1YDR

STRUCTURE OF CAMP-DEPENDENT PROTEIN KINASE, ALPHA-CATALYTIC SUBUNIT IN COMPLEX WITH H7 PROTEIN KINASE INHIBITOR 1-(5-ISOQUINOLINESULFONYL)-2-METHYLPIPERAZINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structures of catalytic subunit of cAMP-dependent protein kinase in complex with isoquinolinesulfonyl protein kinase inhibitors H7, H8, and H89. Structural implications for selectivity.

Engh, R.A.Girod, A.Kinzel, V.Huber, R.Bossemeyer, D.

(1996) J Biol Chem 271: 26157-26164

  • DOI: 10.1074/jbc.271.42.26157
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The discovery of several hundred different protein kinases involved in highly diverse cellular signaling pathways is in stark contrast to the much smaller number of known modulators of cell signaling. Of these, the H series protein kinase inhibitors ...

    The discovery of several hundred different protein kinases involved in highly diverse cellular signaling pathways is in stark contrast to the much smaller number of known modulators of cell signaling. Of these, the H series protein kinase inhibitors (1-(5-isoquinolinesulfonyl)-2-methylpiperazine (H7), N-[2-(methylamino)ethyl]-5-isoquinolinesulfonamide (H8) N-[2-(p-Bromocinnamylamino)ethyl]-5-isoquinolinesulfonamide (H89)) are frequently used to block signaling pathways in studies of cellular regulation. To elucidate inhibition mechanisms at atomic resolution and to enable structure-based drug design of potential therapeutic modulators of signaling pathways, we determined the crystal structures of corresponding complexes with the cAPK catalytic subunit. Complexes with H7 and H8 (2.2 A) and with H89 (2.3 A) define the binding mode of the isoquinoline-sulfonamide derivatives in the ATP-binding site while demonstrating effects of ligand-induced structural change. Specific interactions between the enzyme and the inhibitors include the isoquinoline ring nitrogen ligating to backbone amide of Val-123 and an inhibitor side chain amide bonding to the backbone carbonyl of Glu-170. The conservation of the ATP-binding site of protein kinases allows evaluation of factors governing general selectivity of these inhibitors among kinases. These results should assist efforts in the design of protein kinase inhibitors with specific properties.


    Related Citations: 
    • Phosphotransferase and Substrate Binding Mechanism of the Camp-Dependent Protein Kinase Catalytic Subunit from Porcine Heart as Deduced from the 2.0 A Structure of the Complex with Mn2+ Adenylyl Imidodiphosphate and Inhibitor Peptide Pki(5-24)
      Bossemeyer, D., Engh, R.A., Kinzel, V., Ponstingl, H., Huber, R.
      (1993) EMBO J 12: 849
    • Cloning of the C Alpha Catalytic Subunit of the Bovine Camp-Dependent Protein Kinase
      Wiemann, S., Kinzel, V., Pyerin, W.
      (1992) Biochim Biophys Acta 1171: 93
    • Isoquinolinesulfonamides, Novel and Potent Inhibitors of Cyclic Nucleotide Dependent Protein Kinase and Protein Kinase C
      Hidaka, H., Inagaki, M., Kawamoto, S., Sasaki, Y.
      (1984) Biochemistry 23: 5036

    Organizational Affiliation

    Abteilung Strukturforschung II, Max-Planck Institute for Biochemistry, D-82152 Martinsried, Federal Republic of Germany.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
C-AMP-DEPENDENT PROTEIN KINASEE350Bos taurusMutation(s): 2 
Gene Names: PRKACA
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.11 (UniProt)
Find proteins for P00517 (Bos taurus)
Explore P00517 
Go to UniProtKB:  P00517
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN KINASE INHIBITOR PEPTIDEI20N/AMutation(s): 0 
Find proteins for P61925 (Homo sapiens)
Explore P61925 
Go to UniProtKB:  P61925
NIH Common Fund Data Resources
PHAROS  P61925
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IQP
Query on IQP

Download CCD File 
E
1-(5-ISOQUINOLINESULFONYL)-2-METHYLPIPERAZINE
C14 H17 N3 O2 S
BDVFVCGFMNCYPV-NSHDSACASA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
EL-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
EL-PEPTIDE LINKINGC4 H10 N O6 PTHR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IQPIC50:  3000   nM  BindingDB
IQPIC50:  6641   nM  BindingDB
IQPKi:  3000   nM  Binding MOAD
IQPKi :  3000   nM  PDBBind
IQPKi:  3000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.58α = 90
b = 76.28β = 90
c = 80.58γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
SAINTdata reduction
SAINTdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-04-01
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance