Research workbench
Structure of nicotinamide N-methyltransferase (nnmt) in complex with II399 (P1 space group)
Analyse Structure of nicotinamide N-methyltransferase (nnmt) in complex with II399 (P1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RKL
- Type
- protein
- Length
- 1,050 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nnmt protein
- UniProt
- Q6FH49
- Ligands
- 5R4, SO4
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nnmt protein | protein | 271 | 35% helix, 24% strand | Q6FH49 |
| B | Nnmt protein | protein | 269 | 35% helix, 24% strand | Q6FH49 |
| C | Nnmt protein | protein | 256 | 37% helix, 25% strand | Q6FH49 |
| D | Nnmt protein | protein | 254 | 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 · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.81 | 0.94 | 41 | 5R4 |
| 2 | 232 | 0.80 | 0.93 | 43 | 5R4 |
| 3 | 222 | 0.80 | 0.93 | 44 | 5R4 |
| 4 | 612 | 0.77 | 0.83 | 94 | 5R4 |
| 5 | 236 | 0.61 | 0.81 | 33 | empty |
Interfaces
4 interfaces between chains.
- A–D · 753 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 635 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 495 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 468 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7RKL · Structure of Nicotinamide N-Methyltransferase (NNMT) in complex with II399 (P1 space… · the same entry in another collection · chain D against D, 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 7RKL · PDBe 7RKL · UniProt Q6FH49
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