3F18

Crystal structure of the catalytic domain of human MMP12 complexed with the inhibitor 4-fluoro-N-(2-hydroxyethyl)-N-(2-nitroso-2-oxoethyl)benzenesulfonamide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Exploring the subtleties of drug-receptor interactions: the case of matrix metalloproteinases.

Bertini, I., Calderone, V., Fragai, M., Giachetti, A., Loconte, M., Luchinat, C., Maletta, M., Nativi, C., Yeo, K.J.

(2007) J.Am.Chem.Soc. 129: 2466-2475

  • DOI: 10.1021/ja065156z
  • Primary Citation of Related Structures:  
  • Also Cited By: 4GUY, 3RTU, 3RTT, 3RTS, 3N2V, 3N2U

  • PubMed Abstract: 

    • By solving high-resolution crystal structures of a large number (14 in this case) of adducts of matrix metalloproteinase 12 (MMP12) with strong, nanomolar, inhibitors all derived from a single ligand scaffold, it is shown that the energetics of the l ...

    By solving high-resolution crystal structures of a large number (14 in this case) of adducts of matrix metalloproteinase 12 (MMP12) with strong, nanomolar, inhibitors all derived from a single ligand scaffold, it is shown that the energetics of the ligand-protein interactions can be accounted for directly from the structures to a level of detail that allows us to rationalize for the differential binding affinity between pairs of closely related ligands. In each case, variations in binding affinities can be traced back to slight improvements or worsening of specific interactions with the protein of one or more ligand atoms. Isothermal calorimetry measurements show that the binding of this class of MMP inhibitors is largely enthalpy driven, but a favorable entropic contribution is always present. The binding enthalpy of acetohydroxamic acid (AHA), the prototype zinc-binding group in MMP drug discovery, has been also accurately measured. In principle, this research permits the planning of either improved inhibitors, or inhibitors with improved selectivity for one or another MMP. The present analysis is applicable to any drug target for which structural information on adducts with a series of homologous ligands can be obtained, while structural information obtained from in silico docking is probably not accurate enough for this type of study.

    Related Citations: 
    • X-ray structures of binary and ternary enzyme-product-inhibitor complexes of matrix metalloproteinases.
      Bertini, I.,Calderone, V.,Fragai, M.,Luchinat, C.,Mangani, S.,Terni, B.
      (2003) Angew.Chem.Int.Ed.Engl. 42: 2673

    Organizational Affiliation: 

    Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy. ivanobertini@cerm.unifi.it




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Macrophage metalloelastase
A
158Homo 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
HS5
Query on HS5
Download SDF File 
Download CCD File 
A
2-[(4-fluorophenyl)sulfonyl-(2-hydroxyethyl)amino]-N-oxo-ethanamide
4-fluoro-N-(2-hydroxyethyl)-N-(2-nitroso-2-oxoethyl)benzenesulfonamide
C10 H11 F N2 O5 S
XNNFYDODDRKLAF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA
Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HS5Kd: 29.5 nM BINDINGMOAD
HS5Kd: 39.5 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.166 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 51.709α = 90.00
b = 60.326β = 115.07
c = 53.992γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALAdata scaling
MAR345dtbdata collection
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2008-10-27 
  • Released Date: 2008-11-18 
  • Deposition Author(s): Calderone, V.

Revision History 

  • Version 1.0: 2008-11-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance