MolNFT v1 · #157907 · protein
Structure of ret protein tyrosine kinase domain in complex with nintedanib
6NEC · Proto-oncogene tyrosine-protein kinase receptor ret: “Structure of ret protein tyrosine kinase domain in complex with nintedanib”. X-ray diffraction, 1 ligand (XIN), 4 pockets (best druggability 0.75). MolNFT v1 #157907 on…
- PDB
- 6NEC
- Type
- protein
- Length
- 571 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proto-oncogene tyrosine-protein kinase receptor ret
- EC
- 2.7.10.1
- UniProt
- P07949
- Ligands
- XIN
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase receptor ret (EC 2.7.10.1) | protein | 287 | 40% helix, 21% strand | P07949 |
| C | Proto-oncogene tyrosine-protein kinase receptor ret (EC 2.7.10.1) | protein | 284 | 42% helix, 18% strand | P07949 |
Ligands and binding sites
- XIN · Methyl (3Z)-3-{[(4-{methyl[(4-methylpiperazin-1-yl) acetyl]amino}phenyl)amino](phenyl)methylidene}-2-oxo-2,3-dihydro-1H-indole-6-carboxylate · ligand · 2 copies · chains A, C
- FMT · Formic acid · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 885 | 0.75 | 0.79 | 78 | XIN |
| 2 | 119 | 0.47 | 0.79 | 19 | empty |
| 3 | 67 | 0.39 | 0.79 | 14 | empty |
| 4 | 55 | 0.32 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–C · 1457 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6NEC · Structure of ret protein tyrosine kinase domain in complex with nintedanib · the same entry in another collection · chain A against A, TM-score 1.00
- P07949 · AlphaFold monomer V2.0 prediction for proto-oncogene tyrosine-protein kinase receptor ret… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P07949
- Elsewhere: RCSB PDB 6NEC · PDBe 6NEC · UniProt P07949
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