MolNFT v1 · #124684 · protein
Structure of cavab in complex with amlodipine
5KMD · Ion transport protein: “Structure of cavab in complex with amlodipine”. X-ray diffraction, 3 ligands (MC3, 6UB, CA), 20 pockets (best druggability 0.80). MolNFT v1 #124684 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5KMD
- Type
- protein
- Length
- 876 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ion transport protein
- UniProt
- A8EVM5
- Ligands
- MC3, 6UB, CA
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ion transport protein | protein | 219 | 80% helix, 0% strand | A8EVM5 |
Ligands and binding sites
- MC3 · 1,2-dimyristoyl-rac-glycero-3-phosphocholine · ligand · 14 copies · chains A, D, B, C
- 6UB · amlodipine · ligand · chains C, D
- CA · Calcium ion · metal · 2 copies · chains B, C, D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 545 | 0.80 | 0.86 | 77 | MC3, CA |
| 2 | 139 | 0.65 | 0.86 | 21 | MC3 |
| 3 | 158 | 0.58 | 0.81 | 18 | empty |
| 4 | 343 | 0.57 | 0.75 | 43 | MC3 |
| 5 | 138 | 0.56 | 0.81 | 17 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1528 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1508 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1501 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1488 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 18 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5KMD · Structure of CavAb in complex with amlodipine · 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 5KMD · PDBe 5KMD · UniProt A8EVM5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.