› 6ls4

X-ray diffraction
2.4Å resolution

A novel anti-tumor agent S-40 in complex with tubulin

Released:
DOI: 10.2210/pdb6ls4/pdb
PDB entry 6ls4 coloured by chain, front view.
PDB entry 6ls4 coloured by chain, side view.
PDB entry 6ls4 coloured by chain, top view.
Source organism: Sus scrofa
Primary publication:
A novel orally active microtubule destabilizing agent S-40 targets the colchicine-binding site and shows potent antitumor activity.
Du T, Lin S, Ji M, Xue N, Liu Y, Zhang Z, Zhang K, Zhang J, Zhang Y, Wang Q, Sheng L, Li Y, Lu D, Chen X, Xu H
Cancer Lett 495 22-32 (2020)
PMID: 32931884

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-104077 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Tubulin alpha-1B chain Chains: A, C
Molecule details ›
Chains: A, C
Length: 451 amino acids
Theoretical weight: 50.2 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: Q2XVP4 (Residues: 1-451; Coverage: 100%)
Gene name: TUBA1B
Sequence domains:
Tubulin beta chain Chains: B, D
Molecule details ›
Chains: B, D
Length: 445 amino acids
Theoretical weight: 50 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: P02554 (Residues: 1-445; Coverage: 100%)
Sequence domains:
Stathmin-4 Chain: E
Molecule details ›
Chain: E
Length: 152 amino acids
Theoretical weight: 18.06 KDa
Source organism: Sus scrofa
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A4X1VCH4 (Residues: 76-216; Coverage: 65%)
Gene name: STMN4
Sequence domains: Stathmin family

Ligands and Environments

6 bound ligands:
Ligand GTP 3 x GTP
Ligand MG 6 x MG
Ligand GDP 1 x GDP
Ligand MES 1 x MES
Ligand GOL 1 x GOL
Ligand S40 2 x S40
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P21
Unit cell:
a: 82.68Å b: 102.2Å c: 131.5Å
α: 90° β: 107.42° γ: 90°
R-values:
R R work R free
0.223 0.222 0.24
Expression system: Escherichia coli

Quick links

Citations

1 review citation

The power and the promise of organoid models for cancer precision medicine with next-generation functional diagnostics and pharmaceutical exploitation.
Ma et al. (2021)
3 other articles