Crystal Structure of Benzamide SNX-1321 bound to Hsp90

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

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This is version 1.2 of the entry. See complete history


Application of Chemoproteomics to Drug Discovery: Identification of a Clinical Candidate Targeting Hsp90.

Fadden, P.Huang, K.H.Veal, J.M.Steed, P.M.Barabasz, A.F.Foley, B.Hu, M.Partridge, J.M.Rice, J.Scott, A.Dubois, L.G.Freed, T.A.Silinski, M.A.Barta, T.E.Hughes, P.F.Ommen, A.Ma, W.Smith, E.D.Spangenberg, A.W.Eaves, J.Hanson, G.J.Hinkley, L.Jenks, M.Lewis, M.Otto, J.Pronk, G.J.Verleysen, K.Haystead, T.A.Hall, S.E.

(2010) Chem Biol 17: 686-694

  • DOI: https://doi.org/10.1016/j.chembiol.2010.04.015
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    A chemoproteomics-based drug discovery strategy is presented that utilizes a highly parallel screening platform, encompassing more than 1000 targets, with a focused chemical library prior to target selection. This chemoproteomics-based process enables a data-driven selection of both the biological target and chemical hit after the screen is complete. The methodology has been exemplified for the purine binding proteome (proteins utilizing ATP, NAD, FAD). Screening of an 8000 member library yielded over 1500 unique protein-ligand interactions, which included novel hits for the oncology target Hsp90. The approach, which also provides broad target selectivity information, was used to drive the identification of a potent and orally active Hsp90 inhibitor, SNX-5422, which is currently in phase 1 clinical studies.

  • Organizational Affiliation

    Serenex, Inc., 323 Foster Street, Durham, NC 27701, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heat shock protein HSP 90-alphaA [auth P]232Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P07900 (Homo sapiens)
Explore P07900 
Go to UniProtKB:  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 SD1

Download Ideal Coordinates CCD File 
B [auth P]2-[(3,4,5-trimethoxyphenyl)amino]-4-(2,6,6-trimethyl-4-oxo-4,5,6,7-tetrahydro-1H-indol-1-yl)benzamide
C27 H31 N3 O5
Binding Affinity Annotations 
IDSourceBinding Affinity
SD1 BindingDB:  3MNR IC50: 490 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.773α = 90
b = 90.753β = 90
c = 99.116γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata 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: 2010-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description