3R91 | pdb_00003r91

Macrocyclic lactams as potent Hsp90 inhibitors with excellent tumor exposure and extended biomarker activity.

• PDB DOI: https://doi.org/10.2210/pdb3R91/pdb

• Classification: CHAPERONE/CHAPERONE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-03-24 Released: 2011-05-11 
• Deposition Author(s): Zapf, C.W., Bloom, J.D., McBean, J.L., Dushin, R.G., Nittoli, T., Otteng, M., Ingalls, C., Golas, J.M., Liu, H., Lucas, J., Boschelli, F., Vogan, E., Hu, Y., Levin, J.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 
  0.199 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Macrocyclic lactams as potent Hsp90 inhibitors with excellent tumor exposure and extended biomarker activity.

Zapf, C.W., Bloom, J.D., McBean, J.L., Dushin, R.G., Nittoli, T., Otteng, M., Ingalls, C., Golas, J.M., Liu, H., Lucas, J., Boschelli, F., Hu, Y., Vogan, E., Levin, J.I.

(2011) Bioorg Med Chem Lett 21: 3411-3416

• PubMed: 21515049 
• DOI: https://doi.org/10.1016/j.bmcl.2011.03.112
• Primary Citation Related Structures: 
  3R91


• PubMed Abstract: 
  

  A novel series of macrocyclic ortho-aminobenzamide Hsp90 inhibitors is reported. In continuation of our research in this area, macrocyclic amides and lactams were explored to reduce the risk of hERG liabilities. This effort culminated in the discovery of compound 38, which showed a favorable in vitro profile, and efficiently suppressed proliferation of several relevant cell lines. This compound showed prolonged Hsp90-inhibitory activity at least 24 h post-administration, consistent with elevated and prolonged exposure in the tumor.

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Organizational Affiliation: 
• Medicinal Chemistry, Pfizer, 401 N Middletown Road, Pearl River, NY 10965, United States. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 25.85 kDa 
• Atom Count: 1,968 
• Modeled Residue Count: 207 
• Deposited Residue Count: 226 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock protein HSP 90-alpha	A	226	Homo sapiens	Mutation(s): 0  Gene Names: HSP90A, HSP90AA1, HSPC1, HSPCA 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
06H	B [auth A]	(6S)-4,6,15,15,18-pentamethyl-5,17-dioxo-2,3,4,5,6,7,14,15,16,17-decahydro-1H-12,8-(metheno)[1,4,9]triazacyclotetradecino[9,8-a]indole-9-carboxamide C25 H32 N4 O3 QPCQIBFESZKAHD-HNNXBMFYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.199 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.042	α = 90
b = 90.25	β = 90
c = 97.797	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-11 
Deposition Author(s): Zapf, C.W., Bloom, J.D., McBean, J.L., Dushin, R.G., Nittoli, T., Otteng, M., Ingalls, C., Golas, J.M., Liu, H., Lucas, J., Boschelli, F., Vogan, E., Hu, Y., Levin, J.I.

Revision History  

• Version 1.0: 2011-05-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description