2GM1

Crystal structure of the mitotic kinesin eg5 in complex with mg-adp and n-(3-aminopropyl)-n-((3-benzyl-5-chloro-4-oxo-3,4-dihydropyrrolo[2,1-f][1,2,4]triazin-2-yl)(cyclopropyl)methyl)-4-methylbenzamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.230 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Synthesis and SAR of pyrrolotriazine-4-one based Eg5 inhibitors.

Kim, K.S.Lu, S.Cornelius, L.A.Lombardo, L.J.Borzilleri, R.M.Schroeder, G.M.Sheng, C.Rovnyak, G.Crews, D.Schmidt, R.J.Williams, D.K.Bhide, R.S.Traeger, S.C.McDonnell, P.A.Mueller, L.Sheriff, S.Newitt, J.A.Pudzianowski, A.T.Yang, Z.Wild, R.Lee, F.Y.Batorsky, R.Ryder, J.S.Ortega-Nanos, M.Shen, H.Gottardis, M.Roussell, D.L.

(2006) Bioorg Med Chem Lett 16: 3937-3942

  • DOI: 10.1016/j.bmcl.2006.05.037
  • Primary Citation of Related Structures:  
    2GM1

  • PubMed Abstract: 
  • Synthesis and SAR of substituted pyrrolotriazine-4-one analogues as Eg5 inhibitors are described. Many of these analogues displayed potent inhibitory activities in the Eg5 ATPase and A2780 cell proliferation assays. In addition, pyrrolotriazine-4-one analogue 26 demonstrated in vivo efficacy in an iv P388 murine leukemia model ...

    Synthesis and SAR of substituted pyrrolotriazine-4-one analogues as Eg5 inhibitors are described. Many of these analogues displayed potent inhibitory activities in the Eg5 ATPase and A2780 cell proliferation assays. In addition, pyrrolotriazine-4-one analogue 26 demonstrated in vivo efficacy in an iv P388 murine leukemia model. Both NMR and X-ray crystallographic studies revealed that these analogues bind to an allosteric site on the Eg5 protein.


    Organizational Affiliation

    Department of Drug Discovery, Bristol-Myers Squibb Pharmaceutical Research Institute, Princeton, NJ 08543-4000, USA. kyoung.kim@bms.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
KINESIN-RELATED MOTOR PROTEIN EG5A,
B,
C [auth D],
D [auth E]
368Homo sapiensMutation(s): 0 
Gene Names: EG5KIF11KNSL1TRIP5
UniProt & NIH Common Fund Data Resources
Find proteins for P52732 (Homo sapiens)
Explore P52732 
Go to UniProtKB:  P52732
PHAROS:  P52732
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52732
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2AZ
Query on 2AZ

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
O [auth D],
S [auth E]
N-(3-AMINOPROPYL)-N-[(R)-(3-BENZYL-5-CHLORO-4-OXO-3,4-DIHYDROPYRROLO[2,1-F][1,2,4]TRIAZIN-2-YL)(CYCLOPROPYL)METHYL]-4-METHYLBENZAMIDE
C28 H30 Cl N5 O2
IKORZPHBTIOSSU-XMMPIXPASA-N
 Ligand Interaction
ADP
Query on ADP

Download Ideal Coordinates CCD File 
H [auth A],
L [auth B],
P [auth D],
T [auth E]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
I [auth B],
J [auth B],
M [auth D],
E [auth A],
F [auth A],
I [auth B],
J [auth B],
M [auth D],
N [auth D],
Q [auth E],
R [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
2AZ BindingDB:  2GM1 IC50: 100 (nM) from 1 assay(s)
PDBBind:  2GM1 IC50: 100 (nM) from 1 assay(s)
Binding MOAD:  2GM1 IC50: 100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.230 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.7α = 90
b = 112.6β = 90.2
c = 108.1γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACTdata extraction
CNXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2006-04-05 
  • Released Date: 2006-06-27 
  • Deposition Author(s): Sheriff, S.

Revision History  (Full details and data files)

  • Version 1.0: 2006-06-27
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description