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Co-crystal structure of human nicotinamide N-methyltransferase (nnmt) with tricyclic small molecule inhibitor jbsnf-000107
Analyse Co-crystal structure of human nicotinamide N-methyltransferase (nnmt) with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EU5
- Type
- protein
- Length
- 1,023 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, JDL
- Pockets
- 16 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicotinamide N-methyltransferase (EC 2.1.1.1) | protein | 256 | 38% helix, 27% strand | P40261 |
| B | Nicotinamide N-methyltransferase (EC 2.1.1.1) | protein | 255 | 38% helix, 26% 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 | 255 | 40% helix, 27% strand | P40261 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
- JDL · 6-fluoranyl-10-methyl-1,10-diazatricyclo[6.3.1.0^{4, 12}]dodeca-4,6,8(12)-trien-11-imine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 825 | 0.84 | 0.86 | 99 | empty |
| 2 | 227 | 0.81 | 0.94 | 41 | SAH, JDL |
| 3 | 231 | 0.80 | 0.93 | 44 | SAH, JDL |
| 4 | 148 | 0.77 | 0.94 | 31 | SAH |
| 5 | 143 | 0.77 | 0.94 | 32 | SAH |
Interfaces
5 interfaces between chains.
- A–B · 820 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 704 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 283 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 282 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 239 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7EU5 · Co-crystal structure of Human Nicotinamide N-methyltransferase (NNMT) with tricyclic… · 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 7EU5 · PDBe 7EU5 · UniProt P40261
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