5NY1

Carbonic Anhydrase II Inhibitor RA10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.137 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Ranking Power of the SQM/COSMO Scoring Function on Carbonic Anhydrase II-Inhibitor Complexes.

Brynda, J.Vrzal, L.Gnanasekaran, R.Horejsi, M.Eyrilmez, S.M.Rezac, J.Lepsik, M.Rezacova, P.Hobza, P.Majer, P.Veverka, V.Fanfrlik, J.Pecina, A.

(2018) Chemphyschem 19: 873-879

  • DOI: 10.1002/cphc.201701104
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Accurate prediction of protein-ligand binding affinities is essential for hit-to-lead optimization and virtual screening. The reliability of scoring functions can be improved by implementing of quantum effects. Here, we demonstrate the ranking power ...

    Accurate prediction of protein-ligand binding affinities is essential for hit-to-lead optimization and virtual screening. The reliability of scoring functions can be improved by implementing of quantum effects. Here, we demonstrate the ranking power of the semiempirical quantum mechanics (SQM)/implicit solvent (COSMO) scoring function using a challenging set of 10 inhibitors binding to carbonic anhydrase II via Zn2+ in the active site. This new dataset consists of the high-resolution (1.1 - 1.4 Å) crystal structures and experimentally determined Ki values. It allowed us to evaluate the common approximations, such as representing the solvent implicitly or using a single target conformation combined with a set of ligand docking poses. The SQM/COSMO attained good correlation of R2 0.56 - 0.77 with the experimental inhibitory activities, benefiting from the careful handling of both noncovalent interactions (e.g. charge transfer) and solvation. This proof-of-concept study of SQM/COSMO ranking for metalloprotein-ligand systems demonstrates its potential for hit-to-lead applications.


    Organizational Affiliation

    Institute of Organic Chemistry and Biochemistry and Gilead Science and IOCB Research Center, Academy of Sciences of the Czech Republic, Department of Computational Chemistry, Flemingovo nam. 2, 166 10, Prague, CZECH REPUBLIC.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbonic anhydrase 2
A
257Homo 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
9E5
Query on 9E5

Download SDF File 
Download CCD File 
A
3,6,7-trimethyl-~{N}-[(4-sulfamoylphenyl)methyl]-1-benzofuran-2-carboxamide
C19 H20 N2 O4 S
UTFNKOUSVJRLOG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.137 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.147α = 90.00
b = 41.270β = 104.28
c = 72.147γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Czech Science FoundationCzech RepublicGA15-05677S
IMG of the Czech Academy of SciencesCzech RepublicRVO 61388963
IOCB of the Czech Academy of SciencesCzech RepublicRVO 68378050
Ministry of EducationCzech RepublicLO1304

Revision History 

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-04-18
    Type: Data collection, Database references