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 
  • R-Value Observed: 0.136 

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:  
    3N2U, 3N2V

  • 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 the ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Macrophage metalloelastase A158Homo sapiensMutation(s): 1 
Gene Names: MMP12HME
EC: 3.4.24.65
Find proteins for P39900 (Homo sapiens)
Explore P39900 
Go to UniProtKB:  P39900
NIH Common Fund Data Resources
PHAROS:  P39900
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JT5
Query on JT5

Download Ideal Coordinates 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
ZN
Query on ZN

Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
JT5Ki :  31   nM  PDBBind
JT5Ki:  31   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.136 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.614α = 90
b = 60.277β = 115.2
c = 54.186γ = 90
Software Package:
Software NamePurpose
CrysalisProdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



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
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description