Crystal structure of the KIFC3 motor domain in complex with ADP

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

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This is version 1.2 of the entry. See complete history


Structural basis of small molecule ATPase inhibition of a human mitotic kinesin motor protein.

Park, H.W.Ma, Z.Zhu, H.Jiang, S.Robinson, R.C.Endow, S.A.

(2017) Sci Rep 7: 15121-15121

  • DOI: https://doi.org/10.1038/s41598-017-14754-6
  • Primary Citation of Related Structures:  
    5W3D, 5WDE, 5WDH

  • PubMed Abstract: 

    Kinesin microtubule motor proteins play essential roles in division, including attaching chromosomes to spindles and crosslinking microtubules for spindle assembly. Human kinesin-14 KIFC1 is unique in that cancer cells with amplified centrosomes are dependent on the motor for viable division because of its ability to cluster centrosomes and form bipolar spindles, but it is not required for division in almost all normal cells. Screens for small molecule inhibitors of KIFC1 have yielded several candidates for further development, but obtaining structural data to determine their sites of binding has been difficult. Here we compare a previously unreported KIFC1 crystal structure with new structures of two closely related kinesin-14 proteins, Ncd and KIFC3, to determine the potential binding site of a known KIFC1 ATPase inhibitor, AZ82. We analyze the previously identified kinesin inhibitor binding sites and identify features of AZ82 that favor binding to one of the sites, the α4/α6 site. This selectivity can be explained by unique structural features of the KIFC1 α4/α6 binding site. These features may help improve the drug-like properties of AZ82 and other specific KIFC1 inhibitors.

  • Organizational Affiliation

    Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kinesin-like protein KIFC3330Homo sapiensMutation(s): 0 
Gene Names: KIFC3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BVG8 (Homo sapiens)
Explore Q9BVG8 
Go to UniProtKB:  Q9BVG8
GTEx:  ENSG00000140859 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BVG8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ADP

Download Ideal Coordinates CCD File 
C10 H15 N5 O10 P2
Query on MG

Download Ideal Coordinates CCD File 
Query on UNX

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
CA [auth A]
D [auth A]
DA [auth A]
AA [auth A],
BA [auth A],
CA [auth A],
D [auth A],
DA [auth A],
E [auth A],
EA [auth A],
F [auth A],
FA [auth A],
G [auth A],
GA [auth A],
H [auth A],
HA [auth A],
I [auth A],
IA [auth A],
J [auth A],
JA [auth A],
K [auth A],
KA [auth A],
L [auth A],
LA [auth A],
M [auth A],
MA [auth A],
N [auth A],
NA [auth A],
O [auth A],
OA [auth A],
P [auth A],
PA [auth A],
Q [auth A],
QA [auth A],
R [auth A],
RA [auth A],
S [auth A],
SA [auth A],
T [auth A],
TA [auth A],
U [auth A],
UA [auth A],
V [auth A],
VA [auth A],
W [auth A],
WA [auth A],
X [auth A],
Y [auth A],
Z [auth A]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.85 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: H 3 2
  • Diffraction Data: https://doi.org/10.18430/M35WDE
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 187.608α = 90
b = 187.608β = 90
c = 151.363γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-09
    Type: Initial release
  • Version 1.1: 2017-12-20
    Changes: Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description