5H22 | pdb_00005h22

Hsp90 alpha N-terminal domain in complex with an inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5H22/pdb

• Classification: CHAPERONE/INHIBITOR
• Organism(s): Mus musculus
• Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
• Mutation(s): No 


• Deposited: 2016-10-13 Released: 2017-10-11 
• Deposition Author(s): Kim, E.E., Shin, S.C., Keum, G.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.208 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Synthesis and in vitro antiproliferative activity of C5-benzyl substituted 2-amino-pyrrolo[2,3-d]pyrimidines as potent Hsp90 inhibitors.

Lee, J.H., Shin, S.C., Seo, S.H., Seo, Y.H., Jeong, N., Kim, C.W., Kim, E.E., Keum, G.

(2017) Bioorg Med Chem Lett 27: 237-241

• PubMed: 27914802 
• DOI: https://doi.org/10.1016/j.bmcl.2016.11.062
• Primary Citation Related Structures: 
  5H22


• PubMed Abstract: 
  

  A novel series of heat shock protein 90 (Hsp90) inhibitors was identified by X-ray crystal analysis of complex structures at solvent-exposed exit pocket C. The 2-amino-pyrrolo[2,3-d]pyrimidine derivatives, 7-deazapurines substituted with a benzyl moiety at C5, showed potent Hsp90 inhibition and broad-spectrum antiproliferative activity against NCI-60 cancer cell lines. The most potent compound, 6a, inhibited Hsp90 with an IC ₅₀ of 36nM and showed a submicromolar mean GI ₅₀ value against NCI-60 cell lines. The interaction of 6a at the ATP-binding pocket of Hsp90 was confirmed by X-ray crystallography and Western blot analysis.

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Organizational Affiliation: 
• Center for Neuro-Medicine, Korea Institute of Science and Technology (KIST), Hwarangro 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea; Department of Chemistry, Korea University, Anam-ro 145, Seongbuk-gu, Seoul 02841, Republic of Korea.
Biomedical Research Institute, KIST, Hwarangro 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea; School of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea.
Center for Neuro-Medicine, Korea Institute of Science and Technology (KIST), Hwarangro 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea.
College of Pharmacy, Keimyung University, Daegu 42601, Republic of Korea.
Department of Chemistry, Korea University, Anam-ro 145, Seongbuk-gu, Seoul 02841, Republic of Korea.
School of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea.
Biomedical Research Institute, KIST, Hwarangro 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea. Electronic address: [e-mail].
Center for Neuro-Medicine, Korea Institute of Science and Technology (KIST), Hwarangro 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea. Electronic address: [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: 24.52 kDa 
• Atom Count: 1,936 
• Modeled Residue Count: 209 
• Deposited Residue Count: 215 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hsp90aa1 protein	A	215	Mus musculus	Mutation(s): 0  Gene Names: Hsp90aa1 EC: 3.6.4.10
UniProt & NIH Common Fund Data Resources
Find proteins for P07901 (Mus musculus) Explore P07901  Go to UniProtKB:  P07901
IMPC:  MGI:96250

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7FT	B [auth A]	4-chloranyl-7-[(4-methoxy-3,5-dimethyl-pyridin-2-yl)methyl]-5-(phenylmethyl)pyrrolo[2,3-d]pyrimidin-2-amine C22 H22 Cl N5 O CBDCNHPEKJZUHT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.208 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.787	α = 90
b = 90.581	β = 90
c = 98.943	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data processing
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-10-11 
Deposition Author(s): Kim, E.E., Shin, S.C., Keum, G.C.

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Funding Organization	Location	Grant Number
	Korea, Republic Of	NRF 20110021713

Revision History  

• Version 1.0: 2017-10-11
  Type: Initial release
  
• Version 1.1: 2019-04-24
  Changes: Data collection, Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description