5G0B

An unusual natural product primary sulfonamide: synthesis, carbonic anhydrase inhibition and protein x-ray structure of Psammaplin C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.132 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

An Unusual Natural Product Primary Sulfonamide: Synthesis, Carbonic Anhydrase Inhibition and Protein X-Ray Structures of Psammaplin C.

Mujumdar, P.Teruya, K.Tonissen, K.F.Vullo, D.Supuran, C.T.Peat, T.S.Poulsen, S.

(2016) J.Med.Chem. 59: 5462

  • DOI: 10.1021/acs.jmedchem.6b00443
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Psammaplin C is one of only two described natural product primary sulfonamides. Here we report the synthesis of psammaplin C and evaluate the inhibition profile against therapeutically relevant carbonic anhydrase (CA) zinc metalloenzymes. The compoun ...

    Psammaplin C is one of only two described natural product primary sulfonamides. Here we report the synthesis of psammaplin C and evaluate the inhibition profile against therapeutically relevant carbonic anhydrase (CA) zinc metalloenzymes. The compound exhibited unprecedented inhibition of an important cancer-associated isozyme, hCA XII, with a Ki of 0.79 nM. The compound also displayed good isoform selectivity for hCA XII over other CAs. We present the first reported protein X-ray crystal structures of psammaplin C in complex with human CAs. We engineered the easily crystallized hCA II enzyme to mimic both the hCA IX and hCA XII binding sites and then utilized protein X-ray crystallography to determine the binding pose of psammaplin C within the hCA II, hCA IX, and hCA XII mimic active sites, all to high resolution. This is the first time a natural product primary sulfonamide inhibitor has been assessed for inhibition and binding to CAs.


    Organizational Affiliation

    Eskitis Institute for Drug Discovery, Griffith University , Don Young Road, Nathan, Queensland 4111, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CARBONIC ANHYDRASE 2
A
260Homo sapiensMutation(s): 10 
Gene Names: CA2
EC: 4.2.1.1
Find proteins for P00918 (Homo sapiens)
Go to Gene View: CA2
Go to UniProtKB:  P00918
Small Molecules
Ligands 4 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
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SO4Ki: 89000000 - >300000000 nM (96) BINDINGDB
CLKi: 200000000 nM (96) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.132 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 41.706α = 90.00
b = 41.286β = 104.19
c = 72.130γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-05-25
    Type: Initial release
  • Version 1.1: 2016-06-22
    Type: Database references