3K3B

Co-crystal structure of the human kinesin Eg5 with a novel tetrahydro-beta-carboline


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The discovery of tetrahydro-beta-carbolines as inhibitors of the kinesin Eg5.

Barsanti, P.A.Wang, W.Ni, Z.J.Duhl, D.Brammeier, N.Martin, E.Bussiere, D.Walter, A.O.

(2010) Bioorg.Med.Chem.Lett. 20: 157-160

  • DOI: 10.1016/j.bmcl.2009.11.012

  • PubMed Abstract: 
  • A series of tetrahydro-beta-carbolines were identified by HTS as inhibitors of the kinesin Eg5. Molecular modeling and medicinal chemistry techniques were employed to explore the SAR for this series with a focus of removing potential metabolic liabil ...

    A series of tetrahydro-beta-carbolines were identified by HTS as inhibitors of the kinesin Eg5. Molecular modeling and medicinal chemistry techniques were employed to explore the SAR for this series with a focus of removing potential metabolic liabilities and improving cellular potency.


    Organizational Affiliation

    Global Discovery Chemistry/Oncology and Exploratory Chemistry, Novartis Institutes for Biomedical Research, 5400 Hollis Street, Emeryville, CA 94608, USA. paul.barsanti@novartis.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Kinesin-like protein KIF11
A, B
368Homo sapiensMutation(s): 0 
Gene Names: KIF11 (EG5, KNSL1, TRIP5)
Find proteins for P52732 (Homo sapiens)
Go to Gene View: KIF11
Go to UniProtKB:  P52732
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

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Download CCD File 
A, B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
NO3
Query on NO3

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A, B
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
L31
Query on L31

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Download CCD File 
A, B
3-[(1R)-2-acetyl-6-methyl-2,3,4,9-tetrahydro-1H-beta-carbolin-1-yl]phenol
C20 H20 N2 O2
ZNGGYWGHJZJJDR-HXUWFJFHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
L31IC50: 200 nM (100) BINDINGDB
L31IC50: 200 nM BINDINGMOAD
L31IC50: 200 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 78.970α = 90.00
b = 92.670β = 90.00
c = 102.950γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
EPMRphasing
SCALAdata scaling
PHENIXrefinement
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-02-13
    Type: Refinement description