3WZU | pdb_00003wzu

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 
    0.322 (Depositor), 0.322 (DCC) 
  • R-Value Work: 
    0.236 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 
    0.240 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 

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

  • DOI: https://doi.org/10.1016/j.bmcl.2014.12.011
  • Primary Citation 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.

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

Macromolecule Content 

  • Total Structure Weight: 37.36 kDa 
  • Atom Count: 2,200 
  • Modeled Residue Count: 270 
  • Deposited Residue Count: 324 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dual specificity mitogen-activated protein kinase kinase 7324Homo sapiensMutation(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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14733
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1FM

Query on 1FM


Download:Ideal Coordinates CCD File
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 
IDSourceBinding 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 (Depositor), 0.322 (DCC) 
  • R-Value Work:  0.236 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 0.240 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.395α = 90
b = 71.395β = 90
c = 268.817γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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