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Co-crystal structure of human nicotinamide N-methyltransferase (nnmt) with the bisubstrate-like inhibitor (1)
Analyse Co-crystal structure of human nicotinamide N-methyltransferase (nnmt) with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NBJ
- Type
- protein
- Length
- 1,041 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
- U7H
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicotinamide N-methyltransferase (EC 2.1.1.1) | protein | 269 | 36% helix, 25% strand | P40261 |
| B | Nicotinamide N-methyltransferase (EC 2.1.1.1) | protein | 267 | 36% helix, 24% strand | P40261 |
| C | Nicotinamide N-methyltransferase (EC 2.1.1.1) | protein | 252 | 38% helix, 26% strand | P40261 |
| D | Nicotinamide N-methyltransferase (EC 2.1.1.1) | protein | 253 | 38% helix, 26% strand | P40261 |
Ligands and binding sites
- U7H · 2-hydroxy-1-(4-(isoquinolin-5-yl)piperazin-1-yl)-2-methyl-3-(3-methyl-4-phenyl-1H-pyrazol-1-yl)propan-1-one · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.83 | 0.94 | 42 | U7H |
| 2 | 258 | 0.83 | 0.94 | 43 | U7H |
| 3 | 252 | 0.82 | 0.94 | 43 | U7H |
| 4 | 462 | 0.79 | 0.86 | 62 | U7H |
| 5 | 627 | 0.74 | 0.81 | 69 | empty |
Interfaces
4 interfaces between chains.
- A–B · 601 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 520 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 485 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 461 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7NBJ · Co-crystal structure of Human Nicotinamide N-methyltransferase (NNMT) with the… · the same entry in another collection · chain C against C, 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 7NBJ · PDBe 7NBJ · UniProt P40261
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