Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 52.14 kDa 
• Atom Count: 3787 
• Residue Count: 443 
• Unique protein chains: 1

3HEK

HSP90 N-terminal domain in complex with 1-{4-[(2R)-1-(5-chloro-2,4-dihydroxybenzoyl)pyrrolidin-2-yl]benzyl}-3,3-difluoropyrrolidinium

• DOI: 10.2210/pdb3HEK/pdb

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


• Deposited: 2009-05-08 Released: 2009-09-29 
• Deposition Author(s): Gajiwala, K.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.237 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 

Literature

Solution-phase parallel synthesis of Hsp90 inhibitors

Cho-Schultz, S., Patten, M.J., Huang, B., Elleraas, J., Gajiwala, K.S., Hickey, M.J., Wang, J., Mehta, P.P., Kang, P., Gehring, M.R., Kung, P.P., Sutton, S.C.

(null) J Comb Chem 11: 860-874

• PubMed: 19583220 
• DOI: 10.1021/cc900056d
• Structures With Same Primary Citation


• PubMed Abstract: 
  

As part of an oncology chemistry program directed toward discovery of orally bioavailable inhibitors of the 90 kDa heat shock protein (Hsp90), several solution-phase libraries were designed and prepared. A 2 x 89 library of racemic resorcinol amides was prepared affording 131 purified compounds. After evaluation in a binding assay, followed by an AKT-Luminex cellular assay, three potent analogs had functional activity between 0.1 and 0.3 microM. Resolution by preparative chiral SFC chromatography led to (+)-15, (+)-16, and (+)-17 having functional IC(50) = 27, 43, and 190 nM, respectively. (+)-15 exhibited high clearance in human hepatocytes driven primarily by glucuronidation as confirmed by metabolite identification. A second 8 x 14 exploratory library was designed to investigate heterocyclic replacements of the resorcinol ring. The second library highlights the use of the (-)-sparteine-mediated enantioselective Pd-catalyzed alpha-arylation of N-Boc-pyrrolidine to prepare chiral 2-arylpyrrolidines in parallel.

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Organizational Affiliation: 

Pfizer Global Research and Development, La Jolla Laboratories, 10770 Science Center Drive, San Diego, California 92121, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Heat shock protein HSP 90-alpha	A, B	226	Homo sapiens	Mutation(s): 0  Gene Names: HSP90, HSP90A, HSP90AA1, HSPC1, HSPCA
Find proteins for P07900 (Homo sapiens) Explore P07900  Go to UniProtKB:  P07900
NIH Common Fund Data Resources
PHAROS  P07900 GTEx  ENSG00000080824

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BD0	A, B	(1S,2R)-1-[(5-chloro-2,4-dihydroxyphenyl)carbonyl]-2-{4-[(3,3-difluoropyrrolidin-1-yl)methyl]phenyl}pyrrolidinium C22 H24 Cl F2 N2 O3 MKPBMJPMGDZEOP-GOSISDBHSA-O
PO4	A	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
BD0	Ki :  5.400000095367432   nM  PDBBind
BD0	Ki:  3.5   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.237 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.083	α = 90
b = 80.16	β = 90
c = 117.434	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
CNX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-05-08 
• Released Date: 2009-09-29 
Deposition Author(s): Gajiwala, K.S.

Revision History 

• Version 1.0: 2009-09-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description