MolNFT v1 · #156069 · protein
A novel anti-tumor agent S-40 in complex with tubulin
6LS4 · Tubulin alpha-1B chain: “A novel anti-tumor agent S-40 in complex with tubulin”. X-ray diffraction, 4 ligands (GTP, S40, GDP), 20 pockets (best druggability 0.84). MolNFT v1 #156069 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6LS4
- Type
- protein
- Length
- 1,843 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta chain; Stathmin
- UniProt
- Q2XVP4, P02554, F2Z508
- Ligands
- GTP, S40, GDP, MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 429 | 45% helix, 19% strand | Q2XVP4 |
| B | Tubulin beta chain | protein | 423 | 47% helix, 19% strand | P02554 |
| C | Tubulin alpha-1B chain | protein | 439 | 46% helix, 19% strand | Q2XVP4 |
| D | Tubulin beta chain | protein | 428 | 47% helix, 18% strand | P02554 |
| E | Stathmin | protein | 124 | 77% helix, 14% strand | F2Z508 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, B, C, D
- S40 · 3-[(4-cyclopropylphenyl)sulfonylamino]-4-methyl-N-(pyridin-3-ylmethyl)benzamide · ligand · 2 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- MG · Magnesium ion · metal · 6 copies · chains A, C, B, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, B
- GOL · Glycerol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 857 | 0.84 | 0.86 | 91 | GTP, MG, S40 |
| 2 | 1167 | 0.83 | 0.84 | 107 | GTP, MG, S40 |
| 3 | 427 | 0.80 | 0.88 | 73 | GDP, GOL |
| 4 | 538 | 0.70 | 0.80 | 48 | MES |
| 5 | 534 | 0.68 | 0.78 | 48 | empty |
Interfaces
7 interfaces between chains.
- B–C · 1494 Ų buried · 23 hydrogen bonds · protein-protein
- A–E · 1436 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1367 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1306 Ų buried · 17 hydrogen bonds · protein-protein
- C–E · 830 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6LS4 · A novel anti-tumor agent S-40 in complex with tubulin · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q2XVP4
- Every structure of UniProt P02554
- Every structure of UniProt F2Z508
- Elsewhere: RCSB PDB 6LS4 · PDBe 6LS4 · UniProt Q2XVP4 · UniProt P02554 · UniProt F2Z508
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