MolNFT v1 · #149013 · protein
Crystal structure of ephrin B4 (EPHB4) receptor protein kinase with an isomer of nvp-BHG712
6FNJ · Ephrin type-B receptor 4: “Crystal structure of ephrin B4 (EPHB4) receptor protein kinase with an isomer of nvp-BHG712”. X-ray diffraction, 1 ligand (DWT), 4 pockets (best druggability 0.67). MolNFT v1 #149013 on GenesisL1: 3D…
- PDB
- 6FNJ
- Type
- protein
- Length
- 524 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
- DWT
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ephrin type-B receptor 4 (EC 2.7.10.1) | protein | 262 | 42% helix, 18% strand | P54760 |
Ligands and binding sites
- DWT · 4-methyl-3-[(2-methyl-6-pyridin-3-yl-pyrazolo[3,4-d]pyrimidin-4-yl)amino]-~{N}-[3-(trifluoromethyl) phenyl]benzamide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains 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 | 360 | 0.67 | 0.81 | 39 | DWT |
| 2 | 388 | 0.67 | 0.80 | 43 | DWT |
| 3 | 418 | 0.62 | 0.77 | 33 | empty |
| 4 | 214 | 0.52 | 0.77 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 375 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6FNJ · Crystal Structure of Ephrin B4 (EphB4) Receptor Protein Kinase with an isomer of… · the same entry in another collection · chain A against A, TM-score 1.00
- P54760 · AlphaFold monomer V2.0 prediction for ephrin type-B receptor 4 (P54760) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 6FNJ · PDBe 6FNJ · UniProt P54760
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