Crystal structure of an MMP twin carboxylate based inhibitor LC20 in complex with the MMP-9 catalytic domain

Experimental Data Snapshot

  • Resolution: 1.94 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 

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Crystallization of bi-functional ligand protein complexes.

Antoni, C.Vera, L.Devel, L.Catalani, M.P.Czarny, B.Cassar-Lajeunesse, E.Nuti, E.Rossello, A.Dive, V.Stura, E.A.

(2013) J Struct Biol 182: 246-254

  • DOI: https://doi.org/10.1016/j.jsb.2013.03.015
  • Primary Citation of Related Structures:  
    4H1Q, 4H2E, 4H30, 4H3X, 4H49, 4H76, 4H82, 4H84, 4HMA, 4I03

  • PubMed Abstract: 

    Homodimerization is important in signal transduction and can play a crucial role in many other biological systems. To obtaining structural information for the design of molecules able to control the signalization pathways, the proteins involved will have to be crystallized in complex with ligands that induce dimerization. Bi-functional drugs have been generated by linking two ligands together chemically and the relative crystallizability of complexes with mono-functional and bi-functional ligands has been evaluated. There are problems associated with crystallization with such ligands, but overall, the advantages appear to be greater than the drawbacks. The study involves two matrix metalloproteinases, MMP-12 and MMP-9. Using flexible and rigid linkers we show that it is possible to control the crystal packing and that by changing the ligand-enzyme stoichiometric ratio, one can toggle between having one bi-functional ligand binding to two enzymes and having the same ligand bound to each enzyme. The nature of linker and its point of attachment on the ligand can be varied to aid crystallization, and such variations can also provide valuable structural information about the interactions made by the linker with the protein. We report here the crystallization and structure determination of seven ligand-dimerized complexes. These results suggest that the use of bi-functional drugs can be extended beyond the realm of protein dimerization to include all drug design projects.

  • Organizational Affiliation

    CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines-SIMOPRO, Gif-sur-Yvette F-91191, France. antoni.claudia@cea.fr

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Matrix metalloproteinase-9
A, B
160Homo sapiensMutation(s): 1 
Gene Names: CLG4BMMP9
UniProt & NIH Common Fund Data Resources
Find proteins for P14780 (Homo sapiens)
Explore P14780 
Go to UniProtKB:  P14780
GTEx:  ENSG00000100985 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14780
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 0ZD

Download Ideal Coordinates CCD File 
H [auth A]N,N'-bis(2-[(biphenyl-4ylsulfonyl)[(2R)-1-hydroxy-3-methyl-1-oxobutan-2-yl]-amino]ethyl)benzene-1,3-dicarboxamide
C46 H50 N4 O10 S2
Query on MLT

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Y [auth B]D-MALATE
C4 H6 O5
Query on PEG

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EA [auth B]
FA [auth B]
O [auth A]
P [auth A]
Q [auth A]
EA [auth B],
FA [auth B],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A]
C4 H10 O3
Query on GOL

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AA [auth B],
I [auth A],
J [auth A],
K [auth A],
Z [auth B]
C3 H8 O3
Query on PGO

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BA [auth B]
CA [auth B]
DA [auth B]
L [auth A]
M [auth A]
BA [auth B],
CA [auth B],
DA [auth B],
L [auth A],
M [auth A],
N [auth A]
C3 H8 O2
Query on ZN

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C [auth A],
D [auth A],
T [auth B],
U [auth B]
Query on CA

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E [auth A]
F [auth A]
G [auth A]
V [auth B]
W [auth B]
E [auth A],
F [auth A],
G [auth A],
V [auth B],
W [auth B],
X [auth B]
Binding Affinity Annotations 
IDSourceBinding Affinity
0ZD BindingDB:  4HMA IC50: 26 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.94 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.87α = 90
b = 98.24β = 90
c = 47.44γ = 90
Software Package:
Software NamePurpose
DNAdata collection
XDSdata reduction
XDSdata 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: 2013-04-24
    Type: Initial release
  • Version 1.1: 2013-05-01
    Changes: Database references
  • Version 1.2: 2014-10-08
    Changes: Structure summary
  • Version 1.3: 2015-08-12
    Changes: Database references
  • Version 1.4: 2017-08-09
    Changes: Data collection, Refinement description, Source and taxonomy
  • Version 1.5: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description