3WZU

THE STRUCTURE OF MAP2K7 IN COMPLEX WITH 5Z-7-oxozeaenol

• PDB DOI: https://doi.org/10.2210/pdb3WZU/pdb

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


• Deposited: 2014-10-07 Released: 2015-01-14 
• Deposition Author(s): Sogabe, Y., Hashimoto, Y., Matsumoto, T., Kinoshita, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.01 Å
• R-Value Free: 0.322 
• R-Value Work: 0.236 
• R-Value Observed: 0.240 

Starting Model: experimental

Literature

5Z-7-Oxozeaenol covalently binds to MAP2K7 at Cys218 in an unprecedented manner.

Sogabe, Y., Matsumoto, T., Hashimoto, T., Kirii, Y., Sawa, M., Kinoshita, T.

(2015) Bioorg Med Chem Lett 25: 593-596

• PubMed: 25529738 
• DOI: https://doi.org/10.1016/j.bmcl.2014.12.011
• Primary Citation of Related Structures:  
  3WZU


• PubMed Abstract: 
  

  5Z-7-Oxozeaenol (5Z7O) is a covalent bonding inhibitor against the several protein kinases (e.g., ERK2 and TAK1) that possess a free cysteine at the gatekeeper-2 position. In addition to this cysteine, MAP2K7 has three other cysteine residues that are candidate for covalent bonding by the inhibitor 5Z7O. The crystal structure of the MAP2K7/5Z7O complex revealed that the inhibitor binds to MAP2K7 at a cysteine residue located at the end of the hinge region and not at the gatekeeper-2 residue. The structural insights into the interaction of 5Z7O with MAP2K7 should aid the development of 5Z7O derivatives with improved potency and selectivity.

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Organizational Affiliation: 

Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan.

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: 37.36 kDa 
• Atom Count: 2,200 
• Modelled Residue Count: 270 
• Deposited Residue Count: 324 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity mitogen-activated protein kinase kinase 7	A	324	Homo sapiens	Mutation(s): 0  Gene Names: MAP2K7, JNKK2, MEK7, MKK7, PRKMK7, SKK4 EC: 2.7.12.2
UniProt & NIH Common Fund Data Resources
Find proteins for O14733 (Homo sapiens) Explore O14733  Go to UniProtKB:  O14733
PHAROS:  O14733 GTEx:  ENSG00000076984

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1FM	B [auth A]	(3S,5Z,8S,9S,11E)-8,9,16-trihydroxy-14-methoxy-3-methyl-3,4,9,10-tetrahydro-1H-2-benzoxacyclotetradecine-1,7(8H)-dione C19 H22 O7 NEQZWEXWOFPKOT-BYRRXHGESA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
1FM	BindingDB:  3WZU	IC50: 1300 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.01 Å
• R-Value Free: 0.322 
• R-Value Work: 0.236 
• R-Value Observed: 0.240 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.395	α = 90
b = 71.395	β = 90
c = 268.817	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-14 
Deposition Author(s): Sogabe, Y., Hashimoto, Y., Matsumoto, T., Kinoshita, T.

Revision History  

• Version 1.0: 2015-01-14
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2022-08-24
  Changes: Database references, Derived calculations
• Version 1.3: 2023-11-08
  Changes: Data collection, Refinement description