7ZKX

SRPK2 IN COMPLEX WITH INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

MSC-1186, a Highly Selective Pan-SRPK Inhibitor Based on an Exceptionally Decorated Benzimidazole-Pyrimidine Core.

Schroder, M.Leiendecker, M.Gradler, U.Braun, J.Blum, A.Wanior, M.Berger, B.T.Kramer, A.Muller, S.Esdar, C.Knapp, S.Heinrich, T.

(2023) J Med Chem 66: 837-854

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01705
  • Primary Citation of Related Structures:  
    7ZKS, 7ZKX

  • PubMed Abstract: 

    The highly conserved catalytic sites in protein kinases make it difficult to identify ATP competitive inhibitors with kinome-wide selectivity. Serendipitously, during a dedicated fragment campaign for the focal adhesion kinase (FAK), a scaffold that had lost its initial FAK affinity showed remarkable potency and selectivity for serine-arginine-protein kinases 1-3 (SRPK1-3). Non-conserved interactions with the uniquely structured hinge region of the SRPK family were the key drivers of the exclusive selectivity of the discovered fragment hit. Structure-guided medicinal chemistry efforts led to the SRPK inhibitor MSC-1186 , which fulfills all hallmarks of a reversible chemical probe, including nanomolar cellular potency and excellent kinome-wide selectivity. The combination of MSC-1186 with CDC2-like kinase (CLK) inhibitors showed additive attenuation of SR-protein phosphorylation compared to the single agents. MSC-1186 and negative control ( MSC-5360 ) are chemical probes available via the Structural Genomics Consortium chemical probe program (https://www.sgc-ffm.uni-frankfurt.de/).


  • Organizational Affiliation

    SGC Frankfurt, Goethe University Frankfurt, Buchmann Institute for Life Sciences (BMLS), Riedberg Campus, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SRSF protein kinase 2619Homo sapiensMutation(s): 0 
Gene Names: SRPK2
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P78362 (Homo sapiens)
Explore P78362 
Go to UniProtKB:  P78362
PHAROS:  P78362
GTEx:  ENSG00000135250 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP78362
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IXQ (Subject of Investigation/LOI)
Query on IXQ

Download Ideal Coordinates CCD File 
B [auth A]N-[3-[[[2-(6-chloranyl-5-fluoranyl-1H-benzimidazol-2-yl)pyrimidin-4-yl]amino]methyl]pyridin-2-yl]-N-methyl-methanesulfonamide
C19 H17 Cl F N7 O2 S
SSZBLNIVOGDOJH-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A],
M [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A],
I [auth A],
J [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3
Query on NO3

Download Ideal Coordinates CCD File 
H [auth A],
K [auth A]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
L [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.755α = 90
b = 107.755β = 90
c = 90.228γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2023-02-22 
  • Deposition Author(s): Graedler, U.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-22
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Refinement description