6QG4 | pdb_00006qg4

Structure of the mitogen activated kinase kinase 7 in complex with pyrazolopyrimidine inhibitor 1h

• PDB DOI: https://doi.org/10.2210/pdb6QG4/pdb

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


• Deposited: 2019-01-10 Released: 2019-05-22 
• Deposition Author(s): Wolle, P., Mueller, M.P., Rauh, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.269 (Depositor) 
• R-Value Work: 
  0.234 (Depositor) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

Literature

Characterization of Covalent Pyrazolopyrimidine-MKK7 Complexes and a Report on a Unique DFG-in/Leu-in Conformation of Mitogen-Activated Protein Kinase Kinase 7 (MKK7).

Wolle, P., Engel, J., Smith, S., Goebel, L., Hennes, E., Lategahn, J., Rauh, D.

(2019) J Med Chem 62: 5541-5546

• PubMed: 31083997 
• DOI: https://doi.org/10.1021/acs.jmedchem.9b00472
• Primary Citation Related Structures: 
  6QFL, 6QFR, 6QFT, 6QG4, 6QG7, 6QHO, 6QHR


• PubMed Abstract: 
  

  Pyrazolopyrimidines are well-established as covalent inhibitors of protein kinases such as the epidermal growth factor receptor or Bruton's tyrosine kinase, and we recently described their potential in targeting mitogen-activated protein kinase kinase 7 (MKK7). Herein, we report the structure-activity relationship of pyrazolopyrimidine-based MKK7 inhibitors and solved several complex crystal structures to gain insights into their binding mode. In addition, we present two structures of apo-MKK7, exhibiting a DFG-out and an unprecedented DFG-in/Leu-in conformation.

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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.

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: 36.51 kDa 
• Atom Count: 2,114 
• Modeled Residue Count: 272 
• 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
J0E	B [auth A]	1-[(3~{R})-3-[4-azanyl-3-(4-hydroxyphenyl)pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl]propan-1-one C19 H22 N6 O2 OMHARXNEFRLRTL-CYBMUJFWSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.269 (Depositor) 
• R-Value Work:  0.234 (Depositor) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.2	α = 90
b = 67	β = 90
c = 86.1	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-05-22 
Deposition Author(s): Wolle, P., Mueller, M.P., Rauh, D.

Revision History  

• Version 1.0: 2019-05-22
  Type: Initial release
  
• Version 1.1: 2019-05-29
  Changes: Data collection, Database references
• Version 1.2: 2019-06-12
  Changes: Data collection, Database references
• Version 1.3: 2019-06-26
  Changes: Data collection, Database references
• Version 1.4: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-11-13
  Changes: Structure summary