3K3B

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

• PDB DOI: https://doi.org/10.2210/pdb3K3B/pdb

• Classification: MOTOR PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-10-02 Released: 2009-12-15 
• Deposition Author(s): Bussiere, D.E., Bellamacina, C., Le, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.243 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 

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

• PubMed: 19945875 
• DOI: https://doi.org/10.1016/j.bmcl.2009.11.012
• Primary Citation of Related Structures:  
  3K3B


• 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 liabilities and improving cellular potency.

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Organizational Affiliation: 

Global Discovery Chemistry/Oncology and Exploratory Chemistry, Novartis Institutes for Biomedical Research, 5400 Hollis Street, Emeryville, CA 94608, 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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 83.92 kDa 
• Atom Count: 5,582 
• Modelled Residue Count: 666 
• 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, TRIP5
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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	D [auth A], K [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
L31	E [auth A], L [auth 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
PEG	H [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
NO3	F [auth A], I [auth B]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
CL	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
L31	BindingDB:  3K3B	IC50: 200 (nM) from 1 assay(s)
	PDBBind:  3K3B	IC50: 200 (nM) from 1 assay(s)
	Binding MOAD:  3K3B	IC50: 200 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.243 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.97	α = 90
b = 92.67	β = 90
c = 102.95	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
EPMR	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-15 
Deposition Author(s): Bussiere, D.E., Bellamacina, C., Le, V.

Revision History  

• Version 1.0: 2009-12-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-02-13
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations