3VQH

Bromine SAD partially resolves multiple binding modes for PKA inhibitor H-89


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

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Literature

Anomalous dispersion analysis of inhibitor flexibility: a case study of the kinase inhibitor H-89

Pflug, A.Johnson, K.A.Engh, R.A.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 873-877

  • DOI: 10.1107/S1744309112028655
  • Primary Citation of Related Structures:  
    3VQH

  • PubMed Abstract: 
  • With its ability to show the interactions between drug-target proteins and small-molecule ligands, X-ray crystallography is an essential tool in drug-discovery programmes. However, its usefulness can be limited by crystallization artifacts or by the data resolution, and in particular when assumptions of unimodal binding (and isotropic motion) do not apply ...

    With its ability to show the interactions between drug-target proteins and small-molecule ligands, X-ray crystallography is an essential tool in drug-discovery programmes. However, its usefulness can be limited by crystallization artifacts or by the data resolution, and in particular when assumptions of unimodal binding (and isotropic motion) do not apply. Discrepancies between the modelled crystal structure and the physiological range of structures generally prevent quantitative estimation of binding energies. Improved crystal structure resolution will often not aid energy estimation because the conditions which provide the highest rigidity and resolution are not likely to reflect physiological conditions. Instead, strategies must be employed to measure and model flexibility and multiple binding modes to supplement crystallographic information. One useful tool is the use of anomalous dispersion for small molecules that contain suitable atoms. Here, an analysis of the binding of the kinase inhibitor H-89 to protein kinase A (PKA) is presented. H-89 contains a bromobenzene moiety that apparently binds with multiple conformations in the kinase ATP pocket. Using anomalous dispersion methods, it was possible to resolve these conformations into two distinct binding geometries.


    Organizational Affiliation

    Norwegian Structural Biology Centre, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-dependent protein kinase catalytic subunit alphaA351Homo sapiensMutation(s): 0 
Gene Names: PKACAPRKACA
EC: 2.7.11.11
UniProt & NIH Common Fund Data Resources
Find proteins for P17612 (Homo sapiens)
Explore P17612 
Go to UniProtKB:  P17612
PHAROS:  P17612
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-dependent protein kinase inhibitor alphaB20Homo sapiensMutation(s): 0 
Gene Names: PKIAPRKACN1
UniProt & NIH Common Fund Data Resources
Find proteins for P61925 (Homo sapiens)
Explore P61925 
Go to UniProtKB:  P61925
PHAROS:  P61925
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IQB (Subject of Investigation/LOI)
Query on IQB

Download Ideal Coordinates CCD File 
C [auth A]N-[2-(4-BROMOCINNAMYLAMINO)ETHYL]-5-ISOQUINOLINE SULFONAMIDE
C20 H20 Br N3 O2 S
ZKZXNDJNWUTGDK-NSCUHMNNSA-N
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
D [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-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
IQB BindingDB:  3VQH Ki: min: 48, max: 50 (nM) from 2 assay(s)
Kd: 23 (nM) from 1 assay(s)
IC50: min: 73, max: 100 (nM) from 2 assay(s)
PDBBind:  3VQH IC50: 1200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.73α = 90
b = 75.18β = 90
c = 80.33γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-15
    Type: Initial release
  • Version 1.1: 2014-04-30
    Changes: Database references