5ZR3 | pdb_00005zr3

Crystal structure of Hsp90-alpha N-terminal domain in complex with 4-(3-isopropyl-4-(4-(1-methyl-1H-pyrazol-4-yl)-1H-imidazol-1-yl)-1H-pyrazolo[3,4-b]pyridin-1-yl)-3-methylbenzamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.254 (Depositor), 0.256 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5ZR3

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of 3-Ethyl-4-(3-isopropyl-4-(4-(1-methyl-1 H-pyrazol-4-yl)-1 H-imidazol-1-yl)-1 H-pyrazolo[3,4- b]pyridin-1-yl)benzamide (TAS-116) as a Potent, Selective, and Orally Available HSP90 Inhibitor.

Uno, T.Kawai, Y.Yamashita, S.Oshiumi, H.Yoshimura, C.Mizutani, T.Suzuki, T.Chong, K.T.Shigeno, K.Ohkubo, M.Kodama, Y.Muraoka, H.Funabashi, K.Takahashi, K.Ohkubo, S.Kitade, M.

(2019) J Med Chem 62: 531-551

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b01085
  • Primary Citation Related Structures: 
    5ZR3

  • PubMed Abstract: 

    The molecular chaperone heat shock protein 90 (HSP90) is a promising target for cancer therapy, as it assists in the stabilization of cancer-related proteins, promoting cancer cell growth, and survival. A novel series of HSP90 inhibitors were discovered by structure-activity relationship (SAR)-based optimization of an initial hit compound 11a having a 4-(4-(quinolin-3-yl)-1 H-indol-1-yl)benzamide structure. The pyrazolo[3,4- b]pyridine derivative, 16e (TAS-116), is a selective inhibitor of HSP90α and HSP90β among the HSP90 family proteins and exhibits oral availability in mice. The X-ray cocrystal structure of the 16e analogue 16d demonstrated a unique binding mode at the N-terminal ATP binding site. Oral administration of 16e demonstrated potent antitumor effects in an NCI-H1975 xenograft mouse model without significant body weight loss.


  • Organizational Affiliation
    • Discovery and Preclinical Research Division , Taiho Pharmaceutical Co. Ltd. , Tsukuba , Ibaraki 300-2611 , Japan.

Macromolecule Content 

  • Total Structure Weight: 108.72 kDa 
  • Atom Count: 6,825 
  • Modeled Residue Count: 848 
  • Deposited Residue Count: 948 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Heat shock protein HSP 90-alphaA,
B [auth C],
C [auth E],
D [auth G]
237Homo sapiensMutation(s): 0 
Gene Names: HSP90AA1HSP90AHSPC1HSPCA
EC: 3.6.4.10
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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.254 (Depositor), 0.256 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.4α = 90
b = 95.21β = 91.3
c = 102.36γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-02
    Type: Initial release
  • Version 1.1: 2019-05-01
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description