4AP0

The mitotic kinesin Eg5 in complex with Mg-ADP and ispinesib

PDB DOI: https://doi.org/10.2210/pdb4AP0/pdb

Classification: MOTOR PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-03-30 Released: 2012-09-26
Deposition Author(s): Schuettelkopf, A.W., Talapatra, S.K., Kozielski, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.59 Å
R-Value Free: 0.253
R-Value Work: 0.203
R-Value Observed: 0.206

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

The Structure of the Ternary Eg5-Adp-Ispinesib Complex

Talapatra, S.K., Schuettelkopf, A.W., Kozielski, F.

(2012) Acta Crystallogr D Biol Crystallogr 68: 1311

PubMed: 22993085 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S0907444912027965
Primary Citation of Related Structures:
4AP0

PubMed Abstract:
The human kinesin Eg5 is responsible for bipolar spindle formation during early mitosis. Inhibition of Eg5 triggers the formation of monoastral spindles, leading to mitotic arrest that eventually causes apoptosis. There is increasing evidence that Eg5 constitutes a potential drug target for the development of cancer chemotherapeutics. The most advanced Eg5-targeting agent is ispinesib, which exhibits potent antitumour activity and is currently in multiple phase II clinical trials. In this study, the crystal structure of the Eg5 motor domain in complex with ispinesib, supported by kinetic and thermodynamic binding data, is reported. Ispinesib occupies the same induced-fit pocket in Eg5 as other allosteric inhibitors, making extensive hydrophobic interactions with the protein. The data for the Eg5-ADP-ispinesib complex suffered from pseudo-merohedral twinning and revealed translational noncrystallographic symmetry, leading to challenges in data processing, space-group assignment and structure solution as well as in refinement. These complications may explain the lack of available structural information for this important agent and its analogues. The present structure represents the best interpretation of these data based on extensive data-reduction, structure-solution and refinement trials.

Organizational Affiliation

Molecular Motor Laboratory, The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, Scotland, UK. s.talapatra@beatson.gla.ac.uk

Macromolecule Content

Total Structure Weight: 168.93 kDa
Atom Count: 9,849
Modelled Residue Count: 1,257
Deposited Residue Count: 1,480
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KINESIN-LIKE PROTEIN KIF11	A, B, C, D	370	Homo sapiens	Mutation(s): 0
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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P52732
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G7X Query on G7X Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain V [auth D] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain V [auth D] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain R [auth C] mmCIF format, chain V [auth D]	I [auth A], O [auth B], R [auth C], V [auth D]	ISPINESIB MESILATE C₃₀ H₃₃ Cl N₄ O₂ QJZRFPJCWMNVAV-HHHXNRCGSA-N		Interactions Focus chain I [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain V [auth D] Interactions & Density Focus chain I [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain V [auth D]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain Q [auth C] SDF format, chain T [auth D] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D]	F [auth A], K [auth B], Q [auth C], T [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain T [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain T [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain U [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain U [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain U [auth D]	G [auth A] H [auth A] L [auth B] M [auth B] N [auth B] G [auth A], H [auth A], L [auth B], M [auth B], N [auth B], U [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain U [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain U [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain P [auth C] SDF format, chain S [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D]	E [auth A], J [auth B], P [auth C], S [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain P [auth C] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain P [auth C] Focus chain S [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
G7X	BindingDB: 4AP0	Ki: min: 2.3, max: 2.5 (nM) from 2 assay(s)
	BindingDB: 4AP0	IC50: min: 1.2, max: 47 (nM) from 3 assay(s)
	PDBBind: 4AP0	Kd: 10 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.59 Å
R-Value Free: 0.253
R-Value Work: 0.203
R-Value Observed: 0.206
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.723	α = 90
b = 112.607	β = 90.02
c = 106.913	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-09-26

Deposition Author(s):

Schuettelkopf, A.W.

Talapatra, S.K.

Kozielski, F.

Revision History (Full details and data files)

Version 1.0: 2012-09-26
Type: Initial release
Version 1.1: 2012-10-03
Changes: Database references
Version 1.2: 2019-05-08
Changes: Data collection, Experimental preparation, Other
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description