3HUQ

Thieno[3,2-b]thiophene in complex with T4 lysozyme L99A/M102Q


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site.

Boyce, S.E.Mobley, D.L.Rocklin, G.J.Graves, A.P.Dill, K.A.Shoichet, B.K.

(2009) J.Mol.Biol. 394: 747-763

  • DOI: 10.1016/j.jmb.2009.09.049
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We present a combined experimental and modeling study of organic ligand molecules binding to a slightly polar engineered cavity site in T4 lysozyme (L99A/M102Q). For modeling, we computed alchemical absolute binding free energies. These were blind te ...

    We present a combined experimental and modeling study of organic ligand molecules binding to a slightly polar engineered cavity site in T4 lysozyme (L99A/M102Q). For modeling, we computed alchemical absolute binding free energies. These were blind tests performed prospectively on 13 diverse, previously untested candidate ligand molecules. We predicted that eight compounds would bind to the cavity and five would not; 11 of 13 predictions were correct at this level. The RMS error to the measurable absolute binding energies was 1.8 kcal/mol. In addition, we computed "relative" binding free energies for six phenol derivatives starting from two known ligands: phenol and catechol. The average RMS error in the relative free energy prediction was 2.5 kcal/mol (phenol) and 1.1 kcal/mol (catechol). To understand these results at atomic resolution, we obtained x-ray co-complex structures for nine of the diverse ligands and for all six phenol analogs. The average RMSD of the predicted pose to the experiment was 2.0 A (diverse set), 1.8 A (phenol-derived predictions), and 1.2 A (catechol-derived predictions). We found that predicting accurate affinities and rank-orderings required near-native starting orientations of the ligand in the binding site. Unanticipated binding modes, multiple ligand binding, and protein conformational change all proved challenging for the free energy methods. We believe that these results can help guide future improvements in physics-based absolute binding free energy methods.


    Organizational Affiliation

    Graduate Group in Chemistry and Chemical Biology, University of California-San Francisco, San Francisco, CA 94158-2518, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme
A
162Enterobacteria phage T4Mutations: L99A, M102Q, N144D, S38D
Gene Names: E
EC: 3.2.1.17
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
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
BME
Query on BME

Download SDF File 
Download CCD File 
A
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
J1Z
Query on J1Z

Download SDF File 
Download CCD File 
A
thieno[3,2-b]thiophene
C6 H4 S2
VJYJJHQEVLEOFL-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
J1ZKd: 250000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.170 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 60.060α = 90.00
b = 60.060β = 90.00
c = 96.990γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
XDSdata scaling
ADSCdata collection
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance