MolNFT v1 · #140711 · protein
Co-crystal structure of human nicotinamide N-methyltransferase (nnmt) with small molecule analog of nicotinamide
5YJF: “Co-crystal structure of human nicotinamide N-methyltransferase (nnmt) with small molecule analog of…”. X-ray diffraction, 2 ligands (SAH, 8WO), 15 pockets (best druggability 0.84). MolNFT v1 #140711 on GenesisL1: 3D structure…
- PDB
- 5YJF
- Type
- protein
- Length
- 1,021 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinamide N-methyltransferase
- EC
- 2.1.1.1
- UniProt
- P40261
- Ligands
- SAH, 8WO
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nicotinamide N-methyltransferase (EC 2.1.1.1) | protein | 256 | 38% helix, 27% strand | P40261 |
| C | Nicotinamide N-methyltransferase (EC 2.1.1.1) | protein | 257 | 38% helix, 26% strand | P40261 |
| D | Nicotinamide N-methyltransferase (EC 2.1.1.1) | protein | 252 | 40% helix, 25% strand | P40261 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
- 8WO · 6-methoxy-1-methyl-2H-pyridine-3-carboxamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1081 | 0.84 | 0.85 | 116 | empty |
| 2 | 218 | 0.81 | 0.94 | 43 | SAH, 8WO |
| 3 | 211 | 0.81 | 0.94 | 41 | SAH, 8WO |
| 4 | 210 | 0.80 | 0.94 | 41 | SAH, 8WO |
| 5 | 158 | 0.78 | 0.94 | 30 | SAH |
Interfaces
5 interfaces between chains.
- A–B · 855 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 753 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 333 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 333 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 223 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5YJF · Co-crystal structure of Human Nicotinamide N-methyltransferase (NNMT) with small molecule… · the same entry in another collection · chain B against B, TM-score 1.00
- P40261 · AlphaFold monomer V2.0 prediction for nicotinamide N-methyltransferase (P40261) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P40261
- Elsewhere: RCSB PDB 5YJF · PDBe 5YJF · UniProt P40261
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