5MY8

Crystal structure of SRPK1 in complex with SPHINX31


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Development of Potent, Selective SRPK1 Inhibitors as Potential Topical Therapeutics for Neovascular Eye Disease.

Batson, J.Toop, H.D.Redondo, C.Babaei-Jadidi, R.Chaikuad, A.Wearmouth, S.F.Gibbons, B.Allen, C.Tallant, C.Zhang, J.Du, C.Hancox, J.C.Hawtrey, T.Da Rocha, J.Griffith, R.Knapp, S.Bates, D.O.Morris, J.C.

(2017) ACS Chem Biol 12: 825-832

  • DOI: https://doi.org/10.1021/acschembio.6b01048
  • Primary Citation of Related Structures:  
    5MXX, 5MY8, 5MYV

  • PubMed Abstract: 

    Serine/arginine-protein kinase 1 (SRPK1) regulates alternative splicing of VEGF-A to pro-angiogenic isoforms and SRPK1 inhibition can restore the balance of pro/antiangiogenic isoforms to normal physiological levels. The lack of potency and selectivity of available compounds has limited development of SRPK1 inhibitors, with the control of alternative splicing by splicing factor-specific kinases yet to be translated. We present here compounds that occupy a binding pocket created by the unique helical insert of SRPK1, and trigger a backbone flip in the hinge region, that results in potent (<10 nM) and selective inhibition of SRPK1 kinase activity. Treatment with these inhibitors inhibited SRPK1 activity and phosphorylation of serine/arginine splicing factor 1 (SRSF1), resulting in alternative splicing of VEGF-A from pro-angiogenic to antiangiogenic isoforms. This property resulted in potent inhibition of blood vessel growth in models of choroidal angiogenesis in vivo. This work identifies tool compounds for splice isoform selective targeting of pro-angiogenic VEGF, which may lead to new therapeutic strategies for a diversity of diseases where dysfunctional splicing drives disease development.


  • Organizational Affiliation

    Exonate Ltd , Unit 23, Cambridge Science Park, Cambridge, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SRSF protein kinase 1,SRSF protein kinase 1383Homo sapiensMutation(s): 0 
Gene Names: SRPK1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96SB4 (Homo sapiens)
Explore Q96SB4 
Go to UniProtKB:  Q96SB4
PHAROS:  Q96SB4
GTEx:  ENSG00000096063 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96SB4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RXZ
Query on RXZ

Download Ideal Coordinates CCD File 
Y [auth A]SPHINX31
C27 H24 F3 N5 O2
VURLRACCOCGFDB-UHFFFAOYSA-N
CIT
Query on CIT

Download Ideal Coordinates CCD File 
B [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
D [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
RXZ BindingDB:  5MY8 IC50: min: 3.18, max: 6 (nM) from 3 assay(s)
-TΔS: -1.61e+1 (kJ/mol) from 1 assay(s)
ΔH: -2.50e+1 (kJ/mol) from 1 assay(s)
ΔG: -4.15e+1 (kJ/mol) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.883α = 90
b = 74.883β = 90
c = 310.129γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-10
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Data collection, Database references