4R3M | pdb_00004r3m

Crystal structure of Human Hsp90 with JR9

• PDB DOI: https://doi.org/10.2210/pdb4R3M/pdb

• Classification: Chaperone/Chaperone Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-08-16 Released: 2014-11-05 
• Deposition Author(s): Li, J., Yang, M., Ren, J., Xiong, B., He, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.234 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

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

• PubMed: 25490978 
• DOI: https://doi.org/10.1039/c4ob01865f
• Primary Citation Related Structures: 
  4R3M


• 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.

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Organizational Affiliation: 
• Medicinal Chemistry Department, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 23.84 kDa 
• Atom Count: 1,757 
• Modeled Residue Count: 209 
• Deposited Residue Count: 209 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock protein HSP 90-alpha	A	209	Homo sapiens	Mutation(s): 0  Gene Names: HSP90A, HSP90AA1, HSPC1, HSPCA 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JR9	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 QOEANVPMVDTINQ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.234 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.578	α = 90
b = 90.926	β = 90
c = 98.894	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-05 
Deposition Author(s): Li, J., Yang, M., Ren, J., Xiong, B., He, J.

Revision History  

• 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