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Co-crystal structure of human nicotinamide N-methyltransferase (nnmt) with the tricyclic inhibitor (2)
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
- 7BKG
- Type
- protein
- Length
- 1,050 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, U0Z
- Pockets
- 11 · best druggability 0.80
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 | 272 | 36% helix, 24% strand | P40261 |
| B | Nicotinamide N-methyltransferase (EC 2.1.1.1) | protein | 268 | 37% helix, 24% strand | P40261 |
| C | Nicotinamide N-methyltransferase (EC 2.1.1.1) | protein | 256 | 38% helix, 26% strand | P40261 |
| D | Nicotinamide N-methyltransferase (EC 2.1.1.1) | protein | 254 | 39% helix, 26% strand | P40261 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
- U0Z · 5,6-dihydro-2-imino-2H,4H-thiazolo(5,4,3-IJ)quinoline · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 227 | 0.80 | 0.93 | 46 | SAH, U0Z |
| 2 | 697 | 0.78 | 0.82 | 97 | SAH, U0Z |
| 3 | 171 | 0.76 | 0.92 | 32 | SAH |
| 4 | 154 | 0.76 | 0.93 | 32 | SAH |
| 5 | 58 | 0.71 | 0.98 | 17 | U0Z |
Interfaces
4 interfaces between chains.
- A–B · 740 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 479 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 478 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 466 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7BKG · Co-crystal structure of Human Nicotinamide N-methyltransferase (NNMT) with the tricyclic… · 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 7BKG · PDBe 7BKG · UniProt P40261
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