Crystal Structure of Hsp90-alpha N-domain in complex with N-Butyl-5-[4-(2-fluoro-phenyl)-5-oxo-4,5-dihydro-1H-[1,2,4]triazol-3-yl]-2,4-dihydroxy-N-methyl-benzamide

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

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Protein conformational flexibility modulates kinetics and thermodynamics of drug binding.

Amaral, M.Kokh, D.B.Bomke, J.Wegener, A.Buchstaller, H.P.Eggenweiler, H.M.Matias, P.Sirrenberg, C.Wade, R.C.Frech, M.

(2017) Nat Commun 8: 2276-2276

  • DOI: https://doi.org/10.1038/s41467-017-02258-w
  • Primary Citation of Related Structures:  
    5J20, 5J27, 5J2V, 5J2X, 5J64, 5J6L, 5J6M, 5J6N, 5J80, 5J82, 5J86, 5J8M, 5J8U, 5J9X

  • PubMed Abstract: 

    Structure-based drug design has often been restricted by the rather static picture of protein-ligand complexes presented by crystal structures, despite the widely accepted importance of protein flexibility in biomolecular recognition. Here we report a detailed experimental and computational study of the drug target, human heat shock protein 90, to explore the contribution of protein dynamics to the binding thermodynamics and kinetics of drug-like compounds. We observe that their binding properties depend on whether the protein has a loop or a helical conformation in the binding site of the ligand-bound state. Compounds bound to the helical conformation display slow association and dissociation rates, high-affinity and high cellular efficacy, and predominantly entropically driven binding. An important entropic contribution comes from the greater flexibility of the helical relative to the loop conformation in the ligand-bound state. This unusual mechanism suggests increasing target flexibility in the bound state by ligand design as a new strategy for drug discovery.

  • Organizational Affiliation

    iBET - Instituto de Biologia Experimental e Tecnológica, Oeiras, 2780-157, Portugal. marta.amaral@sanofi.com.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heat shock protein HSP 90-alpha228Homo 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 6GC

Download Ideal Coordinates CCD File 
B [auth A]N-butyl-5-[4-(2-fluorophenyl)-5-oxo-4,5-dihydro-1H-1,2,4-triazol-3-yl]-2,4-dihydroxy-N-methylbenzamide
C20 H21 F N4 O4
Experimental Data & Validation

Experimental Data

  • Resolution: 1.75 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.221α = 90
b = 90.023β = 90
c = 99.546γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description