4JM8

Crystal structure of Cytochrome C Peroxidase W191G-Gateless in complex with 2,6-diaminopyridine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.117 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Blind prediction of charged ligand binding affinities in a model binding site.

Rocklin, G.J.Boyce, S.E.Fischer, M.Fish, I.Mobley, D.L.Shoichet, B.K.Dill, K.A.

(2013) J.Mol.Biol. 425: 4569-4583

  • DOI: 10.1016/j.jmb.2013.07.030
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Predicting absolute protein-ligand binding affinities remains a frontier challenge in ligand discovery and design. This becomes more difficult when ionic interactions are involved because of the large opposing solvation and electrostatic attraction e ...

    Predicting absolute protein-ligand binding affinities remains a frontier challenge in ligand discovery and design. This becomes more difficult when ionic interactions are involved because of the large opposing solvation and electrostatic attraction energies. In a blind test, we examined whether alchemical free-energy calculations could predict binding affinities of 14 charged and 5 neutral compounds previously untested as ligands for a cavity binding site in cytochrome c peroxidase. In this simplified site, polar and cationic ligands compete with solvent to interact with a buried aspartate. Predictions were tested by calorimetry, spectroscopy, and crystallography. Of the 15 compounds predicted to bind, 13 were experimentally confirmed, while 4 compounds were false negative predictions. Predictions had a root-mean-square error of 1.95 kcal/mol to the experimental affinities, and predicted poses had an average RMSD of 1.7Å to the crystallographic poses. This test serves as a benchmark for these thermodynamically rigorous calculations at predicting binding affinities for charged compounds and gives insights into the existing sources of error, which are primarily electrostatic interactions inside proteins. Our experiments also provide a useful set of ionic binding affinities in a simplified system for testing new affinity prediction methods.


    Related Citations: 
    • Docking to a water-filled model binding site in Cytochrome c Peroxidase
      Barelier, S.,Boyce, S.E.,Fischer, M.,Fish, I.,Goodin, D.B.,Shoichet, B.K.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th Street, San Francisco, CA 94143-2550, USA; Biophysics Graduate Program, University of California San Francisco, 1700 4th Street, San Francisco, CA 94143-2550, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c peroxidase
A
289Saccharomyces cerevisiae (strain RM11-1a)Mutation(s): 2 
EC: 1.11.1.-
Find proteins for B3LRE1 (Saccharomyces cerevisiae (strain RM11-1a))
Go to UniProtKB:  B3LRE1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
26D
Query on 26D

Download SDF File 
Download CCD File 
A
PYRIDINE-2,6-DIAMINE
C5 H7 N3
VHNQIURBCCNWDN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.117 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.843α = 90.00
b = 74.519β = 90.00
c = 106.464γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
PDB_EXTRACTdata extraction
REFMACrefinement
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-01
    Type: Initial release
  • Version 1.1: 2013-10-09
    Type: Database references
  • Version 1.2: 2013-11-20
    Type: Database references