MolNFT v1 · #55530 · protein
EPHB4 kinase domain inhibitor complex
2YN8 · Ephrin type-B receptor 4: “EPHB4 kinase domain inhibitor complex”. X-ray diffraction, 1 ligand (STU), 4 pockets (best druggability 0.60). MolNFT v1 #55530 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2YN8
- Type
- protein
- Length
- 513 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ephrin type-B receptor 4
- EC
- 2.7.10.1
- UniProt
- P54760
- Ligands
- STU
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ephrin type-B receptor 4 (EC 2.7.10.1) | protein | 253 | 45% helix, 19% strand | P54760 |
| B | Ephrin type-B receptor 4 (EC 2.7.10.1) | protein | 260 | 43% helix, 18% strand | P54760 |
Ligands and binding sites
- STU · Staurosporine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 223 | 0.60 | 0.81 | 34 | STU |
| 2 | 363 | 0.60 | 0.77 | 30 | empty |
| 3 | 193 | 0.60 | 0.81 | 25 | STU |
| 4 | 255 | 0.55 | 0.77 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 381 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
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 P54760
- Elsewhere: RCSB PDB 2YN8 · PDBe 2YN8 · UniProt P54760
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