MolNFT v1 · #72343 · protein
Structure of endothelial nitric oxide synthase heme domain complexed with 4-(2-(6-(2-(6-amino-4-methylpyridin-2-YL)ETHYL)PYRIDIN-2-yl) ethyl)-6-methylpyridin-2-amine
3N5P: “Structure of endothelial nitric oxide synthase heme domain complexed with…”. X-ray diffraction, 5 ligands (HEM, XFM, CAD), 10 pockets (best druggability 0.83). MolNFT v1 #72343 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3N5P
- Type
- protein
- Length
- 809 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitric oxide synthase
- EC
- 1.14.13.39
- UniProt
- P29473
- Ligands
- HEM, XFM, CAD, H4B, ZN
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitric oxide synthase (EC 1.14.13.39) | protein | 405 | 40% helix, 16% strand | P29473 |
| B | Nitric oxide synthase (EC 1.14.13.39) | protein | 404 | 41% helix, 15% strand | P29473 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- XFM · 6-(2-{6-[2-(2-amino-6-methylpyridin-4-yl)ethyl]pyridin-2-yl}ethyl)-4-methylpyridin-2-amine · ligand · 2 copies · chains A, B
- CAD · Cacodylic acid · ligand · 2 copies · chains A, B
- H4B · 5,6,7,8-tetrahydrobiopterin · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · 4 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1161 | 0.83 | 0.84 | 83 | HEM, ACT, GOL, XFM, H4B |
| 2 | 1175 | 0.83 | 0.84 | 90 | HEM, ACT, GOL, H4B, XFM |
| 3 | 96 | 0.72 | 0.95 | 22 | empty |
| 4 | 93 | 0.54 | 0.85 | 20 | empty |
| 5 | 93 | 0.54 | 0.84 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2885 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 3N5P · Structure of endothelial nitric oxide synthase heme domain complexed with… · 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 P29473
- Elsewhere: RCSB PDB 3N5P · PDBe 3N5P · UniProt P29473
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