4AWQ

Complex of HSP90 ATPase domain with tropane derived inhibitors

• PDB DOI: https://doi.org/10.2210/pdb4AWQ/pdb

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


• Deposited: 2012-06-05 Released: 2012-08-29 
• Deposition Author(s): Lougheed, J.C., Stout, T.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.262 
• R-Value Work: 0.227 
• R-Value Observed: 0.229 

Starting Model: other

Literature

Discovery of Xl888: A Novel Tropane-Derived Small Molecule Inhibitor of Hsp90.

Bussenius, J., Blazey, C.M., Aay, N., Anand, N.K., Arcalas, A., Baik, T., Bowles, O.J., Buhr, C.A., Costanzo, S., Curtis, J.K., Defina, S.C., Dubenko, L., Heuer, T.S., Huang, P., Jaeger, C., Joshi, A., Kennedy, A.R., Kim, A.I., Lara, K., Lee, J., Li, J., Lougheed, J.C., Ma, S., Malek, S., Manalo, J.C., Martini, J.F., Mcgrath, G., Nicoll, M., Nuss, J.M., Pack, M., Peto, C.J., Tsang, T.H., Wang, L., Womble, S.W., Yakes, M., Zhang, W., Rice, K.D.

(2012) Bioorg Med Chem Lett 22: 5396

• PubMed: 22877636 
• DOI: https://doi.org/10.1016/j.bmcl.2012.07.052
• Primary Citation of Related Structures:  
  4AWO, 4AWP, 4AWQ


• PubMed Abstract: 
  

  With structural guidance, tropane-derived HTS hits were modified to optimize for HSP90 inhibition and a desirable in vivo profile. Through an iterative SAR development process 12i (XL888) was discovered and shown to reduce HSP90 client protein content in PD studies. Furthermore, efficacy experiments performed in a NCI-N87 mouse xenograft model demonstrated tumor regression in some dosing regimens.

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Organizational Affiliation: 

Exelixis, Inc., 220 East Grand Ave., South San Francisco, CA 94080, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 52.57 kDa 
• Atom Count: 3,563 
• Modelled Residue Count: 408 
• Deposited Residue Count: 460 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEAT SHOCK PROTEIN HSP 90-ALPHA	A, B	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
592	C [auth A], D [auth B]	N-benzyl-6-[(3-endo)-3-{[(3-methoxy-2-methylphenyl)carbonyl]amino}-8-azabicyclo[3.2.1]oct-8-yl]pyridine-3-carboxamide C29 H32 N4 O3 JXXRMCOYDPMQEY-BKFWDETESA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
592	PDBBind:  4AWQ	IC50: 479 (nM) from 1 assay(s)
	BindingDB:  4AWQ	IC50: min: 479, max: 2800 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.262 
• R-Value Work: 0.227 
• R-Value Observed: 0.229 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.324	α = 70.4
b = 56.769	β = 87.01
c = 57.444	γ = 68.7

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-29 
Deposition Author(s): Lougheed, J.C., Stout, T.J.

Revision History  

• Version 1.0: 2012-08-29
  Type: Initial release
  
• Version 1.1: 2017-06-28
  Changes: Data collection
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description