Kinesin spindle protein Eg5 in complex with STLC-type inhibitor PVEI0138

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.1 of the entry. See complete history


Structural and Thermodynamic Basis of the Enhanced Interaction between Kinesin Spindle Protein Eg5 and STLC-type Inhibitors.

Yokoyama, H.Sawada, J.I.Sato, K.Ogo, N.Kamei, N.Ishikawa, Y.Hara, K.Asai, A.Hashimoto, H.

(2018) ACS Omega 3: 12284-12294

  • DOI: https://doi.org/10.1021/acsomega.8b00778
  • Primary Citation of Related Structures:  
    5ZO7, 5ZO8, 5ZO9

  • PubMed Abstract: 

    For a better understanding of protein-inhibitor interactions, we report structural, thermodynamic, and biological analyses of the interactions between S -trityl-l-cysteine (STLC) derivatives and the motor domain of kinesin spindle protein Eg5. Binding of STLC-type inhibitors to Eg5 was enthalpically driven and entropically unfavorable. The introduction of a para -methoxy substituent in one phenyl ring of STLC enhances its inhibitory activity resulting from a larger enthalpy gain possibly due to the increased shape complementarity. The substituent fits to a recess in the binding pocket. To avoid steric hindrance, the substituted STLC is nudged toward the side opposite to the recess, which enhances the interaction of Eg5 with the remaining part of the inhibitor. Further introduction of an ethylene linkage between two phenyl rings enhances Eg5 inhibitory activity by reducing the loss of entropy in forming the complex. This study provides valuable examples of enhancing protein-inhibitor interactions without forming additional hydrogen bonds.

  • Organizational Affiliation

    Department of Physical Biochemistry, School of Pharmaceutical Sciences and Center for Drug Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kinesin-like protein KIF11
A, B
367Homo sapiensMutation(s): 0 
Gene Names: KIF11EG5KNSL1TRIP5
UniProt & NIH Common Fund Data Resources
Find proteins for P52732 (Homo sapiens)
Explore P52732 
Go to UniProtKB:  P52732
PHAROS:  P52732
GTEx:  ENSG00000138160 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52732
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ADP

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
C10 H15 N5 O10 P2
Query on 5C5

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
(2R)-2-azanyl-3-[[2-(4-methoxyphenyl)-2-tricyclo[^{3,8}]pentadeca-1(11),3,5,7,12,14-hexaenyl]sulfanyl]propanoic acid
C25 H25 N O3 S
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
O4 S
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
Binding Affinity Annotations 
IDSourceBinding Affinity
5C5 BindingDB:  5ZO7 IC50: 14 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.231 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.347α = 90
b = 50.58β = 102.2
c = 93.689γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan17K07316

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2019-09-11
    Changes: Data collection, Database references, Structure summary