4FLH

Crystal structure of human PI3K-gamma in complex with AMG511

• PDB DOI:  https://doi.org/10.2210/pdb4FLH/pdb

• Classification: Transferase/Inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2012-06-14 Released: 2012-08-29 
• Deposition Author(s): Whittington, D.A., Tang, J., Yakowec, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.244 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 

Literature

Selective Class I Phosphoinositide 3-Kinase Inhibitors: Optimization of a Series of Pyridyltriazines Leading to the Identification of a Clinical Candidate, AMG 511.

Norman, M.H., Andrews, K.L., Bo, Y.Y., Booker, S.K., Caenepeel, S., Cee, V.J., D'Angelo, N.D., Freeman, D.J., Herberich, B.J., Hong, F.T., Jackson, C.L., Jiang, J., Lanman, B.A., Liu, L., McCarter, J.D., Mullady, E.L., Nishimura, N., Pettus, L.H., Reed, A.B., Miguel, T.S., Smith, A.L., Stec, M.M., Tadesse, S., Tasker, A., Aidasani, D., Zhu, X., Subramanian, R., Tamayo, N.A., Wang, L., Whittington, D.A., Wu, B., Wu, T., Wurz, R.P., Yang, K., Zalameda, L., Zhang, N., Hughes, P.E.

(2012) J Med Chem 55: 7796-7816

• PubMed: 22897589 
• DOI: https://doi.org/10.1021/jm300846z
• Primary Citation of Related Structures:  
  4FLH


• PubMed Abstract: 
  

The phosphoinositide 3-kinase family catalyzes the phosphorylation of phosphatidylinositol-4,5-diphosphate to phosphatidylinositol-3,4,5-triphosphate, a secondary messenger which plays a critical role in important cellular functions such as metabolism, cell growth, and cell survival. Our efforts to identify potent, efficacious, and orally available phosphatidylinositol 3-kinase (PI3K) inhibitors as potential cancer therapeutics have resulted in the discovery of 4-(2-((6-methoxypyridin-3-yl)amino)-5-((4-(methylsulfonyl)piperazin-1-yl)methyl)pyridin-3-yl)-6-methyl-1,3,5-triazin-2-amine (1). In this paper, we describe the optimization of compound 1, which led to the design and synthesis of pyridyltriazine 31, a potent pan inhibitor of class I PI3Ks with a superior pharmacokinetic profile. Compound 31 was shown to potently block the targeted PI3K pathway in a mouse liver pharmacodynamic model and inhibit tumor growth in a U87 malignant glioma glioblastoma xenograft model. On the basis of its excellent in vivo efficacy and pharmacokinetic profile, compound 31 was selected for further evaluation as a clinical candidate and was designated AMG 511.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, USA. [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: 110.73 kDa 
• Atom Count: 6,905 
• Modelled Residue Count: 840 
• Deposited Residue Count: 960 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform	A	960	Homo sapiens	Mutation(s): 0  Gene Names: PIK3CG EC: 2.7.1.153 (PDB Primary Data), 2.7.11.1 (PDB Primary Data), 2.7.1.137 (UniProt), 2.7.1.154 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P48736 (Homo sapiens) Explore P48736  Go to UniProtKB:  P48736
PHAROS:  P48736

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
14K	F [auth A]	4-(2-[(5-fluoro-6-methoxypyridin-3-yl)amino]-5-{(1R)-1-[4-(methylsulfonyl)piperazin-1-yl]ethyl}pyridin-3-yl)-6-methyl-1,3,5-triazin-2-amine C22 H28 F N9 O3 S KUGIFHQBIIHRIZ-CYBMUJFWSA-N
SO4	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
14K	PDBBind:  4FLH	Ki: 1 (nM) from 1 assay(s)
	BindingDB:  4FLH	Ki: 1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.244 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.059	α = 90
b = 67.803	β = 95.27
c = 107.523	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-29 
Deposition Author(s): Whittington, D.A., Tang, J., Yakowec, P.

Revision History  

• Version 1.0: 2012-08-29
  Type: Initial release
  
• Version 1.1: 2012-10-03
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description