6T5C

Human Carbonic anhydrase II bound by anthracene-9-sulfonamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.126 

wwPDB Validation 3D Report Full Report



Literature

Isoform-Selective Enzyme Inhibitors by Exploring Pocket Size According to the Lock-and-Key Principle.

Dudutiene, V.Zubriene, A.Kairys, V.Smirnov, A.Smirnoviene, J.Leitans, J.Kazaks, A.Tars, K.Manakova, L.Grazulis, S.Matulis, D.

(2020) Biophys J 

  • DOI: 10.1016/j.bpj.2020.08.037
  • Primary Citation of Related Structures:  
    6T4O, 6T4N, 6T4P, 6T5P, 6T5Q, 6T5C, 6T81

  • PubMed Abstract: 
  • In the design of high-affinity and enzyme isoform-selective inhibitors, we applied an approach of augmenting the substituents attached to the benzenesulfonamide scaffold in three ways, namely, substitutions at the 3,5- or 2,4,6-positions or expansion ...

    In the design of high-affinity and enzyme isoform-selective inhibitors, we applied an approach of augmenting the substituents attached to the benzenesulfonamide scaffold in three ways, namely, substitutions at the 3,5- or 2,4,6-positions or expansion of the condensed ring system. The increased size of the substituents determined the spatial limitations of the active sites of the 12 catalytically active human carbonic anhydrase (CA) isoforms until no binding was observed because of the inability of the compounds to fit in the active site. This approach led to the discovery of high-affinity and high-selectivity compounds for the anticancer target CA IX and antiobesity target CA VB. The x-ray crystallographic structures of compounds bound to CA IX showed the positions of the bound compounds, whereas computational modeling confirmed that steric clashes prevent the binding of these compounds to other isoforms and thus avoid undesired side effects. Such an approach, based on the Lock-and-Key principle, could be used for the development of enzyme-specific drug candidate compounds.


    Organizational Affiliation

    Department of Biothermodynamics and Drug Design, Vilnius University, Vilnius, Lithuania. Electronic address: matulis@ibt.lt.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
carbonic anhydrase 2A260Homo sapiensMutation(s): 0 
Gene Names: CA2
EC: 4.2.1.1
Find proteins for P00918 (Homo sapiens)
Explore P00918 
Go to UniProtKB:  P00918
NIH Common Fund Data Resources
PHAROS  P00918
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MJT
Query on MJT

Download CCD File 
A
anthracene-9-sulfonamide
C14 H11 N O2 S
FKFZOFZWJNHJDE-UHFFFAOYSA-N
 Ligand Interaction
BCN
Query on BCN

Download CCD File 
A
BICINE
C6 H13 N O4
FSVCELGFZIQNCK-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.126 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.309α = 90
b = 41.313β = 104.26
c = 71.971γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-10-14
    Type: Initial release