Structure of HSP90 bound with a novel fragment

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 

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Fragment-based Identification of Hsp90 Inhibitors.

Barker, J.J.Barker, O.Boggio, R.Chauhan, V.Cheng, R.K.Corden, V.Courtney, S.M.Edwards, N.Falque, V.M.Fusar, F.Gardiner, M.Hamelin, E.M.Hesterkamp, T.Ichihara, O.Jones, R.S.Mather, O.Mercurio, C.Minucci, S.Montalbetti, C.A.Muller, A.Patel, D.Phillips, B.G.Varasi, M.Whittaker, M.Winkler, D.Yarnold, C.J.

(2009) ChemMedChem 4: 963-966

  • DOI: https://doi.org/10.1002/cmdc.200900011
  • Primary Citation of Related Structures:  
    3FT5, 3FT8

  • PubMed Abstract: 

    Heat shock protein 90 (Hsp90) plays a key role in stress response and protection of the cell against the effects of mutation. Herein we report the identification of an Hsp90 inhibitor identified by fragment screening using a high-concentration biochemical assay, as well as its optimisation by in silico searching coupled with a structure-based drug design (SBDD) approach.

  • Organizational Affiliation

    Evotec, 114 Milton Park, Abingdon, Oxfordshire, OX10 4SA UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heat shock protein HSP 90-alpha249Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P07900 (Homo sapiens)
Explore P07900 
Go to UniProtKB:  P07900
PHAROS:  P07900
GTEx:  ENSG00000080824 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07900
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MO8

Download Ideal Coordinates CCD File 
B [auth A]4-methyl-7,8-dihydro-5H-thiopyrano[4,3-d]pyrimidin-2-amine
C8 H11 N3 S
Binding Affinity Annotations 
IDSourceBinding Affinity
MO8 Binding MOAD:  3FT5 IC50: 1.50e+4 (nM) from 1 assay(s)
PDBBind:  3FT5 IC50: 1.50e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.083α = 90
b = 89.009β = 90
c = 99.715γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations