4U93

Crystal Structure of Hsp90-alpha N-domain Bound to the Inhibitor NVP-HSP990

• PDB DOI: https://doi.org/10.2210/pdb4U93/pdb

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


• Deposited: 2014-08-05 Released: 2014-11-19 
• Deposition Author(s): Bellamacina, C.R., Shafer, C.M., Bussiere, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.213 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 

Literature

Design, Structure-Activity Relationship, and in Vivo Characterization of the Development Candidate NVP-HSP990.

McBride, C.M., Levine, B., Xia, Y., Bellamacina, C., Machajewski, T., Gao, Z., Renhowe, P., Antonios-McCrea, W., Barsanti, P., Brinner, K., Costales, A., Doughan, B., Lin, X., Louie, A., McKenna, M., Mendenhall, K., Poon, D., Rico, A., Wang, M., Williams, T.E., Abrams, T., Fong, S., Hendrickson, T., Lei, D., Lin, J., Menezes, D., Pryer, N., Taverna, P., Xu, Y., Zhou, Y., Shafer, C.M.

(2014) J Med Chem 57: 9124-9129

• PubMed: 25368984 
• DOI: https://doi.org/10.1021/jm501107q
• Primary Citation of Related Structures:  
  4U93, 4W7T


• PubMed Abstract: 
  

  Utilizing structure-based drug design, a novel dihydropyridopyrimidinone series which exhibited potent Hsp90 inhibition, good pharmacokinetics upon oral administration, and an excellent pharmacokinetic/pharmacodynamic relationship in vivo was developed from a commercial hit. The exploration of this series led to the selection of NVP-HSP990 as a development candidate.

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Organizational Affiliation: 

Global Discovery Chemistry/Oncology & Exploratory Chemistry, Novartis Institutes for Biomedical Research , 5300 Chiron Way, Emeryville, California 94608, United States.

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: 26.98 kDa 
• Atom Count: 2,031 
• Modelled Residue Count: 207 
• Deposited Residue Count: 236 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock protein HSP 90-alpha	A	236	Homo sapiens	Mutation(s): 0
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
990	B [auth A]	(7R)-2-amino-7-[4-fluoro-2-(6-methoxypyridin-2-yl)phenyl]-4-methyl-7,8-dihydropyrido[4,3-d]pyrimidin-5(6H)-one C20 H18 F N5 O2 WSMQUUGTQYPVPD-OAHLLOKOSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
990	BindingDB:  4U93	IC50: 13 (nM) from 1 assay(s)
	Binding MOAD:  4U93	IC50: 13 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.213 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.726	α = 90
b = 99.237	β = 90
c = 91.561	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
MOLREP	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-19 
Deposition Author(s): Bellamacina, C.R., Shafer, C.M., Bussiere, D.

Revision History  

• Version 1.0: 2014-11-19
  Type: Initial release
  
• Version 1.1: 2014-11-26
  Changes: Database references
• Version 1.2: 2016-07-20
  Changes: Data collection
• Version 1.3: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references