Crystal Structure of Hsp90-alpha N-Domain in complex with Indazole derivative

Experimental Data Snapshot

  • Resolution: 1.82 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

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Ligand Desolvation Steers On-Rate and Impacts Drug Residence Time of Heat Shock Protein 90 (Hsp90) Inhibitors.

Schuetz, D.A.Richter, L.Amaral, M.Grandits, M.Gradler, U.Musil, D.Buchstaller, H.P.Eggenweiler, H.M.Frech, M.Ecker, G.F.

(2018) J Med Chem 61: 4397-4411

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b00080
  • Primary Citation of Related Structures:  
    5LNY, 5LNZ, 5LO0, 5LO1, 5NYH, 5OCI, 5OD7, 5ODX

  • PubMed Abstract: 

    Residence time and more recently the association rate constant k on are increasingly acknowledged as important parameters for in vivo efficacy and safety of drugs. However, their broader consideration in drug development is limited by a lack of knowledge of how to optimize these parameters. In this study on a set of 176 heat shock protein 90 inhibitors, structure-kinetic relationships, X-ray crystallography, and molecular dynamics simulations were combined to retrieve a concrete scheme of how to rationally slow down on-rates. We discovered that an increased ligand desolvation barrier by introducing polar substituents resulted in a significant k on decrease. The slowdown was accomplished by introducing polar moieties to those parts of the ligand that point toward a hydrophobic cavity. We validated this scheme by increasing polarity of three Hsp90 inhibitors and observed a 9-, 13-, and 45-fold slowdown of on-rates and a 9-fold prolongation in residence time. This prolongation was driven by transition state destabilization rather than ground state stabilization.

  • Organizational Affiliation

    Department of Pharmaceutical Chemistry , University of Vienna , UZA 2, Althanstrasse 14 , 1090 Vienna , Austria.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heat shock protein HSP 90-alpha229Homo 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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 9RZ

Download Ideal Coordinates CCD File 
B [auth A]3-[(3~{S})-3-methoxypiperidin-1-yl]carbonyl-~{N}-methyl-~{N}-(4-morpholin-4-ylphenyl)-6-oxidanyl-1~{H}-indazole-5-carboxamide
C26 H31 N5 O5
Query on DMS

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
C2 H6 O S
Binding Affinity Annotations 
IDSourceBinding Affinity
9RZ BindingDB:  5ODX Kd: 195 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.82 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.88α = 90
b = 88.837β = 90
c = 97.558γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata 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: 2018-04-18
    Type: Initial release
  • Version 1.1: 2018-05-23
    Changes: Data collection, Database references
  • Version 1.2: 2018-06-06
    Changes: Data collection, Database references
  • Version 1.3: 2018-12-19
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2019-10-16
    Changes: Data collection
  • Version 1.5: 2024-05-08
    Changes: Data collection, Database references