MolNFT v1 · #155400 · protein
Human PDE5 catalytic core in complex with avanafil
6L6E · Cgmp-specific 3',5'-cyclic phosphodiesterase: “Human PDE5 catalytic core in complex with avanafil”. X-ray diffraction, 4 ligands (E6L, ZN, MG), 3 pockets (best druggability 0.74). MolNFT v1 #155400 on GenesisL1: 3D structure…
- PDB
- 6L6E
- Type
- protein
- Length
- 324 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cgmp-specific 3',5'-cyclic phosphodiesterase
- EC
- 3.1.4.35
- UniProt
- O76074
- Ligands
- E6L, ZN, MG, SO4
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cgmp-specific 3',5'-cyclic phosphodiesterase (EC 3.1.4.35) | protein | 324 | 72% helix, 0% strand | O76074 |
Ligands and binding sites
- E6L · 4-[(3-chloranyl-4-methoxy-phenyl)methylamino]-2-[(2S)-2-(hydroxymethyl)pyrrolidin-1-yl]-N-(pyrimidin-2-ylmethyl)pyrimid ine-5-carboxamide · ligand · chains A
- ZN · Zinc ion · metal · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 416 | 0.74 | 0.84 | 37 | E6L, MG, SO4 |
| 2 | 60 | 0.57 | 0.90 | 19 | empty |
| 3 | 85 | 0.47 | 0.82 | 21 | empty |
Compared structures
- 6L6E · Human PDE5 catalytic core in complex with avanafil · 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 O76074
- Elsewhere: RCSB PDB 6L6E · PDBe 6L6E · UniProt O76074
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