MolNFT v1 · #154535 · protein
Structure basis for diltiazem block of a voltage-gated calcium channel
6KEB · Ion transport protein: “Structure basis for diltiazem block of a voltage-gated calcium channel”. X-ray diffraction, 3 ligands (PX4, D6C, CA), 20 pockets (best druggability 0.83). MolNFT v1 #154535 on GenesisL1: 3D structure, binding…
- PDB
- 6KEB
- Type
- protein
- Length
- 885 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ion transport protein
- UniProt
- A8EVM5
- Ligands
- PX4, D6C, CA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Ion transport protein | protein | 219 | 74% helix, 0% strand | A8EVM5 |
| D | Ion transport protein | protein | 228 | 81% helix, 0% strand | A8EVM5 |
Ligands and binding sites
- PX4 · 1,2-dimyristoyl-sn-glycero-3-phosphocholine · ligand · 12 copies · chains A, C, B, D
- D6C · [(2~{S},3~{R})-5-[2-(dimethylamino)ethyl]-2-(4-methoxyphenyl)-4-oxidanylidene-2,3-dihydro-1,5-benzothiazepin-3-yl] ethanoate · ligand · chains B, C, D
- CA · Calcium ion · metal · 2 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1060 | 0.83 | 0.83 | 91 | CA, D6C |
| 2 | 178 | 0.63 | 0.83 | 23 | PX4 |
| 3 | 162 | 0.57 | 0.80 | 19 | empty |
| 4 | 202 | 0.55 | 0.78 | 19 | empty |
| 5 | 146 | 0.54 | 0.80 | 20 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1645 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1545 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1543 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1519 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 22 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6KEB · Structure basis for Diltiazem block of a voltage-gated calcium channel · the same entry in another collection · chain A against A, TM-score 1.00
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
- Elsewhere: RCSB PDB 6KEB · PDBe 6KEB · UniProt A8EVM5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.