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

• PDB DOI: https://doi.org/10.2210/pdb2GM1/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


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

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Experimental Data Snapshot

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

Starting Model: experimental

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

• PubMed: 16730979 
• DOI: https://doi.org/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. Both NMR and X-ray crystallographic studies revealed that these analogues bind to an allosteric site on the Eg5 protein.

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Organizational Affiliation: 

Department of Drug Discovery, Bristol-Myers Squibb Pharmaceutical Research Institute, Princeton, NJ 08543-4000, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 168.14 kDa 
• Atom Count: 10,443 
• Modelled Residue Count: 1,297 
• Deposited Residue Count: 1,472 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KINESIN-RELATED MOTOR PROTEIN EG5	A, B, C [auth D], D [auth E]	368	Homo sapiens	Mutation(s): 0  Gene Names: EG5
UniProt & NIH Common Fund Data Resources
Find proteins for P52732 (Homo sapiens) Explore P52732  Go to UniProtKB:  P52732
PHAROS:  P52732 GTEx:  ENSG00000138160

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2AZ	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
ADP	H [auth A], L [auth B], P [auth D], T [auth E]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	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

Binding Affinity Annotations
ID	Source	Binding Affinity
2AZ	PDBBind:  2GM1	IC50: 100 (nM) from 1 assay(s)
	BindingDB:  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 = 64.7	α = 90
b = 112.6	β = 90.2
c = 108.1	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
PDB_EXTRACT	data extraction
CNX	refinement

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-04-03
  Changes: Refinement description