6IB0 | pdb_00006ib0

The structure of MKK7 in complex with the covalent 4-amino-pyrazolopyrimidine 3a

• PDB DOI: https://doi.org/10.2210/pdb6IB0/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-11-28 Released: 2019-02-27 
• Deposition Author(s): Wolle, P., Hardick, J., Mueller, M.P., Rauh, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.271 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

Targeting the MKK7-JNK (Mitogen-Activated Protein Kinase Kinase 7-c-Jun N-Terminal Kinase) Pathway with Covalent Inhibitors.

Wolle, P., Hardick, J., Cronin, S.J.F., Engel, J., Baumann, M., Lategahn, J., Penninger, J.M., Rauh, D.

(2019) J Med Chem 62: 2843-2848

• PubMed: 30768270 
• DOI: https://doi.org/10.1021/acs.jmedchem.9b00102
• Primary Citation Related Structures: 
  6IB0, 6IB2


• PubMed Abstract: 
  

  The protein kinase MKK7 is linked to neuronal development and the onset of cancer. The field, however, lacks high-quality functional probes that would allow for the dissection of its detailed functions. Against this background, we describe an effective covalent inhibitor of MKK7 based on the pyrazolopyrimidine scaffold.

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Organizational Affiliation: 
• Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Strasse 4a , 44227 Dortmund , Germany.
Drug Discovery Hub Dortmund (DDHD) am Zentrum für Integrierte Wirkstoffforschung (ZIW) , 44227 Dortmund , Germany.
Institute of Molecular Biotechnology, Austrian Academy of Sciences , Dr. Bohr Gasse 3 , AT-1030 Vienna , Austria.
Lead Discovery Center GmbH , Otto-Hahn-Strasse 15 , 44227 Dortmund , Germany.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 36.64 kDa 
• Atom Count: 2,323 
• Modeled Residue Count: 290 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity mitogen-activated protein kinase kinase 7	A	318	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
H8Z	B [auth A]	1-[(3~{R})-3-(4-azanyl-3-ethynyl-pyrazolo[3,4-d]pyrimidin-1-yl)piperidin-1-yl]prop-2-en-1-one C15 H16 N6 O XXFDMGXYEIKFNZ-SNVBAGLBSA-N
PG4	C [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
H8Z	BindingDB:  6IB0	IC50: 30 (nM) from 1 assay(s)
		EC50: 1.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.271 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.4	α = 90
b = 66	β = 90
c = 86.4	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-02-27 
Deposition Author(s): Wolle, P., Hardick, J., Mueller, M.P., Rauh, D.

Revision History  

• Version 1.0: 2019-02-27
  Type: Initial release
  
• Version 1.1: 2019-03-27
  Changes: Data collection, Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary