MolNFT v1 · #182996 · protein
Co-crystal structure of human nicotinamide N-methyltransferase (nnmt) with the bisubstrate-like inhibitor (33)
7NBM: “Co-crystal structure of human nicotinamide N-methyltransferase (nnmt) with the bisubstrate-like inhibitor (33)”. X-ray diffraction, 1 ligand (U7K), 9 pockets (best druggability 0.84). MolNFT v1 #182996 on GenesisL1: 3D structure…
- PDB
- 7NBM
- Type
- protein
- Length
- 1,038 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
- U7K
- Pockets
- 9 · best druggability 0.84
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 | 268 | 37% helix, 25% strand | P40261 |
| B | Nicotinamide N-methyltransferase (EC 2.1.1.1) | protein | 265 | 36% helix, 25% strand | P40261 |
| C | Nicotinamide N-methyltransferase (EC 2.1.1.1) | protein | 253 | 38% helix, 25% strand | P40261 |
| D | Nicotinamide N-methyltransferase (EC 2.1.1.1) | protein | 252 | 37% helix, 27% strand | P40261 |
Ligands and binding sites
- U7K · (E)-3-((5,6-dihydro-2H,4H-thiazolo[5,4,3-ij]quinolin-2-ylidene)amino)-2-hydroxy-1-(4-(isoquinolin-5-yl) piperazin-1-yl)-2-methylpropan-1-one · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.84 | 0.95 | 44 | U7K |
| 2 | 241 | 0.82 | 0.95 | 41 | U7K |
| 3 | 258 | 0.82 | 0.94 | 40 | U7K |
| 4 | 423 | 0.79 | 0.87 | 57 | U7K |
| 5 | 422 | 0.72 | 0.83 | 66 | empty |
Interfaces
4 interfaces between chains.
- A–B · 693 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 501 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 488 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 415 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7NBM · Co-crystal structure of Human Nicotinamide N-methyltransferase (NNMT) with the… · the same entry in another collection · chain D against D, TM-score 1.00
- P40261 · AlphaFold monomer V2.0 prediction for nicotinamide N-methyltransferase (P40261) · a predicted model of the same protein · chain D 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 7NBM · PDBe 7NBM · UniProt P40261
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