MolNFT v1 · #126986 · protein
Kinase domain of human EPHB1, G703C mutant, covalently bound to a quinazoline-based inhibitor
5MJB · Ephrin type-B receptor 1: “Kinase domain of human EPHB1, G703C mutant, covalently bound to a quinazoline-based inhibitor”. X-ray diffraction, 2 ligands (7O3, SO4), 7 pockets (best druggability 0.77). MolNFT v1 #126986 on GenesisL1…
- PDB
- 5MJB
- Type
- protein
- Length
- 558 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ephrin type-B receptor 1
- EC
- 2.7.10.1
- UniProt
- P54762
- Ligands
- 7O3, SO4
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ephrin type-B receptor 1 (EC 2.7.10.1) | protein | 278 | 40% helix, 18% strand | P54762 |
| B | Ephrin type-B receptor 1 (EC 2.7.10.1) | protein | 280 | 39% helix, 18% strand | P54762 |
Ligands and binding sites
- 7O3 · 2-chloranyl-~{N}-[4-[(2-chloranyl-5-oxidanyl-phenyl) amino]quinazolin-7-yl]ethanamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1058 | 0.77 | 0.80 | 81 | SO4 |
| 2 | 317 | 0.65 | 0.80 | 36 | 7O3 |
| 3 | 282 | 0.65 | 0.81 | 33 | 7O3 |
| 4 | 172 | 0.58 | 0.82 | 33 | empty |
| 5 | 91 | 0.44 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1261 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 2 covalent (phosphorylation, covalent ligand).
Compared structures
- 5MJB · Kinase domain of human EphB1, G703C mutant, covalently bound to a quinazoline-based… · the same entry in another collection · chain A against A, TM-score 1.00
- P54762 · AlphaFold monomer V2.0 prediction for ephrin type-B receptor 1 (P54762) · 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 P54762
- Elsewhere: RCSB PDB 5MJB · PDBe 5MJB · UniProt P54762
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