MolNFT v1 · #125358 · protein
EPHB3 kinase domain covalently bound to an irreversible inhibitor (compound 3)
5L6O · Ephrin type-B receptor 3: “EPHB3 kinase domain covalently bound to an irreversible inhibitor (compound 3)”. X-ray diffraction, 1 ligand (6P6), 2 pockets (best druggability 0.67). MolNFT v1 #125358 on GenesisL1: 3D structure, binding…
- PDB
- 5L6O
- Type
- protein
- Length
- 267 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ephrin type-B receptor 3
- EC
- 2.7.10.1
- UniProt
- P54753
- Ligands
- 6P6
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ephrin type-B receptor 3 (EC 2.7.10.1) | protein | 267 | 40% helix, 16% strand | P54753 |
Ligands and binding sites
- 6P6 · 1-(4-phenylazanylquinazolin-7-yl)ethanone · ligand · chains A
- DIO · 1,4-diethylene dioxide · additive · 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 | 200 | 0.67 | 0.85 | 25 | 6P6 |
| 2 | 268 | 0.50 | 0.74 | 45 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5L6O · EphB3 kinase domain covalently bound to an irreversible inhibitor (compound 3) · the same entry in another collection · chain A against A, TM-score 1.00
- P54753 · AlphaFold monomer V2.0 prediction for ephrin type-B receptor 3 (P54753) · 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 P54753
- Elsewhere: RCSB PDB 5L6O · PDBe 5L6O · UniProt P54753
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