Research workbench
Structure of nicotinamide N-methyltransferase (nnmt) in complex with inhibitor LL320
Analyse Structure of nicotinamide N-methyltransferase (nnmt) in complex with inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PVS
- Type
- protein
- Length
- 1,055 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nnmt protein
- UniProt
- Q6FH49
- Ligands
- P0V
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nnmt protein | protein | 270 | 36% helix, 24% strand | Q6FH49 |
| C | Nnmt protein | protein | 257 | 37% helix, 25% strand | Q6FH49 |
| D | Nnmt protein | protein | 258 | 36% helix, 25% strand | Q6FH49 |
Ligands and binding sites
- P0V · 9-(5-{[(3R)-3-amino-3-carboxypropyl][3-(3-carbamoylphenyl)prop-2-yn-1-yl]amino}-5-deoxy-alpha-D-lyxofuranosyl)-9H-purin-6-amine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 247 | 0.82 | 0.94 | 43 | P0V |
| 2 | 255 | 0.81 | 0.93 | 42 | P0V |
| 3 | 231 | 0.80 | 0.93 | 40 | P0V |
| 4 | 487 | 0.77 | 0.85 | 69 | P0V |
| 5 | 276 | 0.66 | 0.82 | 51 | empty |
Interfaces
4 interfaces between chains.
- B–D · 769 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 648 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 447 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 440 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6PVS · Structure of Nicotinamide N-Methyltransferase (NNMT) in complex with inhibitor LL320 · 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 Q6FH49
- Elsewhere: RCSB PDB 6PVS · PDBe 6PVS · UniProt Q6FH49
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