5NHJ

Human Erk2 with an Erk1/2 inhibitor

• PDB DOI:  https://doi.org/10.2210/pdb5NHJ/pdb

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


• Deposited: 2017-03-21 Released: 2017-04-19 
• Deposition Author(s): Debreczeni, J.E., Ward, R.A., Bethel, P., Cook, C., Davies, E., Eckersley, K., Fairley, G., Feron, L., Flemington, V., Graham, M.A., Greenwood, R., Hopcroft, P., Howard, T.D., Hudson, J., James, M., Jones, C.D., Jones, C.R., Lamont, S., Lewis, R., Lindsay, N., Roberts, K., Simpson, I., StGallay, S., Swallow, S., Tonge, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 0.207 
• R-Value Work: 0.201 
• R-Value Observed: 0.202 

Literature

Structure-Guided Discovery of Potent and Selective Inhibitors of ERK1/2 from a Modestly Active and Promiscuous Chemical Start Point.

Ward, R.A., Bethel, P., Cook, C., Davies, E., Debreczeni, J.E., Fairley, G., Feron, L., Flemington, V., Graham, M.A., Greenwood, R., Griffin, N., Hanson, L., Hopcroft, P., Howard, T.D., Hudson, J., James, M., Jones, C.D., Jones, C.R., Lamont, S., Lewis, R., Lindsay, N., Roberts, K., Simpson, I., St-Gallay, S., Swallow, S., Tang, J., Tonge, M., Wang, Z., Zhai, B.

(2017) J Med Chem 60: 3438-3450

• PubMed: 28376306 
• DOI: https://doi.org/10.1021/acs.jmedchem.7b00267
• Primary Citation of Related Structures:  
  5NGU, 5NHF, 5NHH, 5NHJ, 5NHL, 5NHO, 5NHP, 5NHV


• PubMed Abstract: 
  

There are a number of small-molecule inhibitors targeting the RAS/RAF/MEK/ERK signaling pathway that have either been approved or are in clinical development for oncology across a range of disease indications. The inhibition of ERK1/2 is of significant current interest, as cell lines with acquired resistance to BRAF and MEK inhibitors have been shown to maintain sensitivity to ERK1/2 inhibition in preclinical models. This article reports on our recent work to identify novel, potent, and selective reversible ERK1/2 inhibitors from a low-molecular-weight, modestly active, and highly promiscuous chemical start point, compound 4. To guide and inform the evolution of this series, inhibitor binding mode information from X-ray crystal structures was critical in the rapid exploration of this template to compound 35, which was active when tested in in vivo antitumor efficacy experiments.

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Organizational Affiliation: 

Pharmaron Beijing Co., Ltd. , 6 Taihe Road BDA, Beijing, 100176, P.R. China.

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: 44.47 kDa 
• Atom Count: 2,961 
• Modelled Residue Count: 345 
• Deposited Residue Count: 381 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 1	A	381	Homo sapiens	Mutation(s): 0  Gene Names: MAPK1, ERK2, PRKM1, PRKM2 EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P28482 (Homo sapiens) Explore P28482  Go to UniProtKB:  P28482
PHAROS:  P28482

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8XE	D [auth A]	5-(2-methoxyethyl)-2-[2-[(2-methylpyrazol-3-yl)amino]pyrimidin-4-yl]-6,7-dihydro-1~{H}-pyrrolo[3,2-c]pyridin-4-one C18 H21 N7 O2 HKLUILZKCLFHGM-UHFFFAOYSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
8XE	Binding MOAD:  5NHJ	IC50: 5.39 (nM) from 1 assay(s)
	BindingDB:  5NHJ	IC50: min: 2.5, max: 1600 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 0.207 
• R-Value Work: 0.201 
• R-Value Observed: 0.202 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.025	α = 90
b = 71.158	β = 112.03
c = 61.398	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-19 
Deposition Author(s): Debreczeni, J.E., Ward, R.A., Bethel, P., Cook, C., Davies, E., Eckersley, K., Fairley, G., Feron, L., Flemington, V., Graham, M.A., Greenwood, R., Hopcroft, P., Howard, T.D., Hudson, J., James, M., Jones, C.D., Jones, C.R., Lamont, S., Lewis, R., Lindsay, N., Roberts, K., Simpson, I., StGallay, S., Swallow, S., Tonge, M.

Revision History  

• Version 1.0: 2017-04-19
  Type: Initial release
  
• Version 1.1: 2017-05-10
  Changes: Database references