4BQJ | pdb_00004bqj

structure of HSP90 with an inhibitor bound

• PDB DOI: https://doi.org/10.2210/pdb4BQJ/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2013-05-30 Released: 2013-10-23 
• Deposition Author(s): Casale, E., Brasca, M.G., Mantegani, S., Amboldi, N., Bindi, S., Caronni, D., Ceccarelli, W., Colombo, N., DePonti, A., Donati, D., Ermoli, A., Fachin, G., Felder, E.R., Ferguson, R.D., Fiorelli, C., Guanci, M., Isacchi, A., Pesenti, E., Polucci, P., Riceputi, L., Sola, F., Visco, C., Zuccotto, F., Fogliatto, G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.221 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Literature

Discovery of Nms-E973 as Novel, Selective and Potent Inhibitor of Heat Shock Protein 90 (Hsp90).

Brasca, M.G., Mantegani, S., Amboldi, N., Bindi, S., Caronni, D., Casale, E., Ceccarelli, W., Colombo, N., De Ponti, A., Donati, D., Ermoli, A., Fachin, G., Felder, E.R., Ferguson, R.D., Fiorelli, C., Guanci, M., Isacchi, A., Pesenti, E., Polucci, P., Riceputi, L., Sola, F., Visco, C., Zuccotto, F., Fogliatto, G.

(2013) Bioorg Med Chem 21: 7047

• PubMed: 24100158 
• DOI: https://doi.org/10.1016/j.bmc.2013.09.018
• Primary Citation Related Structures: 
  4BQG, 4BQJ


• PubMed Abstract: 
  

  Novel small molecule inhibitors of heat shock protein 90 (Hsp90) were discovered with the help of a fragment based drug discovery approach (FBDD) and subsequent optimization with a combination of structure guided design, parallel synthesis and application of medicinal chemistry principles. These efforts led to the identification of compound 18 (NMS-E973), which displayed significant efficacy in a human ovarian A2780 xenograft tumor model, with a mechanism of action confirmed in vivo by typical modulation of known Hsp90 client proteins, and with a favorable pharmacokinetic and safety profile.

---

Organizational Affiliation: 
• Nerviano Medical Sciences S.r.l., Oncology, Viale Pasteur 10, 20014 Nerviano, MI, Italy. 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: 26.2 kDa 
• Atom Count: 1,828 
• Modeled Residue Count: 213 
• Deposited Residue Count: 230 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEAT SHOCK PROTEIN HSP 90-ALPHA	A	230	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XKL	B [auth A]	5-[2,4-dihydroxy-6-(4-nitrophenoxy)phenyl]-N-ethyl-1,2-oxazole-3-carboxamide C18 H15 N3 O7 DAESMMVDEWYEKZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.221 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.699	α = 90
b = 40.855	β = 115.83
c = 54.221	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-23 
Deposition Author(s): Casale, E., Brasca, M.G., Mantegani, S., Amboldi, N., Bindi, S., Caronni, D., Ceccarelli, W., Colombo, N., DePonti, A., Donati, D., Ermoli, A., Fachin, G., Felder, E.R., Ferguson, R.D., Fiorelli, C., Guanci, M., Isacchi, A., Pesenti, E., Polucci, P., Riceputi, L., Sola, F., Visco, C., Zuccotto, F., Fogliatto, G.

Revision History  

• Version 1.0: 2013-10-23
  Type: Initial release
  
• Version 1.1: 2013-10-30
  Changes: Database references
• Version 1.2: 2017-06-28
  Changes: Data collection
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other