary Citation of Related Structures:  
  1ZP5


• PubMed Abstract: 
  

  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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Organizational Affiliation: 

Dipartimento di Scienze del Farmaco, Università degli Studi 'G. d'Annunzio', Chieti, Italy.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 18.63 kDa 
• Atom Count: 1,435 
• Modeled Residue Count: 163 
• Deposited Residue Count: 163 
• Unique protein chains: 1

Macromolecules

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 GTEx:  ENSG00000118113

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2NI	F [auth A]	N-{2-[(4'-CYANO-1,1'-BIPHENYL-4-YL)OXY]ETHYL}-N'-HYDROXY-N-METHYLUREA C17 H17 N3 O3 GVMUNGGWXRKCEU-UHFFFAOYSA-N
ZN	D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
2NI	BindingDB:  1ZP5	IC50: 1.20e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.251 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.387	α = 90
b = 52.675	β = 90
c = 67.331	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-06 
Deposition Author(s): Campestre, C., Agamennone, M., Tortorella, P., Preziuso, S., Biasone, A., Gavuzzo, E., Pochetti, G., Mazza, F., Tschesche, H., Gallina, C.

Revision History  

• Version 1.0: 2005-12-06
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2018-01-24
  Changes: Database references
• Version 1.5: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description