4W7T

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

PDB DOI: https://doi.org/10.2210/pdb4W7T/pdb

Classification: CHAPERONE/INHIBITOR
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2014-08-22 Released: 2014-11-26
Deposition Author(s): Bellamacina, C.R., Shafer, C.M., Bussiere, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.210
R-Value Work: 0.171
R-Value Observed: 0.173

Starting Model: other
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 26.86 kDa
Atom Count: 2,007
Modelled Residue Count: 207
Deposited Residue Count: 236
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock protein HSP 90-alpha	A	236	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07900
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3JC Query on 3JC Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(7S)-2-amino-4-methyl-7-phenyl-7,8-dihydroquinazolin-5(6H)-one C₁₅ H₁₅ N₃ O PHMJMYBSWXYOLM-NSHDSACASA-N		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.210
R-Value Work: 0.171
R-Value Observed: 0.173
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.095	α = 90
b = 89.983	β = 90
c = 97.985	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
EPMR	phasing
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-11-26

Deposition Author(s):

Bellamacina, C.R.

Shafer, C.M.

Bussiere, D.

Revision History (Full details and data files)

Version 1.0: 2014-11-26
Type: Initial release
Version 1.1: 2023-12-27
Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
Version 1.2: 2024-04-03
Changes: Refinement description