MolNFT v1 · #117833 · protein
Human NAV1.7-VSD4-navab in complex with gx-936.
5EK0 · Chimera of bacterial ion transport protein and human sodium…: “Human NAV1.7-VSD4-navab in complex with gx-936.”. X-ray diffraction, 2 ligands (PX4, 5P2), 20 pockets (best druggability 0.84). MolNFT v1 #117833 on GenesisL1: 3D…
- PDB
- 5EK0
- Type
- protein
- Length
- 979 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chimera of bacterial ion transport protein and human sodium channel protein type 9…
- UniProt
- A8EVM5, Q15858
- Ligands
- PX4, 5P2
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 82% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chimera of bacterial ion transport protein and human sodium channel protein type 9 subunit alpha | protein | 250 | 82% helix, 0% strand | A8EVM5, Q15858 |
| B | Chimera of bacterial ion transport protein and human sodium channel protein type 9 subunit alpha | protein | 245 | 81% helix, 0% strand | A8EVM5, Q15858 |
| C, D | Chimera of bacterial ion transport protein and human sodium channel protein type 9 subunit alpha | protein | 242 | 83% helix, 0% strand | A8EVM5, Q15858 |
Ligands and binding sites
- PX4 · 1,2-dimyristoyl-sn-glycero-3-phosphocholine · ligand · 21 copies · chains A, D, B, C
- 5P2 · 3-cyano-4-[2-[2-(1-ethylazetidin-3-yl)pyrazol-3-yl]-4-(trifluoromethyl)phenoxy]-~{N}-(1,2,4-thiadiazol-5-yl)benzenesulfonamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 826 | 0.84 | 0.86 | 84 | PX4 |
| 2 | 325 | 0.69 | 0.83 | 42 | 5P2 |
| 3 | 165 | 0.68 | 0.87 | 19 | 5P2 |
| 4 | 182 | 0.66 | 0.86 | 27 | 5P2 |
| 5 | 182 | 0.65 | 0.85 | 24 | 5P2 |
Interfaces
6 interfaces between chains.
- A–B · 2135 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 2107 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 2080 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 2073 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 106 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5EK0 · Human Nav1.7-VSD4-NavAb in complex with GX-936. · the same entry in another collection · chain A against A, TM-score 1.00
- Q15858 · AlphaFold monomer V2.0 prediction for sodium channel protein type 9 subunit alpha (Q15858) · a predicted model of the same protein · chain B against A, TM-score 0.86
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 A8EVM5
- Every structure of UniProt Q15858
- Elsewhere: RCSB PDB 5EK0 · PDBe 5EK0 · UniProt A8EVM5 · UniProt Q15858
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