4A9C | pdb_00004a9c

Crystal structure of human SHIP2 in complex with biphenyl 2,3',4,5',6- pentakisphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.221 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.1 of the entry. See complete history


Literature

A Synthetic Polyphosphoinositide Headgroup Surrogate in Complex with Ship2 Provides a Rationale for Drug Discovery.

Mills, S.J.Persson, C.Cozier, G.Thomas, M.P.Tresaugues, L.Erneux, C.Riley, A.M.Nordlund, P.Potter, B.V.L.

(2012) ACS Chem Biol 7: 822

  • DOI: https://doi.org/10.1021/cb200494d
  • Primary Citation of Related Structures:  
    4A9C

  • PubMed Abstract: 

    Phosphoinositides regulate many cellular processes, and cellular levels are controlled by kinases and phosphatases. SHIP2 (SH2 (Src homology 2)-domain-containing inositol-phosphatase-2) plays a critical role in phosphoinositide signaling, cleaving the 5-phosphate from phosphatidylinositol 3,4,5-trisphosphate. SHIP2 is thought to be involved in type-2 diabetes and obesity, conditions that could therefore be open to pharmacological modulation of the enzyme. However, rational design of SHIP2 inhibitors has been limited by the absence of a high-resolution structure. Here, we present a 2.1 Å resolution crystal structure of the phosphatase domain of SHIP2 bound to the synthetic ligand biphenyl 2,3',4,5',6-pentakisphosphate (BiPh(2,3',4,5',6)P(5)). BiPh(2,3',4,5',6)P(5) is not a SHIP2 substrate but inhibits Ins(1,3,4,5)P(4) hydrolysis with an IC(50) of 24.8 ± 3.0 μM, (K(m) for Ins(1,3,4,5)P(4) is 215 ± 28 μM). Molecular dynamics simulations suggest that when BiPh(2,3',4,5',6)P(5) binds to SHIP2, a flexible loop folds over and encloses the ligand. Compounds targeting such a closed conformation might therefore deliver SHIP2-specific drugs.


  • Organizational Affiliation

    Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Bath BA2 7AY, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHOSPHATIDYLINOSITOL-3,4,5-TRISPHOSPHATE 5-PHOSPHATASE 2
A, B
316Homo sapiensMutation(s): 0 
EC: 3.1.3.86
UniProt & NIH Common Fund Data Resources
Find proteins for O15357 (Homo sapiens)
Explore O15357 
Go to UniProtKB:  O15357
PHAROS:  O15357
GTEx:  ENSG00000165458 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15357
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B5F
Query on B5F

Download Ideal Coordinates CCD File 
C [auth B]BIPHENYL 2,3',4,5',6-PENTAKISPHOSPHATE
C12 H15 O20 P5
ZCSNVIKBMFGCLE-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
B5F BindingDB:  4A9C IC50: min: 29, max: 3600 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.221 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.246α = 90
b = 61.52β = 91.94
c = 114.742γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

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 B5FClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-30
    Type: Initial release
  • Version 1.1: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description