4BXN | pdb_00004bxn

Eg5(WT) complex

PDB DOI: https://doi.org/10.2210/pdb4BXN/pdb

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

Deposited: 2013-07-15 Released: 2013-07-31
Deposition Author(s): Talapatra, S.K., Anthony, N.G., Mackay, S.P., Kozielski, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.79 Å
R-Value Free:
0.274 (Depositor), 0.288 (DCC)
R-Value Work:
0.230 (Depositor), 0.279 (DCC)
R-Value Observed:
0.233 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

The Mitotic Kinesin Eg5 Overcomes Inhibition to the Phase I/II Clinical Candidate Sb743921 by an Allosteric Resistance Mechanism.

Talapatra, S.K., Anthony, N.G., Mackay, S.P., Kozielski, F.

(2013) J Med Chem 56: 6317

PubMed: 23875972 Search on PubMed
DOI: https://doi.org/10.1021/jm4006274
Primary Citation Related Structures:
4A1Z, 4A28, 4AS7, 4B7B, 4BXN

PubMed Abstract:
Development of drug resistance during cancer chemotherapy is one of the major causes of chemotherapeutic failure for the majority of clinical agents. The aim of this study was to investigate the underlying molecular mechanism of resistance developed by the mitotic kinesin Eg5 against the potent second-generation ispinesib analogue SB743921 (1), a phase I/II clinical candidate. Biochemical and biophysical data demonstrate that point mutations in the inhibitor-binding pocket decrease the efficacy of 1 by several 1000-fold. Surprisingly, the structures of wild-type and mutant Eg5 in complex with 1 display no apparent structural changes in the binding configuration of the drug candidate. Furthermore, ITC and modeling approaches reveal that resistance to 1 is not through conventional steric effects at the binding site but through reduced flexibility and changes in energy fluctuation pathways through the protein that influence its function. This is a phenomenon we have called "resistance by allostery".

Organizational Affiliation

The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BS, Scotland, U.K. s.talapatra@ed.ac.uk

Macromolecule Content

Total Structure Weight: 86.76 kDa
Atom Count: 5,521
Modeled Residue Count: 692
Deposited Residue Count: 736
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KINESIN-LIKE PROTEIN KIF11	A, B	368	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P52732
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6LX Query on 6LX Download:Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain N [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain N [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain N [auth A]	DA [auth B], N [auth A]	N-(3-aminopropyl)-N-[(1R)-1-(3-benzyl-7-chloro-4-oxo-4H-chromen-2-yl)-2-methylpropyl]-4-methylbenzamide C₃₁ H₃₃ Cl N₂ O₃ PGXYIBJJCLWJST-MUUNZHRXSA-N		Interactions Focus chain DA [auth B] Focus chain N [auth A] Interactions & Density Focus chain DA [auth B] Focus chain N [auth A]
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain S [auth B] MOL2 format, chain C [auth A] MOL2 format, chain S [auth B] mmCIF format, chain C [auth A] mmCIF format, chain S [auth B]	C [auth A], S [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain S [auth B] Interactions & Density Focus chain C [auth A] Focus chain S [auth B]
CD Query on CD Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain EA [auth B] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain GA [auth B] SDF format, chain H [auth A] SDF format, chain HA [auth B] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth B] D [auth A] E [auth A] AA [auth B], BA [auth B], CA [auth B], D [auth A], E [auth A], EA [auth B], F [auth A], G [auth A], GA [auth B], H [auth A], HA [auth B], I [auth A], J [auth A], K [auth A], L [auth A], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain D [auth A] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain D [auth A] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain M [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A]	FA [auth B] IA [auth B] JA [auth B] M [auth A] O [auth A] FA [auth B], IA [auth B], JA [auth B], M [auth A], O [auth A], P [auth A], Q [auth A], R [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain FA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain M [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain FA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain M [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
6LX	BindingDB: 4BXN	Ki: 0.5 (nM) from 1 assay(s)
		Kd: 10 (nM) from 1 assay(s)
		IC50: 0.14 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.79 Å
R-Value Free: 0.274 (Depositor), 0.288 (DCC)
R-Value Work: 0.230 (Depositor), 0.279 (DCC)
R-Value Observed: 0.233 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.426	α = 90
b = 81.426	β = 90
c = 115.202	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
CCP4	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-07-31

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-07-31
Type: Initial release
Version 1.1: 2013-09-04
Changes: Database references
Version 1.2: 2014-09-17
Changes: Atomic model, Derived calculations, Non-polymer description
Version 1.3: 2019-11-20
Changes: Advisory, Derived calculations, Other
Version 1.4: 2023-03-08
Changes: Advisory, Database references, Derived calculations
Version 1.5: 2024-02-07
Changes: Data collection, Refinement description
Version 1.6: 2025-10-01
Changes: Advisory, Derived calculations, Structure summary