Research workbench
NMR-guided design of potent and selective EPHA4 agonistic ligands
Analyse NMR-guided design of potent and selective EPHA4 agonistic ligands in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OFV
- Type
- protein
- Length
- 188 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ephrin type-a receptor 4; EPHA4 agonist ligand
- EC
- 2.7.10.1
- UniProt
- P54764
- Ligands
- VDK, VDQ
- Pockets
- 2 · best druggability 0.39
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ephrin type-a receptor 4 (EC 2.7.10.1) | protein | 184 | 5% helix, 51% strand | P54764 |
| B | EPHA4 agonist ligand | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- VDK · [(1S,3S)-3-carboxycyclohexyl]azanium · ligand · chains A, B
- VDQ · 4-morpholin-4-ylaniline · ligand · chains A, B
- ACT · Acetate ion · additive
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.39 | 0.78 | 13 | empty |
| 2 | 53 | 0.30 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 425 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified, 2 covalent, 2 disulfide (nonstandard, covalent ligand, disulfide).
Compared structures
- 7OFV · NMR-guided design of potent and selective EphA4 agonistic ligands · the same entry in another collection · chain A against A, TM-score 1.00
- P54764 · AlphaFold monomer V2.0 prediction for ephrin type-a receptor 4 (P54764) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 P54764
- Elsewhere: RCSB PDB 7OFV · PDBe 7OFV · UniProt P54764
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