Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 34.63 kDa 
• Atom Count: 2337 
• Modelled Residue Count: 280 
• Deposited Residue Count: 301 
• Unique protein chains: 1

4AN3

Crystal structures of human MEK1 with carboxamide-based allosteric inhibitor XL518 (GDC-0973), or related analogs.

• DOI: 10.2210/pdb4AN3/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2012-03-15 Released: 2012-12-19 
• Deposition Author(s): Rice, K.D., Aay, N., Anand, N.K., Blazey, C.M., Bowles, O.J., Bussenius, J., Costanzo, S., Curtis, J.K., Defina, S.C., Dubenko, L., Engst, S., Joshi, A.A., Kennedy, A.R., Kim, A.I., Koltun, E.S., Lougheed, J.C., Manalo, J.C.L., Martini, J.F., Nuss, J.M., Peto, C.J., Tsang, T.H., Yu, P., Johnston, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.283 
• R-Value Work: 0.226 
• R-Value Observed: 0.229 

Literature

Novel Carboxamide-Based Allosteric Mek Inhibitors: Discovery and Optimization Efforts Toward Xl518 (Gdc-0973)

Rice, K.D., Aay, N., Anand, N.K., Blazey, C.M., Bowles, O.J., Bussenius, J., Costanzo, S., Curtis, J.K., Defina, S.C., Dubenko, L., Engst, S., Joshi, A.A., Kennedy, A.R., Kim, A.I., Koltun, E.S., Lougheed, J.C., Manalo, J.C.L., Martini, J.F., Nuss, J.M., Peto, C.J., Tsang, T.H., Yu, P., Johnston, S.

(2012) ACS Med Chem Lett 3: 416

• PubMed: 24900486 
• DOI: 10.1021/ml300049d
• Primary Citation of Related Structures:  
  4AN9, 4AN2, 4AN3, 4ANB


• PubMed Abstract: 
  

The ERK/MAP kinase cascade is a key mechanism subject to dysregulation in cancer and is constitutively activated or highly upregulated in many tumor types. Mutations associated with upstream pathway components RAS and Raf occur frequently and contribute to the oncogenic phenotype through activation of MEK and then ERK. Inhibitors of MEK have been shown to effectively block upregulated ERK/MAPK signaling in a range of cancer cell lines and have further demonstrated early evidence of efficacy in the clinic for the treatment of cancer. Guided by structural insight, a strategy aimed at the identification of an optimal diphenylamine-based MEK inhibitor with an improved metabolism and safety profile versus PD-0325901 led to the discovery of development candidate 1-({3,4-difluoro-2-[(2-fluoro-4-iodophenyl)amino]phenyl}carbonyl)-3-[(2S)-piperidin-2-yl]azetidin-3-ol (XL518, GDC-0973) (1). XL518 exhibits robust in vitro and in vivo potency and efficacy in preclinical models with sustained duration of action and is currently in early stage clinical trials.

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Organizational Affiliation: 

Exelixis Inc. , 210 East Grand Avenue, South San Francisco, California 94080, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 1	A	301	Homo sapiens	Mutation(s): 3  Gene Names: MAP2K1, MEK1, PRKMK1 EC: 2.7.12.2
Find proteins for Q02750 (Homo sapiens) Explore Q02750  Go to UniProtKB:  Q02750
NIH Common Fund Data Resources
PHAROS:  Q02750 GTEx:  ENSG00000169032

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	A	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
5Y0	A	N-[(2S)-2,3-bis(oxidanyl)propoxy]-3,4-bis(fluoranyl)-2-[(2-fluoranyl-4-iodanyl-phenyl)amino]benzamide C16 H14 F3 I N2 O4 SUDAHWBOROXANE-VIFPVBQESA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
5Y0	IC50 :  0.6000000238418579   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.283 
• R-Value Work: 0.226 
• R-Value Observed: 0.229 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.659	α = 90
b = 108.659	β = 90
c = 50.113	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-03-15 
• Released Date: 2012-12-19 
Deposition Author(s): Rice, K.D., Aay, N., Anand, N.K., Blazey, C.M., Bowles, O.J., Bussenius, J., Costanzo, S., Curtis, J.K., Defina, S.C., Dubenko, L., Engst, S., Joshi, A.A., Kennedy, A.R., Kim, A.I., Koltun, E.S., Lougheed, J.C., Manalo, J.C.L., Martini, J.F., Nuss, J.M., Peto, C.J., Tsang, T.H., Yu, P., Johnston, S.

Revision History  

• Version 1.0: 2012-12-19
  Type: Initial release
  
• Version 1.1: 2014-06-18
  Changes: Database references
• Version 1.2: 2019-05-08
  Changes: Data collection, Experimental preparation, Other