5ODX

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

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: 10.1021/acs.jmedchem.8b00080
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Residence time and more recently the association rate constant k <sub>on </sub> 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 l ...

    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

    Instituto de Biologia Experimental e Tecnol├│gica , Oeiras , Portugal.,Medicinal Chemistry , Merck KGaA , 64293 Darmstadt , Germany.,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
229Homo 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
9RZ
Query on 9RZ

Download SDF File 
Download CCD File 
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
RSPZSUZMTGTRAT-IBGZPJMESA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
9RZKd: 195 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.193 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 69.880α = 90.00
b = 88.837β = 90.00
c = 97.558γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
XDSdata reduction
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-04-18
    Type: Initial release
  • Version 1.1: 2018-05-23
    Type: Data collection, Database references
  • Version 1.2: 2018-06-06
    Type: Data collection, Database references
  • Version 1.3: 2018-12-19
    Type: Advisory, Data collection, Derived calculations
  • Version 1.4: 2019-10-16
    Type: Data collection