3DNE

cAMP-dependent protein kinase PKA catalytic subunit with PKI-5-24


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystallography-independent determination of ligand binding modes

Orts, J.Tuma, J.Reese, M.Grimm, S.K.Monecke, P.Bartoschek, S.Schiffer, A.Wendt, K.U.Griesinger, C.Carlomagno, T.

(2008) Angew Chem Int Ed Engl 47: 7736-7740


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-dependent protein kinase catalytic subunit alphaA350Bos taurusMutation(s): 0 
Gene Names: PRKACA
EC: 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
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-dependent protein kinase inhibitor alphaB [auth I]20N/AMutation(s): 0 
UniProt
Find proteins for P61926 (Oryctolagus cuniculus)
Explore P61926 
Go to UniProtKB:  P61926
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LL1 (Subject of Investigation/LOI)
Query on LL1

Download Ideal Coordinates CCD File 
C [auth A]3-pyridin-4-yl-1H-indazole
C12 H9 N3
MSRXUUDVRNWSTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
AL-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
AL-PEPTIDE LINKINGC4 H10 N O6 PTHR
Binding Affinity Annotations 
IDSourceBinding Affinity
LL1 PDBBind:  3DNE Ki: 6000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.841α = 90
b = 75.438β = 90
c = 79.76γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
APRVphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-10-09
    Changes: Derived calculations