8AHI

PAC-FragmentDEL: Photoactivated covalent capture of DNA encoded fragments for hit discovery


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.155 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted M56Click on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

PAC-FragmentDEL - photoactivated covalent capture of DNA-encoded fragments for hit discovery.

Ma, H.Murray, J.B.Luo, H.Cheng, X.Chen, Q.Song, C.Duan, C.Tan, P.Zhang, L.Liu, J.Morgan, B.A.Li, J.Wan, J.Baker, L.M.Finnie, W.Guetzoyan, L.Harris, R.Hendrickson, N.Matassova, N.Simmonite, H.Smith, J.Hubbard, R.E.Liu, G.

(2022) RSC Med Chem 13: 1341-1349

  • DOI: https://doi.org/10.1039/d2md00197g
  • Primary Citation of Related Structures:  
    8AHE, 8AHF, 8AHG, 8AHH, 8AHI

  • PubMed Abstract: 

    We describe a novel approach for screening fragments against a protein that combines the sensitivity of DNA-encoded library technology with the ability of fragments to explore what will bind. Each of the members of the library consists of a fragment which is linked to a photoactivatable diazirine moiety. Split and pool synthesis combines each fragment with a set of linkers with the version of the library reported here containing some 70k different compounds, each with an individual DNA code. Incubation of the library with a protein sample is followed by photoactivation, washing and subsequent PCR and sequencing which allows the individual fragment hits to be identified. We illustrate how the approach allows successful hit fragment identification using only microgram quantities of material for two targets. PAK4 is a kinase for which conventional fragment screening has generated many advance leads. The as yet undrugged target, 2-epimerase, presents a more challenging active site for identification of hit compounds. In both cases, PAC-FragmentDEL identified fragments validated as hits by ligand-observed NMR measurements and crystal structure determination of off-DNA sample binding to the proteins.


  • Organizational Affiliation

    HitGen Inc. Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District Chengdu 610000 Sichuan P. R. China huiyong.ma@hitgen.com hd.luo@hitgen.com xm.cheng@hitgen.com qx.chen@hitgen.com chao.song@hitgen.com cong.duan@hitgen.com ping.tan@hitgen.com lf.zhang@hitgen.com jian.liu@hitgen.com barry.morgan@hitgen.com jin.li@hitgen.com jq.wan@hitgen.com gs.liu@hitgen.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PAK 4297Homo sapiensMutation(s): 1 
Gene Names: PAK4KIAA1142
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O96013 (Homo sapiens)
Explore O96013 
Go to UniProtKB:  O96013
PHAROS:  O96013
GTEx:  ENSG00000130669 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO96013
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
M56 (Subject of Investigation/LOI)
Query on M56

Download Ideal Coordinates CCD File 
B [auth A]~{N}-methyl-1,3-benzothiazole-6-carboxamide
C9 H8 N2 O S
KSBMLBBPMOTYRO-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.155 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.913α = 90
b = 61.913β = 90
c = 181.903γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted M56Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-14
    Type: Initial release
  • Version 1.1: 2022-12-07
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description