4QKZ

X-ray structure of the catalytic domain of MMP-8 with the inhibitor ML115

• PDB DOI: https://doi.org/10.2210/pdb4QKZ/pdb

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


• Deposited: 2014-06-10 Released: 2015-06-17 
• Deposition Author(s): Pochetti, G., Montanari, R., Capelli, D., Tortorella, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.194 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 

Literature

Bone-Seeking Matrix Metalloproteinase Inhibitors for the Treatment of Skeletal Malignancy.

Laghezza, A., Piemontese, L., Brunetti, L., Caradonna, A., Agamennone, M., Di Pizio, A., Pochetti, G., Montanari, R., Capelli, D., Tauro, M., Loiodice, F., Tortorella, P.

(2020) Pharmaceuticals (Basel) 13

• PubMed: 32492898 
• DOI: https://doi.org/10.3390/ph13060113
• Primary Citation of Related Structures:  
  4QKZ


• PubMed Abstract: 
  

  Matrix metalloproteinases (MMPs) are a family of enzymes involved at different stages of cancer progression and metastasis. We previously identified a novel class of bisphosphonic inhibitors, selective for MMPs crucial for bone remodeling, such as MMP-2. Due to the increasing relevance of specific MMPs at various stages of tumor malignancy, we focused on improving potency towards certain isoforms. Here, we tackled MMP-9 because of its confirmed role in tumor invasion, metastasis, angiogenesis, and immuno-response, making it an ideal target for cancer therapy. Using a computational analysis, we designed and characterized potent MMP-2/MMP-9 inhibitors. This is a promising approach to develop and clinically translate inhibitors that could be used in combination with standard care therapy for the treatment of skeletal malignancies.

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Organizational Affiliation: 

Department of Pharmacy and Pharmaceutical Sciences, University of Bari "A. Moro", via E. Orabona 4, 70125 Bari, Italy.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 18.93 kDa 
• Atom Count: 1,469 
• Modelled 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QZK	F [auth A]	{[(biphenyl-4-ylsulfonyl)amino]methanediyl}bis(phosphonic acid) C13 H15 N O8 P2 S SZOCMHFDKYEXMY-UHFFFAOYSA-N
MES	G [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.194 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.91	α = 90
b = 68.69	β = 90
c = 70.69	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-06-17 
Deposition Author(s): Pochetti, G., Montanari, R., Capelli, D., Tortorella, P.

Revision History  

• Version 1.0: 2015-06-17
  Type: Initial release
  
• Version 1.1: 2023-07-26
  Changes: Database references, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Refinement description