3INW | pdb_00003inw

HSP90 N-TERMINAL DOMAIN with pochoxime A

• PDB DOI: https://doi.org/10.2210/pdb3INW/pdb

• Classification: CHAPERONE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-08-13 Released: 2010-08-18 
• Deposition Author(s): Korndoerfer, I.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.242 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.183 (Depositor) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Inhibition of HSP90 with pochoximes: SAR and structure-based insights.

Barluenga, S., Fontaine, J.G., Wang, C., Aouadi, K., Chen, R., Beebe, K., Neckers, L., Winssinger, N.

(2009) Chembiochem 10: 2753-2759

• PubMed: 19856365 
• DOI: https://doi.org/10.1002/cbic.200900494
• Primary Citation Related Structures: 
  3INW, 3INX


• PubMed Abstract: 
  

  The pochoximes, based on the radicicol pharmacophore, are potent inhibitors of heat shock protein 90 (HSP90) that retain their activity in vivo. Herein we report an extended library that broadly explores the structure-activity relationship (SAR) of the pochoximes with four points of diversity. Several modifications were identified that afford improved cellular efficacy, new opportunities for conjugation, and further diversifications. Cocrystal structures of pochoximes A and B with HSP90 show that pochoximes bind to a different conformation of HSP90 than radicicol and provide a rationale for the enhanced affinity of the pochoximes relative to radicicol and the pochonins.

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Organizational Affiliation: 
• Institut de Science et d'Ingénierie Supramoleculaires, Université de Strasbourg, CNRS (UMR7006), 8 Allée Gaspard Monge, 67000 Strasbourg, France.

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: 26.23 kDa 
• Atom Count: 1,954 
• Modeled Residue Count: 207 
• Deposited Residue Count: 228 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock protein HSP 90-alpha	A	228	Homo sapiens	Mutation(s): 0  Gene Names: HSP90AA1, HSP90A, 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JZB	C [auth A]	(5E,9E,11E)-13-chloro-14,16-dihydroxy-3,4,7,8-tetrahydro-1H-2-benzoxacyclotetradecine-1,11(12H)-dione 11-[O-(2-oxo-2-piperidin-1-ylethyl)oxime] C24 H29 Cl N2 O6 XNRNAVTUUGISQH-VCKBHWIVSA-N
DMS	B [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.242 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.183 (Depositor) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.05	α = 90
b = 90.69	β = 90
c = 98.75	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-18 
Deposition Author(s): Korndoerfer, I.P.

Revision History  

• Version 1.0: 2010-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description