3PP1

Crystal Structure of the Human Mitogen-activated protein kinase kinase 1 (MEK 1) in complex with ligand and MgATP

• PDB DOI: https://doi.org/10.2210/pdb3PP1/pdb

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


• Deposited: 2010-11-23 Released: 2011-02-23 
• Deposition Author(s): Dougan, D.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.219 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Literature

Discovery of TAK-733, a potent and selective MEK allosteric site inhibitor for the treatment of cancer.

Dong, Q., Dougan, D.R., Gong, X., Halkowycz, P., Jin, B., Kanouni, T., O'Connell, S.M., Scorah, N., Shi, L., Wallace, M.B., Zhou, F.

(2011) Bioorg Med Chem Lett 21: 1315-1319

• PubMed: 21310613 
• DOI: https://doi.org/10.1016/j.bmcl.2011.01.071
• Primary Citation of Related Structures:  
  3PP1


• PubMed Abstract: 
  

  A novel 5-phenylamino-8-methylpyrido[2,3-d]pyrimidine-4,7(3H,8H)-dione series of MEK inhibitors has been developed using structure-based drug design. Lead optimization of this series led to the discovery of TAK-733. This was advanced to Phase I clinical studies for cancer treatment.

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Organizational Affiliation: 

Takeda San Diego, San Diego, CA 92121, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37.73 kDa 
• Atom Count: 2,416 
• Modelled Residue Count: 291 
• Deposited Residue Count: 328 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity mitogen-activated protein kinase kinase 1	A	328	Homo sapiens	Mutation(s): 0  Gene Names: MAP2K1, Mapk/erk kinase 1, 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	B [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
IZG	D [auth A]	3-[(2R)-2,3-dihydroxypropyl]-6-fluoro-5-[(2-fluoro-4-iodophenyl)amino]-8-methylpyrido[2,3-d]pyrimidine-4,7(3H,8H)-dione C17 H15 F2 I N4 O4 RCLQNICOARASSR-SECBINFHSA-N
ACT	E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
IZG	BindingDB:  3PP1	IC50: min: 1.8, max: 6.9 (nM) from 4 assay(s)
	PDBBind:  3PP1	IC50: 3.2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.219 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.086	α = 90
b = 82.086	β = 90
c = 129.254	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-23 
Deposition Author(s): Dougan, D.R.

Revision History  

• Version 1.0: 2011-02-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations