2FME

Crystal structure of the mitotic kinesin eg5 (ksp) in complex with mg-adp and (r)-4-(3-hydroxyphenyl)-n,n,7,8-tetramethyl-3,4-dihydroisoquinoline-2(1h)-carboxamide

• PDB DOI: https://doi.org/10.2210/pdb2FME/pdb

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


• Deposited: 2006-01-09 Released: 2006-04-18 
• Deposition Author(s): Sheriff, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.305 
• R-Value Work: 0.280 

Starting Model: other

Literature

Inhibitors of human mitotic kinesin Eg5: Characterization of the 4-phenyl-tetrahydroisoquinoline lead series

Tarby, C.M., Kaltenbach III, R.F., Huynh, T., Pudzianowski, A., Shen, H., Ortega-Nanos, M., Sheriff, S., Newitt, J.A., McDonnell, P.A., Burford, N., Fairchild, C.R., Vaccaro, W., Chen, Z., Borzilleri, R.M., Naglich, J., Lombardo, L.J., Gottardis, M., Trainor, G.L., Roussell, D.L.

(2006) Bioorg Med Chem Lett 16: 2095-2100

• PubMed: 16458511 
• DOI: https://doi.org/10.1016/j.bmcl.2006.01.056
• Primary Citation of Related Structures:  
  2FME


• PubMed Abstract: 
  

  In a high-throughput screening effort, a series of tetrahydroisoquinolines was identified as modest inhibitors of human Eg5. A medicinal chemistry optimization effort led to the identification of R-4-(3-hydroxyphenyl)-N,N-7,8-tetramethyl-3,4-dihydroisoquinoline-2(1H)-carboxamide (32a) as a potent inhibitor of human Eg5 (ATPase IC50 104 nM) with good anti-proliferative activity in A2780 cells (IC50 234 nM).

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Organizational Affiliation: 

Bristol-Myers Squibb Company, Route 206 and Province Line Road, Princeton, NJ 08543, 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.

Macromolecule Content

• Total Structure Weight: 83.66 kDa 
• Atom Count: 5,282 
• Modelled Residue Count: 650 
• Deposited Residue Count: 736 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kinesin-like protein KIF11	A, B	368	Homo sapiens	Mutation(s): 0  Gene Names: KIF11, EG5, KNSL1
UniProt & NIH Common Fund Data Resources
Find proteins for P52732 (Homo sapiens) Explore P52732  Go to UniProtKB:  P52732
GTEx:  ENSG00000138160

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	E [auth A], H [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
3QC	D [auth A], G [auth B]	(4R)-4-(3-HYDROXYPHENYL)-N,N,7,8-TETRAMETHYL-3,4-DIHYDROISOQUINOLINE-2(1H)-CARBOXAMIDE C20 H24 N2 O2 HPVCRUIDFODATB-LJQANCHMSA-N
MG	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3QC	BindingDB:  2FME	IC50: min: 104, max: 306 (nM) from 2 assay(s)
	PDBBind:  2FME	IC50: 104 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.305 
• R-Value Work: 0.280 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.8	α = 90
b = 80	β = 96.5
c = 69.2	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-18 
Deposition Author(s): Sheriff, S.

Revision History  

• Version 1.0: 2006-04-18
  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