Crystal structure of MMP9 in complex with inhibitor BE4.

Experimental Data Snapshot

  • Resolution: 1.10 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 

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Ligand Structure Quality Assessment 

This is version 2.1 of the entry. See complete history


Development of Thioaryl-Based Matrix Metalloproteinase-12 Inhibitors with Alternative Zinc-Binding Groups: Synthesis, Potentiometric, NMR, and Crystallographic Studies.

Nuti, E.Cuffaro, D.Bernardini, E.Camodeca, C.Panelli, L.Chaves, S.Ciccone, L.Tepshi, L.Vera, L.Orlandini, E.Nencetti, S.Stura, E.A.Santos, M.A.Dive, V.Rossello, A.

(2018) J Med Chem 61: 4421-4435

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b00096
  • Primary Citation of Related Structures:  
    6EKN, 6ELA, 6ENM, 6EOX, 6ESM

  • PubMed Abstract: 

    Matrix metalloproteinase-12 (MMP-12) selective inhibitors could play a role in the treatment of lung inflammatory and cardiovascular diseases. In the present study, the previously reported 4-methoxybiphenylsulfonyl hydroxamate and carboxylate based inhibitors (1b and 2b) were modified to enhance their selectivity for MMP-12. In the newly synthesized thioaryl derivatives, the nature of the zinc binding group (ZBG) and the sulfur oxidation state were changed. Biological assays carried out in vitro on human MMPs with the resulting compounds led to identification of a sulfide, 4a, bearing an N-1-hydroxypiperidine-2,6-dione (HPD) group as new ZBG. Compound 4a is a promising hit compound since it displayed a nanomolar affinity for MMP-12 with a marked selectivity over MMP-9, MMP-1, and MMP-14. Solution complexation studies with Zn 2+ were performed to characterize the chelating abilities of the new compounds and confirmed the bidentate binding mode of HPD derivatives. X-ray crystallography studies using MMP-12 and MMP-9 catalytic domains were carried out to rationalize the biological results.

  • Organizational Affiliation

    Dipartimento di Farmacia , Università di Pisa , Via Bonanno 6 , 56126 Pisa , Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Matrix metalloproteinase-9,Matrix metalloproteinase-9160Homo sapiensMutation(s): 1 
Gene Names: MMP9CLG4B
UniProt & NIH Common Fund Data Resources
Find proteins for P14780 (Homo sapiens)
Explore P14780 
Go to UniProtKB:  P14780
PHAROS:  P14780
GTEx:  ENSG00000100985 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14780
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B9Z (Subject of Investigation/LOI)
Query on B9Z

Download Ideal Coordinates CCD File 
G [auth A](2~{S})-2-[2-[4-(4-methoxyphenyl)phenyl]sulfanylphenyl]pentanedioic acid
C24 H22 O5 S
Query on PZE

Download Ideal Coordinates CCD File 
H [auth A]piperazine
C4 H10 N2
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
Query on CA

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
Binding Affinity Annotations 
IDSourceBinding Affinity
B9Z BindingDB:  6ESM IC50: 2960 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.10 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.69α = 90
b = 39.69β = 90
c = 163.66γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 2.0: 2018-06-06
    Changes: Atomic model, Data collection, Database references
  • Version 2.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description