6HHR

Hsp90 in complex with 5-(2,4-Dihydroxy-phenyl)-4-(2-fluoro-phenyl)-2,4-dihydro-[1,2,4]triazole-3-thione


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Predicting Residence Time and Drug Unbinding Pathway through Scaled Molecular Dynamics.

Schuetz, D.A.Bernetti, M.Bertazzo, M.Musil, D.Eggenweiler, H.M.Recanatini, M.Masetti, M.Ecker, G.F.Cavalli, A.

(2019) J.Chem.Inf.Model. 59: 535-549

  • DOI: 10.1021/acs.jcim.8b00614

  • PubMed Abstract: 
  • Computational approaches currently assist medicinal chemistry through the entire drug discovery pipeline. However, while several computational tools and strategies are available to predict binding affinity, predicting the drug-target binding kinetics ...

    Computational approaches currently assist medicinal chemistry through the entire drug discovery pipeline. However, while several computational tools and strategies are available to predict binding affinity, predicting the drug-target binding kinetics is still a matter of ongoing research. Here, we challenge scaled molecular dynamics simulations to assess the off-rates for a series of structurally diverse inhibitors of the heat shock protein 90 (Hsp90) covering 3 orders of magnitude in their experimental residence times. The derived computational predictions are in overall good agreement with experimental data. Aside from the estimation of exit times, unbinding pathways were assessed through dimensionality reduction techniques. The data analysis framework proposed in this work could lead to better understanding of the mechanistic aspects related to the observed kinetic behavior.


    Organizational Affiliation

    Medicinal Chemistry , Merck KGaA , 64293 Darmstadt , Germany.,Computational Sciences , Istituto Italiano di Tecnologia , via Morego 30 , 16163 Genova , Italy.,Department of Pharmacy and Biotechnology , Alma Mater Studiorum-Universit├á di Bologna , via Belmeloro 6 , I-40126 Bologna , Italy.,Department of Pharmaceutical Chemistry , University of Vienna , UZA 2, Althanstrasse 14 , 1090 Vienna , Austria.,Discovery Technologies , Merck KGaA , Frankfurter Stra├če 250 , 64293 Darmstadt , Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Heat shock protein HSP 90-alpha
A
208Homo sapiensMutation(s): 0 
Gene Names: HSP90AA1 (HSP90A, HSPC1, HSPCA)
Find proteins for P07900 (Homo sapiens)
Go to Gene View: HSP90AA1
Go to UniProtKB:  P07900
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G5E
Query on G5E

Download SDF File 
Download CCD File 
A
3-[2,4-bis(oxidanyl)phenyl]-4-(2-fluorophenyl)-1~{H}-1,2,4-triazole-5-thione
C14 H10 F N3 O2 S
UAZGBVUYMVWWQS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.183 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 65.830α = 90.00
b = 89.410β = 90.00
c = 99.330γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
HKL-2000data reduction
BUSTERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-07-10
    Type: Initial release