3MBL | pdb_00003mbl

Crystal Structure of the human mitogen-activated protein kinase kinase 1 (MEK 1) in complex with ligand and MgADP

• PDB DOI: https://doi.org/10.2210/pdb3MBL/pdb

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


• Deposited: 2010-03-25 Released: 2010-07-28 
• Deposition Author(s): Dougan, D.R., Mol, C.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.215 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Literature

Structure-based design and synthesis of pyrrole derivatives as MEK inhibitors.

Wallace, M.B., Adams, M.E., Kanouni, T., Mol, C.D., Dougan, D.R., Feher, V.A., O'Connell, S.M., Shi, L., Halkowycz, P., Dong, Q.

(2010) Bioorg Med Chem Lett 20: 4156-4158

• PubMed: 20621728 
• DOI: https://doi.org/10.1016/j.bmcl.2010.05.058
• Primary Citation Related Structures: 
  3MBL


• PubMed Abstract: 
  

  A novel series of pyrrole inhibitors of MEK kinase has been developed using structure-based drug design. Optimization of the series led to the identification of potent inhibitors with good pharmaceutical properties.

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Organizational Affiliation: 
• Takeda San Diego, 10410 Science Center Drive, San Diego, CA 92121, United States. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 37.55 kDa 
• Atom Count: 2,420 
• Modeled Residue Count: 290 
• 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, MEK 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LSG	D [auth A]	5-acetyl-2-[(2-fluoro-4-iodophenyl)amino]-N-(2-hydroxyethoxy)-1-methyl-1H-pyrrole-3-carboxamide C16 H17 F I N3 O4 WRHOGNMBUWCIAC-UHFFFAOYSA-N
ADP	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
LSG	BindingDB:  3MBL	IC50: 18 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.215 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.982	α = 90
b = 81.982	β = 90
c = 129.928	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-28 
Deposition Author(s): Dougan, D.R., Mol, C.D.

Revision History  

• Version 1.0: 2010-07-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations