6QA4

ERK2 mini-fragment binding

• PDB DOI: https://doi.org/10.2210/pdb6QA4/pdb

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


• Deposited: 2018-12-18 Released: 2019-06-26 
• Deposition Author(s): O'Reilly, M., Cleasby, A., Davies, T.G., Hall, R., Ludlow, F., Murray, C.W., Tisi, D., Jhoti, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.215 
• R-Value Work: 0.173 
• R-Value Observed: 0.176 

Literature

Crystallographic screening using ultra-low-molecular-weight ligands to guide drug design.

O'Reilly, M., Cleasby, A., Davies, T.G., Hall, R.J., Ludlow, R.F., Murray, C.W., Tisi, D., Jhoti, H.

(2019) Drug Discov Today 24: 1081-1086

• PubMed: 30878562 
• DOI: https://doi.org/10.1016/j.drudis.2019.03.009
• Primary Citation of Related Structures:  
  6Q7K, 6Q7S, 6Q7T, 6QA1, 6QA3, 6QA4, 6QAG, 6QAH, 6QAL, 6QAQ, 6QAW


• PubMed Abstract: 
  

  We present a novel crystallographic screening methodology (MiniFrags) that employs high-concentration aqueous soaks with a chemically diverse and ultra-low-molecular-weight library (heavy atom count 5-7) to identify ligand-binding hot and warm spots on proteins. We propose that MiniFrag screening represents a highly effective method for guiding optimisation of fragment-derived lead compounds or chemical tools and that the high screening hit rates reflect enhanced sampling of chemical space.

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Organizational Affiliation: 

Astex Pharmaceuticals,436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, UK.

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: mass spectrometry

Macromolecule Content

• Total Structure Weight: 43.03 kDa 
• Atom Count: 3,205 
• Modelled Residue Count: 337 
• Deposited Residue Count: 368 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 1	A	368	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 GTEx:  ENSG00000100030

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
HRZ	C [auth A], D [auth A], E [auth A], F [auth A]	1~{H}-pyridin-2-one C5 H5 N O UBQKCCHYAOITMY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.215 
• R-Value Work: 0.173 
• R-Value Observed: 0.176 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.293	α = 90
b = 69.633	β = 108.96
c = 60.156	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-06-26 
Deposition Author(s): O'Reilly, M., Cleasby, A., Davies, T.G., Hall, R., Ludlow, F., Murray, C.W., Tisi, D., Jhoti, H.

Revision History  

• Version 1.0: 2019-06-26
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Database references, Structure summary