3P4V

Human carbonic anhydrase II in complex with (+)-Xylariamide A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Natural Product-Based Phenols as Novel Probes for Mycobacterial and Fungal Carbonic Anhydrases.

Davis, R.A.Hofmann, A.Osman, A.Hall, R.A.Muhlschlegel, F.A.Vullo, D.Innocenti, A.Supuran, C.T.Poulsen, S.A.

(2011) J.Med.Chem. 54: 1682-1692

  • DOI: 10.1021/jm1013242
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In order to discover novel probes that may help in the investigation and control of infectious diseases through a new mechanism of action, we have evaluated a library of phenol-based natural products (NPs) for enzyme inhibition against four recently ...

    In order to discover novel probes that may help in the investigation and control of infectious diseases through a new mechanism of action, we have evaluated a library of phenol-based natural products (NPs) for enzyme inhibition against four recently characterized pathogen β-family carbonic anhydrases (CAs). These include CAs from Mycobacterium tuberculosis, Candida albicans, and Cryptococcus neoformans as well as α-family human CA I and CA II for comparison. Many of the NPs selectively inhibited the mycobacterial and fungal β-CAs, with the two best performing compounds displaying submicromolar inhibition with a preference for fungal over human CA inhibition of more than 2 orders of magnitude. These compounds provide the first example of non-sulfonamide inhibitors that display β over α CA enzyme selectivity. Structural characterization of the library compounds in complex with human CA II revealed a novel binding mode whereby a methyl ester interacts via a water molecule with the active site zinc.


    Organizational Affiliation

    Eskitis Institute, Griffith University, Nathan, Queensland 4111, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbonic anhydrase 2
A
260Homo sapiensMutation(s): 0 
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 2 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
PMX
Query on PMX

Download SDF File 
Download CCD File 
A
3-chloro-N-[(2E)-4-methoxy-4-oxobut-2-enoyl]-L-tyrosine
(+)-Xylariamide A
C14 H14 Cl N O6
KCOKHEIACSQLBQ-YEZKRMTDSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PMXKi: 8000 nM BINDINGMOAD
PMXKi: 8000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.162 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.312α = 90.00
b = 41.298β = 104.89
c = 72.427γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXphasing
PHENIXrefinement
Blu-Icedata collection
XDSdata reduction
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-04-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance