6QAH

ERK2 mini-fragment binding

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


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

  • 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 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.

    Organizational Affiliation: 

    Astex Pharmaceuticals,436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, UK. Electronic address: harren.jhoti@astx.com.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 1A368Homo sapiensMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28482
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
HVB
Query on HVB
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]		1-azanylpropylideneazanium
C3 H9 N2
GNFWGDKKNWGGJY-UHFFFAOYSA-O		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME		A L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.742α = 90
b = 69.782β = 109.6
c = 60.599γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release