5NYA

Carbonic Anhydrase II Inhibitor RA13


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.117 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

Pecina, A.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.

(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 including quantum effects. Here, we demonstrate the ranking power of the ...

    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 including quantum effects. Here, we demonstrate the ranking power of the semiempirical quantum mechanics (SQM)/implicit solvent (COSMO) scoring function by using a challenging set of 10 inhibitors binding to carbonic anhydrase II through Zn 2+ in the active site. This new dataset consists of the high-resolution (1.1-1.4 Å) crystal structures and experimentally determined inhibitory constant (K i ) values. It allows for evaluation of the common approximations, such as representing the solvent implicitly or by using a single target conformation combined with a set of ligand docking poses. SQM/COSMO attained a good correlation of R 2 of 0.56-0.77 with the experimental inhibitory activities, benefiting from 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

    Regional Centre of Advanced Technologies and Materials, Palacký University, 77146, Olomouc, Czech Republic.,Palacký University, 77146, Olomouc, Czech Republic.,Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Current address: Department of Chemistry, Pondicherry University, Puducherry, 605014, India.,Institute of Molecular Genetics of, Czech Academy of Sciences, Videnska 1083, 14220, Prague 4, 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 3 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
GUA
Query on GUA

Download SDF File 
Download CCD File 
A
GLUTARIC ACID
C5 H8 O4
JFCQEDHGNNZCLN-UHFFFAOYSA-N
 Ligand Interaction
FB2
Query on FB2

Download SDF File 
Download CCD File 
A
benzenesulfonamide
C6 H7 N O2 S
KHBQMWCZKVMBLN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.117 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.227α = 90.00
b = 41.209β = 104.29
c = 72.152γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

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: 2018-01-24
    Type: Experimental preparation
  • Version 1.2: 2018-04-18
    Type: Data collection, Database references