5MY8 | pdb_00005my8

Crystal structure of SRPK1 in complex with SPHINX31


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.200 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.166 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5MY8

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 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.

Macromolecule Content 

  • Total Structure Weight: 45.71 kDa 
  • Atom Count: 3,511 
  • Modeled Residue Count: 355 
  • Deposited Residue Count: 383 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.200 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.166 (Depositor) 
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

View Full Validation Report



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