MolNFT v1 · #186636 · protein
Structure of nicotinamide N-methyltransferase (nnmt) in complex with II399 (C2 space group)
7RKK · Nnmt protein: “Structure of nicotinamide N-methyltransferase (nnmt) in complex with II399 (C2 space group)”. X-ray diffraction, 1 ligand (5R4), 6 pockets (best druggability 0.84). MolNFT v1 #186636 on GenesisL1: 3D structure…
- PDB
- 7RKK
- Type
- protein
- Length
- 528 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nnmt protein
- UniProt
- Q6FH49
- Ligands
- 5R4
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nnmt protein | protein | 270 | 36% helix, 24% strand | Q6FH49 |
| B | Nnmt protein | protein | 258 | 37% helix, 26% strand | Q6FH49 |
Ligands and binding sites
- 5R4 · 3-[3-(acetyl{[(1R,2R,3S,4R)-4-(4-chloro-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-2,3-dihydroxycyclopentyl]methyl}amino)prop-1-yn-1-yl]benzamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.84 | 0.97 | 42 | 5R4 |
| 2 | 236 | 0.81 | 0.94 | 42 | 5R4 |
| 3 | 172 | 0.53 | 0.79 | 19 | empty |
| 4 | 125 | 0.49 | 0.79 | 18 | empty |
| 5 | 102 | 0.41 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 763 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 7RKK · Structure of Nicotinamide N-Methyltransferase (NNMT) in complex with II399 (C2 space… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q6FH49
- Elsewhere: RCSB PDB 7RKK · PDBe 7RKK · UniProt Q6FH49
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