MolNFT v1 · #149012 · protein
Crystal structure of ephrin B4 (EPHB4) receptor protein kinase with nvp-BHG712
6FNI · Ephrin type-B receptor 4: “Crystal structure of ephrin B4 (EPHB4) receptor protein kinase with nvp-BHG712”. X-ray diffraction, 1 ligand (DXH), 1 pocket (best druggability 0.75). MolNFT v1 #149012 on GenesisL1: 3D structure, binding…
- PDB
- 6FNI
- Type
- protein
- Length
- 261 residues
- Chains
- 1
- 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
- DXH
- Pockets
- 1 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ephrin type-B receptor 4 (EC 2.7.10.1) | protein | 261 | 41% helix, 19% strand | P54760 |
Ligands and binding sites
- DXH · 4-methyl-3-[(1-methyl-6-pyridin-3-yl-pyrazolo[3,4-d]pyrimidin-4-yl)amino]-~{N}-[3-(trifluoromethyl) phenyl]benzamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 359 | 0.75 | 0.86 | 45 | DXH |
Compared structures
- 6FNI · Crystal Structure of Ephrin B4 (EphB4) Receptor Protein Kinase with NVP-BHG712 · 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 A 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 6FNI · PDBe 6FNI · UniProt P54760
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