5L79

Crystal structure of MMP12 in complex with RXP470.1 conjugated with fluorophore Cy5,5 in space group P21212.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Synthesis and in Vitro and in Vivo Evaluation of MMP-12 Selective Optical Probes.

Bordenave, T.Helle, M.Beau, F.Georgiadis, D.Tepshi, L.Bernes, M.Ye, Y.Levenez, L.Poquet, E.Nozach, H.Razavian, M.Toczek, J.Stura, E.A.Dive, V.Sadeghi, M.M.Devel, L.

(2016) Bioconjug.Chem. 27: 2407-2417

  • DOI: 10.1021/acs.bioconjchem.6b00377
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In designing new tracers consisting of a small peptide conjugated to a reporter of comparable size, particular attention needs to be paid to the selection of the reporter group, which can dictate both the in vitro and the in vivo performances of the ...

    In designing new tracers consisting of a small peptide conjugated to a reporter of comparable size, particular attention needs to be paid to the selection of the reporter group, which can dictate both the in vitro and the in vivo performances of the whole conjugate. In the case of fluorescent tracers, this is particularly true given the large numbers of available dye moieties differing in their structures and properties. Here, we have investigated the in vitro and in vivo properties of a novel series of MMP-12 selective probes composed of cyanine dyes varying in their structure, net charge, and hydrophilic character, tethered through a linker to a potent and specific MMP-12 phosphinic pseudopeptide inhibitor. The impact of linker length has been also explored. The crystallographic structure of one tracer in complex with MMP-12 has been obtained, providing the first crystal structure of a Cy5.5-derived probe and confirming that the binding of the targeting moiety is unaffected. MMP-12 remains the tracers' privileged target, as attested by their affinity selectivity profile evaluated in solution toward a panel of 12 metalloproteases. In vivo assessment of four selected probes has highlighted not only the impact of the dye structure but also that of the linker length on the probes' blood clearance rates and their biodistributions. These experiments have also provided valuable data on the stability of the dye moieties in vivo. This has permitted the identification of one probe, which combines favorable binding to MMP-12 in solution and on cells with optimized in vivo performance including blood clearance rate suitable for short-time imaging. Through this series of tracers, we have identified various critical factors modulating the tracers' in vivo behavior, which is both useful for the development and optimization of MMP-12 selective radiolabeled tracers and informative for the design of fluorescent probes in general.


    Organizational Affiliation

    Service d'ingénierie moléculaire des protéines (SIMOPRO), IBITECS, CEA, Université Paris-Saclay , Gif-sur-Yvette F-91191, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Macrophage metalloelastase
A
159Homo sapiensMutation(s): 1 
Gene Names: MMP12 (HME)
EC: 3.4.24.65
Find proteins for P39900 (Homo sapiens)
Go to Gene View: MMP12
Go to UniProtKB:  P39900
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
R47
Query on R47

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A
N-[(2S)-3-[(S)-(4-bromophenyl)(hydroxy)phosphoryl]-2-{[3-(3'-chlorobiphenyl-4-yl)-1,2-oxazol-5-yl]methyl}propanoyl]-L-alpha-glutamyl-L-alpha-glutamine
RXP470.1
C35 H35 Br Cl N4 O10 P
PTUCPHGSAFOJAU-MGONOCMRSA-N
 Ligand Interaction
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
6PJ
Query on 6PJ

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A
CY5.5-PEG2
C50 H65 N3 O16 S4
ZUDVNXAIDCSDCG-HWRGAIJTSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
R47Ki: 0.2 - 0.3 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.206 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 70.900α = 90.00
b = 62.790β = 90.00
c = 37.740γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
MOLREPphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-09-14
    Type: Initial release
  • Version 1.1: 2016-09-21
    Type: Database references
  • Version 1.2: 2016-10-26
    Type: Database references
  • Version 2.0: 2018-06-20
    Type: Atomic model, Data collection, Derived calculations, Structure summary