1BX6

CRYSTAL STRUCTURE OF THE POTENT NATURAL PRODUCT INHIBITOR BALANOL IN COMPLEX WITH THE CATALYTIC SUBUNIT OF CAMP-DEPENDENT PROTEIN KINASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.340 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the potent natural product inhibitor balanol in complex with the catalytic subunit of cAMP-dependent protein kinase.

Narayana, N.Diller, T.C.Koide, K.Bunnage, M.E.Nicolaou, K.C.Brunton, L.L.Xuong, N.H.Ten Eyck, L.F.Taylor, S.S.

(1999) Biochemistry 38: 2367-2376

  • DOI: 10.1021/bi9820659

  • PubMed Abstract: 
  • Endogenous protein kinase inhibitors are essential for a wide range of physiological functions. These endogenous inhibitors may mimic peptide substrates as in the case of the heat-stable protein kinase inhibitor (PKI), or they may mimic nucleotide tr ...

    Endogenous protein kinase inhibitors are essential for a wide range of physiological functions. These endogenous inhibitors may mimic peptide substrates as in the case of the heat-stable protein kinase inhibitor (PKI), or they may mimic nucleotide triphosphates. Natural product inhibitors, endogenous to the unique organisms producing them, can be potent exogenous inhibitors against foreign protein kinases. Balanol is a natural product inhibitor exhibiting low nanomolar Ki values against serine and threonine specific kinases, while being ineffective against protein tyrosine kinases. To elucidate balanol's specific inhibitory effects and provide a basis for understanding inhibition-regulated biological processes, a 2.1 A resolution crystal structure of balanol in complex with cAMP-dependent protein kinase (cAPK) was determined. The structure reveals conserved binding regions and displays extensive complementary interactions between balanol and conserved cAPK residues. This report describes the structure of a protein kinase crystallized with a natural ATP mimetic in the absence of metal ions and peptide inhibitor.


    Related Citations: 
    • A Binary Complex of the Catalytic Subunit of Camp-Dependent Protein Kinase and Adenosine Further Defines Conformational Flexibility
      Narayana, N.,Cox, S.,Xuong, N.H.,Ten Eyck, L.F.,Taylor, S.S.
      (1997) Structure 5: 921
    • Crystal Structure of a Polyhistidine-Tagged Recombinant Catalytic Subunit of Camp-Dependent Protein Kinase Complexed with the Peptide Inhibitor Pki(5-24) and Adenosine
      Narayana, N.,Cox, S.,Shaltiel, S.,Taylor, S.S.,Xuong, N.H.
      (1997) Biochemistry 36: 4438
    • Expression of the Catalytic Subunit of Camp-Dependent Protein Kinase in Escherichia Coli: Multiple Isozymes Reflect Different Phosphorylation States
      Herberg, F.W.,Bell, S.M.,Taylor, S.S.
      (1993) Protein Eng. 6: 771
    • Crystal Structure of the Catalytic Subunit of Camp-Dependent Protein Kinase Complexed with Mgatp and Peptide Inhibitor
      Zheng, J.,Knighton, D.R.,Ten Eyck, L.F.,Karlsson, R.,Xuong, N.H.,Taylor, S.S.,Sowadski, J.M.
      (1993) Biochemistry 32: 2154
    • Structure of a Peptide Inhibitor Bound to the Catalytic Subunit of Cyclic Adenosine Monophosphate-Dependent Protein Kinase
      Knighton, D.R.,Zheng, J.H.,Ten Eyck, L.F.,Xuong, N.H.,Taylor, S.S.,Sowadski, J.M.
      (1991) Science 253: 414
    • Crystal Structure of the Catalytic Subunit of Cyclic Adenosine Monophosphate-Dependent Protein Kinase
      Knighton, D.R.,Zheng, J.H.,Ten Eyck, L.F.,Ashford, V.A.,Xuong, N.H.,Taylor, S.S.,Sowadski, J.M.
      (1991) Science 253: 407


    Organizational Affiliation

    The Howard Hughes Medical Institute, Department of Biology, University of California, San Diego, La Jolla, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CAMP-DEPENDENT PROTEIN KINASE
A
350Mus musculusGene Names: Prkaca (Pkaca)
EC: 2.7.11.11
Find proteins for P05132 (Mus musculus)
Go to UniProtKB:  P05132
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BA1
Query on BA1

Download SDF File 
Download CCD File 
A
BALANOL
C28 H26 N2 O10
XYUFCXJZFZPEJD-XMSQKQJNSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BA1Ki: 4.7 nM (96) BINDINGDB
BA1IC50: 40 - 60 nM (97) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.340 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.190α = 90.00
b = 73.180β = 90.00
c = 99.770γ = 90.00
Software Package:
Software NamePurpose
UCSDdata reduction
TNTrefinement
UCSDdata scaling
X-PLORphasing
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-04-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance