Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 41.44 kDa 
• Atom Count: 2782 
• Modelled Residue Count: 340 
• Deposited Residue Count: 358 
• Unique protein chains: 1

7PUS

ERK5 in complex with Pyrrole Carboxamide scaffold

• PDB DOI: 10.2210/pdb7PUS/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2021-09-30 Released: 2022-05-11 
• Deposition Author(s): Tucker, J.A., Martin, M.P., Endicott, J.A., Noble, M.E.N.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.285 
• R-Value Work: 0.219 

wwPDB Validation 

Currently 7PUS does not have a validation slider image.

Literature

Parallel Optimization of Potency and Pharmacokinetics Leading to the Discovery of a Pyrrole Carboxamide ERK5 Kinase Domain Inhibitor.

Miller, D.C., Reuillon, T., Molyneux, L., Blackburn, T., Cook, S.J., Edwards, N., Endicott, J.A., Golding, B.T., Griffin, R.J., Hardcastle, I., Harnor, S.J., Heptinstall, A., Lochhead, P., Martin, M.P., Martin, N.C., Myers, S., Newell, D.R., Noble, R.A., Phillips, N., Rigoreau, L., Thomas, H., Tucker, J.A., Wang, L.Z., Waring, M.J., Wong, A.C., Wedge, S.R., Noble, M.E.M., Cano, C.

(2022) J Med Chem 

• PubMed: 35468293 
• DOI: 10.1021/acs.jmedchem.1c01756
• Primary Citation of Related Structures:  
  7PUS


• PubMed Abstract: 
  

The nonclassical extracellular signal-related kinase 5 (ERK5) mitogen-activated protein kinase pathway has been implicated in increased cellular proliferation, migration, survival, and angiogenesis; hence, ERK5 inhibition may be an attractive approach for cancer treatment. However, the development of selective ERK5 inhibitors has been challenging. Previously, we described the development of a pyrrole carboxamide high-throughput screening hit into a selective, submicromolar inhibitor of ERK5 kinase activity. Improvement in the ERK5 potency was necessary for the identification of a tool ERK5 inhibitor for target validation studies. Herein, we describe the optimization of this series to identify nanomolar pyrrole carboxamide inhibitors of ERK5 incorporating a basic center, which suffered from poor oral bioavailability. Parallel optimization of potency and in vitro pharmacokinetic parameters led to the identification of a nonbasic pyrazole analogue with an optimal balance of ERK5 inhibition and oral exposure.

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Organizational Affiliation: 

Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 7	A [auth AAA]	358	Homo sapiens	Mutation(s): 0  Gene Names: MAPK7, BMK1, ERK5, PRKM7 EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q13164 (Homo sapiens) Explore Q13164  Go to UniProtKB:  Q13164
PHAROS:  Q13164 GTEx:  ENSG00000166484

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
86E (Subject of Investigation/LOI)	B [auth AAA]	4-[3,6-bis(chloranyl)-2-fluoranyl-phenyl]carbonyl-~{N}-(1-methylpyrazol-4-yl)-1~{H}-pyrrole-2-carboxamide C16 H11 Cl2 F N4 O2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.285 
• R-Value Work: 0.219 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.671	α = 90
b = 91.671	β = 90
c = 113.81	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
DIALS	data reduction
pointless	data scaling
PHASER	phasing

Structure Validation

Currently 7PUS does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Deposited Date: 2021-09-30 
• Released Date: 2022-05-11 
Deposition Author(s): Tucker, J.A., Martin, M.P., Endicott, J.A., Noble, M.E.N.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	--

Revision History  

• Version 1.0: 2022-05-11
  Type: Initial release