3V04

Discovery of Novel Allosteric MEK Inhibitors Possessing Classical and Non-classical Bidentate Ser212 Interactions.

• PDB DOI: https://doi.org/10.2210/pdb3V04/pdb

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


• Deposited: 2011-12-07 Released: 2012-05-09 
• Deposition Author(s): Heald, R., Jackson, P., Savy, P., Jones, M., Gancia, E., Burton, B., Newman, R., Boggs, J., Chan, E., Chan, J., Choo, E., Merchant, M., Ultsch, M., Wiesmann, C., Belvin, M., Price, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.243 
• R-Value Work: 0.212 
• R-Value Observed: 0.213 

Starting Model: experimental

Literature

Discovery of Novel Allosteric Mitogen-Activated Protein Kinase Kinase (MEK) 1,2 Inhibitors Possessing Bidentate Ser212 Interactions.

Heald, R.A., Jackson, P., Savy, P., Jones, M., Gancia, E., Burton, B., Newman, R., Boggs, J., Chan, E., Chan, J., Choo, E., Merchant, M., Rudewicz, P., Ultsch, M., Wiesmann, C., Yue, Q., Belvin, M., Price, S.

(2012) J Med Chem 55: 4594-4604

• PubMed: 22506516 
• DOI: https://doi.org/10.1021/jm2017094
• Primary Citation of Related Structures:  
  3V01, 3V04


• PubMed Abstract: 
  

  Using structure-based design, two novel series of highly potent biaryl amine mitogen-activated protein kinase kinase (MEK) inhibitors have been discovered. These series contain an H-bond acceptor, in a shifted position compared with previously disclosed compounds, and an adjacent H-bond donor, resulting in a bidentate interaction with the Ser212 residue of MEK1. The most potent compound identified, 1 (G-894), is orally active in in vivo pharmacodynamic and tumor xenograft models.

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Organizational Affiliation: 

Argenta, 8/9 Spire Green Centre, Flex Meadow, Harlow, Essex CM19 5TR, UK. [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: 38.92 kDa 
• Atom Count: 2,318 
• Modelled Residue Count: 289 
• Deposited Residue Count: 341 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity mitogen-activated protein kinase kinase 1	A	341	Homo sapiens	Mutation(s): 0  Gene Names: MAP2K1, MEK1, PRKMK1 EC: 2.7.12.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q02750 (Homo sapiens) Explore Q02750  Go to UniProtKB:  Q02750
PHAROS:  Q02750 GTEx:  ENSG00000169032

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	C [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
V04	B [auth A]	4-[(2-fluoro-4-iodophenyl)amino]-N-(2-hydroxyethoxy)-1H-indazole-5-carboxamide C16 H14 F I N4 O3 YMRXJLXWVAGVBT-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
V04	BindingDB:  3V04	IC50: 13 (nM) from 1 assay(s)
		EC50: min: 0.2, max: 0.4 (nM) from 2 assay(s)
	PDBBind:  3V04	IC50: 13 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.243 
• R-Value Work: 0.212 
• R-Value Observed: 0.213 
• Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.113	α = 90
b = 82.113	β = 90
c = 129.303	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-09 
Deposition Author(s): Heald, R., Jackson, P., Savy, P., Jones, M., Gancia, E., Burton, B., Newman, R., Boggs, J., Chan, E., Chan, J., Choo, E., Merchant, M., Ultsch, M., Wiesmann, C., Belvin, M., Price, S.

Revision History  

• Version 1.0: 2012-05-09
  Type: Initial release
  
• Version 1.1: 2012-07-18
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description