Crystal structure of Human Hsp90 with JR9

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Multi-substituted 8-aminoimidazo[1,2-a]pyrazines by Groebke-Blackburn-Bienayme reaction and their Hsp90 inhibitory activity.

Ren, J.Yang, M.Liu, H.Cao, D.Chen, D.Li, J.Tang, L.He, J.Chen, Y.L.Geng, M.Xiong, B.Shen, J.

(2015) Org Biomol Chem 13: 1531-1535

  • DOI: https://doi.org/10.1039/c4ob01865f
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Using a 2,3-diamino pyrazine substrate and yttrium triflate catalyst, various 2-alkyl and aryl substituted 3,8-diaminoimidazo[1,2-a]pyrazines were efficiently prepared through Groebke-Blackburn-Bienaymé MCR. In particular, a novel 2-piperonyl 3,8-diaminoimidazo[1,2-a]pyrazine structure was prepared exclusively with this new method and was found to have moderate Hsp90 inhibitory activity. A crystalline complex with N-terminus ATP domain of Hsp90 and one of the new Hsp90 inhibitors was also obtained to elucidate the origin of activity of 2-piperonyl 3,8-diaminoimidazo[1,2-a]pyrazines.

  • Organizational Affiliation

    Medicinal Chemistry Department, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China. bxiong@simm.ac.cn.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heat shock protein HSP 90-alpha209Homo 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 JR9

Download Ideal Coordinates CCD File 
B [auth A]N~3~-benzyl-2-[(6-bromo-1,3-benzodioxol-5-yl)methyl]imidazo[1,2-a]pyrazine-3,8-diamine
C21 H18 Br N5 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.578α = 90
b = 90.926β = 90
c = 98.894γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
HKL-2000data reduction
HKL-2000data 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: 2014-11-05
    Type: Initial release
  • Version 1.1: 2015-11-25
    Changes: Database references
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations