1OSF

Human Hsp90 in complex with 17-desmethoxy-17-N,N-Dimethylaminoethylamino-Geldanamycin

• PDB DOI: https://doi.org/10.2210/pdb1OSF/pdb

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


• Deposited: 2003-03-19 Released: 2003-05-27 
• Deposition Author(s): Jez, J.M., Chen, J.C.-H., Rastelli, G., Stroud, R.M., Santi, D.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.219 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 

Literature

Crystal Structure and Molecular Modeling of 17-DMAG in Complex with Human Hsp90

Jez, J.M., Chen, J.C., Rastelli, G., Stroud, R.M., Santi, D.V.

(2003) Chem Biol 10: 361-368

• PubMed: 12725864 
• DOI: https://doi.org/10.1016/s1074-5521(03)00075-9
• Primary Citation of Related Structures:  
  1OSF


• PubMed Abstract: 
  

  Hsp90 is an attractive chemotherapeutic target because it chaperones the folding of proteins found in multiple signal transduction pathways. We describe the 1.75 A resolution crystal structure of human Hsp90 alpha (residues 9-236) complexed with 17-desmethoxy-17-N,N-dimethylaminoethylamino-geldanamycin (17-DMAG). The structure revealed an altered set of interactions between the 17-substituent and the protein compared to geldanamycin and the 17-dimethylaminoethyl moiety pointing into solvent, but otherwise was similar to that reported for the complex with geldanamycin. Targeted molecular dynamics simulations and energetic analysis indicate that geldanamycin undergoes two major conformational changes when it binds Hsp90, with the key step of the conversion being the trans to cis conformational change of the macrocycle amide bond. We speculate that 17-DMAG analogs constrained to a cis-amide in the ground state could provide a significant increase in affinity for Hsp90.

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Organizational Affiliation: 

Kosan Biosciences, Inc., 3832 Bay Center Place, Hayward, CA 94545, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25.1 kDa 
• Atom Count: 2,040 
• Modelled Residue Count: 215 
• Deposited Residue Count: 215 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
heat shock 90kDa protein 1, alpha; heat shock 90kD protein 1, alpha	A	215	Homo sapiens	Mutation(s): 0  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KOS	B [auth A]	17-DESMETHOXY-17-N,N-DIMETHYLAMINOETHYLAMINO-GELDANAMYCIN C32 H48 N4 O8 KUFRQPKVAWMTJO-LMZWQJSESA-N
MPD	C [auth A], D [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
ACY	E [auth A], F [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
KOS	BindingDB:  1OSF	IC50: min: 4.5, max: 1410 (nM) from 8 assay(s)
		EC50: 7.9 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.219 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.71	α = 90
b = 41.68	β = 102.81
c = 55.98	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
CNS	refinement
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-05-27 
Deposition Author(s): Jez, J.M., Chen, J.C.-H., Rastelli, G., Stroud, R.M., Santi, D.V.

Revision History  

• Version 1.0: 2003-05-27
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations