MolNFT v1 · #183684 · protein
Structure of ret kinase domain bound to inhibitor jb-48
7NZN · Proto-oncogene tyrosine-protein kinase receptor ret: “Structure of ret kinase domain bound to inhibitor jb-48”. X-ray diffraction, 1 ligand (VJH), 2 pockets (best druggability 0.59). MolNFT v1 #183684 on GenesisL1: 3D structure…
- PDB
- 7NZN
- Type
- protein
- Length
- 289 residues
- Chains
- 1
- 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
- VJH
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase receptor ret (EC 2.7.10.1) | protein | 289 | 40% helix, 21% strand | P07949 |
Ligands and binding sites
- VJH · 2-[4-[[4-[1-[2-(dimethylamino)ethyl]pyrazol-4-yl]-6-[(3-methyl-1~{H}-pyrazol-5-yl)amino]pyrimidin-2-yl]amino]phenyl]-~{N}-(3-fluorophenyl)ethanamide · ligand · chains A
- FMT · Formic acid · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 207 | 0.59 | 0.81 | 34 | VJH |
| 2 | 89 | 0.33 | 0.74 | 19 | empty |
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 7NZN · Structure of RET kinase domain bound to inhibitor JB-48 · 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 0.94
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 7NZN · PDBe 7NZN · UniProt P07949
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