8YRK | pdb_00008yrk

Tubulin-Compound KY216: stathmin-like domain complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 
    0.226 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8YRK

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

KY216-tubulin complex captures VASH2 to inhibit NSCLC metastasis.

He, X.Y.Liu, C.Y.Ding, X.Y.Lin, Q.Leng, J.F.Xiao, C.M.Zang, X.Wang, M.Y.Yin, Y.Kong, L.Y.Xia, Y.Z.

(2025) Nat Commun 17: 191-191

  • DOI: https://doi.org/10.1038/s41467-025-66817-2
  • Primary Citation Related Structures: 
    8YRK

  • PubMed Abstract: 

    Metastasis significantly impacts the mortality rate of non-small cell lung cancer (NSCLC) patients. Numerous microtubule-targeting agents (MTAs) reveal anti-metastatic efficacy, but the mechanism remains unclear. In this research, we employ KY216, a microtubule inhibitor, to generate a crystal in complex with αβ-tubulin, and illustrate that the KY216-tubulin combination binds vasohibin-2 (VASH2) to restrain NSCLC metastasis. Through crystal structure analysis, specific interaction sites between KY216 and curved tubulin are identified. KY216 decreases VASH2 levels, hindering the epithelial-mesenchymal transition (EMT) process in NSCLC. Moreover, the MTA enhances the binding of VASH2 to α-tubulin, prevents the activation of zinc finger E-box binding homolog 1 (ZEB1) by VASH2, promotes detyrosination of α-tubulin, and ultimately suppresses EMT. Additionally, KY216 elevates the levels of miR-429 to target the 3'-untranslated region (3' UTR) of VASH2 and ZEB1 transcripts and inhibits EMT, at least partially, via the miR-429/VASH2/ZEB1 axis to block NSCLC metastasis. Overall, our investigation offers valuable insights into the roles of MTAs and VASH2 in NSCLC metastasis.


  • Organizational Affiliation
    • Basic Medical Research Innovation Center for Anti-Cancer Drugs, MOE and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.

Macromolecule Content 

  • Total Structure Weight: 265.37 kDa 
  • Atom Count: 17,720 
  • Modeled Residue Count: 2,191 
  • Deposited Residue Count: 2,317 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Detyrosinated tubulin alpha-1B chain
A, C
450Sus scrofaMutation(s): 0 
EC: 3.6.5
UniProt
Find proteins for Q2XVP4 (Sus scrofa)
Explore Q2XVP4 
Go to UniProtKB:  Q2XVP4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2XVP4
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubulin beta chain
B, D
445Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287AGU7 (Sus scrofa)
Explore A0A287AGU7 
Go to UniProtKB:  A0A287AGU7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A287AGU7
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Stathmin-4143Mus musculusMutation(s): 0 
Gene Names: Stmn4
UniProt & NIH Common Fund Data Resources
Find proteins for P63042 (Mus musculus)
Explore P63042 
Go to UniProtKB:  P63042
IMPC:  MGI:1931224
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63042
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubulin tyrosine ligase384Gallus gallusMutation(s): 0 
Gene Names: TTL
EC: 6.3.2.25
UniProt
Find proteins for A0A8V0Z8P0 (Gallus gallus)
Explore A0A8V0Z8P0 
Go to UniProtKB:  A0A8V0Z8P0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8V0Z8P0
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP

Query on GTP



Download:Ideal Coordinates CCD File
G [auth A],
Q [auth C]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ACP

Query on ACP



Download:Ideal Coordinates CCD File
X [auth F]PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
GDP

Query on GDP



Download:Ideal Coordinates CCD File
K [auth B],
U [auth D]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
A1D62
(Subject of Investigation/LOI)

Query on A1D62



Download:Ideal Coordinates CCD File
P [auth B],
W [auth D]
(11R,16S)-11-(3,5-dichloro-4-methoxyphenyl)-4,7-dioxa-12,14-diazatetracyclo[8.7.0.03,8.012,16]heptadeca-1,3(8),9-triene-13,15-dione
C20 H16 Cl2 N2 O5
GANPPQNYXDZLNS-WMLDXEAASA-N
MES

Query on MES



Download:Ideal Coordinates CCD File
M [auth B],
N [auth B]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
O [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
S [auth C]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
I [auth A],
R [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
J [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
H [auth A],
L [auth B],
T [auth D],
V [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free:  0.226 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.097α = 90
b = 158.982β = 90
c = 179.057γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
FRFSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81973524

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-02
    Type: Initial release
  • Version 1.1: 2026-04-22
    Changes: Database references