2UVM

Structure of PKBalpha PH domain in complex with a novel inositol headgroup surrogate, benzene 1,2,3,4-tetrakisphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.252 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Novel Inositol Phospholipid Headgroup Surrogate Crystallised in the Pleckstrin Homology Domain of Protein Kinase Balpha.

Mills, S.J.Komander, D.Trusselle, M.N.Safrany, S.T.Van Aalten, D.M.F.Potter, B.V.L.

(2007) Acs Chem.Biol. 2: 242

  • DOI: 10.1021/cb700019r

  • PubMed Abstract: 
  • Protein kinase B (PKB/Akt) plays a key role in cell signaling. The PH domain of PKB binds phosphatidylinositol 3,4,5-trisphosphate translocating PKB to the plasma membrane for activation by 3-phosphoinositide-dependent protein kinase 1. The crystal s ...

    Protein kinase B (PKB/Akt) plays a key role in cell signaling. The PH domain of PKB binds phosphatidylinositol 3,4,5-trisphosphate translocating PKB to the plasma membrane for activation by 3-phosphoinositide-dependent protein kinase 1. The crystal structure of the headgroup inositol 1,3,4,5-tetrakisphosphate Ins(1,3,4,5)P4-PKB complex facilitates in silico ligand design. The novel achiral analogue benzene 1,2,3,4-tetrakisphosphate (Bz(1,2,3,4)P4) possesses phosphate regiochemistry different from that of Ins(1,3,4,5)P4 and surprisingly binds with similar affinity as the natural headgroup. Bz(1,2,3,4)P4 co-crystallizes with the PKBalpha PH domain in a fashion also predictable in silico. The 2-phosphate of Bz(1,2,3,4)P4 does not interact with any residue, and the D5-phosphate of Ins(1,3,4,5)P4 is not mimicked by Bz(1,2,3,4)P4. Bz(1,2,3,4)P4 is an example of a simple inositol phosphate surrogate crystallized in a protein, and this approach could be applied to design modulators of inositol polyphosphate binding proteins.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RAC-ALPHA SERINE/THREONINE-PROTEIN KINASE
A
123Homo sapiensMutation(s): 0 
Gene Names: AKT1 (PKB, RAC)
EC: 2.7.11.1
Find proteins for P31749 (Homo sapiens)
Go to Gene View: AKT1
Go to UniProtKB:  P31749
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GVF
Query on GVF

Download SDF File 
Download CCD File 
A
BENZENE-1,2,3,4-TETRAYL TETRAKIS[DIHYDROGEN (PHOSPHATE)]
C6 H10 O16 P4
UKRGHRHHBNLNDD-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GVFKi: 80 nM (100) BINDINGDB
GVFKi: 80 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.252 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 80.029α = 90.00
b = 34.040β = 112.25
c = 44.944γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-04-17
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance