3ZLY

Crystal structure of MEK1 in complex with fragment 8

• PDB DOI: https://doi.org/10.2210/pdb3ZLY/pdb

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


• Deposited: 2013-02-04 Released: 2013-05-22 
• Deposition Author(s): Amaning, K., Lowinsky, M., Vallee, F., Steier, V., Marcireau, C., Ugolini, A., Delorme, C., McCort, G., Andouche, C., Vougier, S., Llopart, S., Halland, N., Rak, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 0.248 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

Literature

The Use of Virtual Screening and Differential Scanning Fluorimetry for the Rapid Identification of Fragments Active Against Mek1.

Amaning, K., Lowinski, M., Vallee, F., Steier, V., Marcireau, C., Ugolini, A., Delorme, C., Foucalt, F., Mccort, G., Derimay, N., Andouche, C., Vougier, S., Llopart, S., Halland, N., Rak, A.

(2013) Bioorg Med Chem Lett 23: 3620

• PubMed: 23648182 
• DOI: https://doi.org/10.1016/j.bmcl.2013.04.003
• Primary Citation of Related Structures:  
  3ZLS, 3ZLW, 3ZLX, 3ZLY, 3ZM4


• PubMed Abstract: 
  

  We report the analysis of an in-house fragment screening campaign for the oncology target MEK1. The application of virtual screening (VS) as a primary fragment screening approach, followed by biophysical validation using differential screening fluorimetry (DSF), with resultant binding mode determination by X-ray crystallography (X-ray), is presented as the most time and cost-effective combination of in silico and in vitro methods to identify fragments. We demonstrate the effectiveness of the VS-DSF workflow for the early identification of fragments to both 'jump-start' the drug discovery project and to complement biochemical screening data.

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Organizational Affiliation: 

Sanofi, Structure Design and Informatics,13 Quai Guesde, B.P.14, F-94408 Vitry-Sur-Seine, France. [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: 39.08 kDa 
• Atom Count: 2,536 
• Modelled Residue Count: 310 
• Deposited Residue Count: 348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 1	A	348	Homo sapiens	Mutation(s): 3  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YSO	B [auth A]	3-AMINO-1H-INDAZOLE-4-CARBONITRILE C8 H6 N4 KVXRKRURRSOVSJ-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
YSO	BindingDB:  3ZLY	IC50: 3.00e+5 (nM) from 1 assay(s)
	PDBBind:  3ZLY	IC50: 3.00e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 0.248 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.759	α = 90
b = 76.759	β = 90
c = 221.768	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-22 
Deposition Author(s): Amaning, K., Lowinsky, M., Vallee, F., Steier, V., Marcireau, C., Ugolini, A., Delorme, C., McCort, G., Andouche, C., Vougier, S., Llopart, S., Halland, N., Rak, A.

Revision History  

• Version 1.0: 2013-05-22
  Type: Initial release
  
• Version 1.1: 2013-05-29
  Changes: Database references
• Version 1.2: 2018-05-02
  Changes: Data collection, Experimental preparation
• Version 1.3: 2019-04-24
  Changes: Data collection, Source and taxonomy
• Version 1.4: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other