Research workbench
Structure of bovine endothelial nitric oxide synthase heme domain in complex with 4-(2-(((2-aminoquinolin-7-YL)METHYL)AMINO)ETHYL)-2- methylbenzonitrile
Analyse Structure of bovine endothelial nitric oxide synthase heme domain in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VV8
- Type
- protein
- Length
- 820 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitric oxide synthase, endothelial
- EC
- 1.14.13.39
- UniProt
- P29473
- Ligands
- HEM, H4B, 9P7, CAD, ZN
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitric oxide synthase, endothelial (EC 1.14.13.39) | protein | 416 | 39% helix, 16% strand | P29473 |
| B | Nitric oxide synthase, endothelial (EC 1.14.13.39) | protein | 404 | 40% helix, 16% strand | P29473 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- H4B · 5,6,7,8-tetrahydrobiopterin · ligand · 2 copies · chains A, B
- 9P7 · 4-(2-{[(2-aminoquinolin-7-yl)methyl]amino}ethyl)-2-methylbenzonitrile · ligand · 2 copies · chains A, B
- CAD · Cacodylic acid · ligand · chains B
- ZN · Zinc ion · metal · chains A, B
- ACT · Acetate ion · additive · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.85 | 0.85 | 84 | HEM, H4B, 9P7, ACT, GOL |
| 2 | 1080 | 0.84 | 0.85 | 90 | HEM, H4B, 9P7, ACT, GOL |
| 3 | 89 | 0.72 | 0.95 | 22 | empty |
| 4 | 355 | 0.62 | 0.78 | 49 | empty |
| 5 | 89 | 0.55 | 0.85 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2886 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (artifact).
Compared structures
- 5VV8 · Structure of bovine endothelial nitric oxide synthase heme domain in complex 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 5VV8 · PDBe 5VV8 · UniProt P29473
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