3N2V

Crystal structure of the catalytic domain of human MMP12 complexed with the inhibitor N-hydroxy-2-(N-hydroxyethyl)biphenyl-4-ylsulfonamido)acetamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.132 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-based approach to nanomolar, water soluble matrix metalloproteinases inhibitors (MMPIs).

Attolino, E.Calderone, V.Dragoni, E.Fragai, M.Richichi, B.Luchinat, C.Nativi, C.

(2010) Eur.J.Med.Chem. 45: 5919-5925

  • DOI: 10.1016/j.ejmech.2010.09.057
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • N-arylsulfonyl-based MMPs inhibitors (MMPIs) are among the most prominent inhibitors possessing nanomolar affinity. However, their poor bioavailability remains critical for the drug development of this family of molecules. The structural analysis of ...

    N-arylsulfonyl-based MMPs inhibitors (MMPIs) are among the most prominent inhibitors possessing nanomolar affinity. However, their poor bioavailability remains critical for the drug development of this family of molecules. The structural analysis of the complex of NNGH (the most representative member of the family) with MMP-12 provided us with the basis to effectively design simple NNGH analogues with enhanced solubility in water. Following this approach, the sec-butyl residue, not directly involved in the binding with MMP, has been replaced with hydrophilic residues thus yielding new potent inhibitors soluble in water.


    Related Citations: 
    • 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


    Organizational Affiliation

    ProtEra s.r.l. viale delle Idee, 22 I-50019 Sesto F.no (FI), Italy.




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
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
JT5
Query on JT5

Download SDF File 
Download CCD File 
A
N~2~-(biphenyl-4-ylsulfonyl)-N-hydroxy-N~2~-(2-hydroxyethyl)glycinamide
C16 H18 N2 O5 S
QQDWEVONJRXVDB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
JT5Ki: 31 nM (99) BINDINGDB
JT5Ki: 31 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.132 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 51.614α = 90.00
b = 60.277β = 115.20
c = 54.186γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
CrysalisProdata collection
MOSFLMdata reduction
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-05-19 
  • Released Date: 2010-11-10 
  • Deposition Author(s): Calderone, V.

Revision History 

  • Version 1.0: 2010-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description