5N5K

Human catalytic MMP-12 in complex with 5-(1,2-dithiolan-3-yl)-N-(3-hydroxypropyl)pentanamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Lipoyl-Homotaurine Derivative (ADM_12) Reverts Oxaliplatin-Induced Neuropathy and Reduces Cancer Cells Malignancy by Inhibiting Carbonic Anhydrase IX (CAIX).

Fragai, M.Comito, G.Di Cesare Mannelli, L.Gualdani, R.Calderone, V.Louka, A.Richichi, B.Francesconi, O.Angeli, A.Nocentini, A.Gratteri, P.Chiarugi, P.Ghelardini, C.Tadini-Buoninsegni, F.Supuran, C.T.Nativi, C.

(2017) J. Med. Chem. 60: 9003-9011

  • DOI: 10.1021/acs.jmedchem.7b01237
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Oxaliplatin (OXA) is a valuable and largely used cancer drug which induces a serious and intractable neuropathy. The lipoyl-homotaurine derivative (ADM_12) reverts in vivo OXA-induced neuropathy, and it is an effective antagonist of the nociceptive s ...

    Oxaliplatin (OXA) is a valuable and largely used cancer drug which induces a serious and intractable neuropathy. The lipoyl-homotaurine derivative (ADM_12) reverts in vivo OXA-induced neuropathy, and it is an effective antagonist of the nociceptive sensor channel TRPA1. Unprecedentedly, this safe analgesic showed a synergy with OXA in vitro and proved to inhibit CA IX, a relevant therapeutic target, clearly interfering with pancreatic cancer cells' aggressiveness.


    Organizational Affiliation

    Department of Chemistry, University of Florence , via della Lastruccia 3-13, 50019 Sesto Fiorentino, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Macrophage metalloelastase
A
156Homo 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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HAE
Query on HAE

Download SDF File 
Download CCD File 
A
ACETOHYDROXAMIC ACID
C2 H5 N O2
RRUDCFGSUDOHDG-UHFFFAOYSA-N
 Ligand Interaction
8NW
Query on 8NW

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Download CCD File 
A
5-[(3~{S})-1,2-dithiolan-3-yl]-~{N}-(3-oxidanylpropyl)pentanamide
C11 H21 N O2 S2
QPQPASXMSHOHIW-JTQLQIEISA-N
 Ligand Interaction
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.167 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 50.790α = 90.00
b = 60.170β = 114.61
c = 53.730γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-02-14 
  • Released Date: 2017-11-01 
  • Deposition Author(s): Calderone, V.

Revision History 

  • Version 1.0: 2017-11-01
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Database references