Research workbench
Structure of human nnmt in complex with bisubstrate inhibitor MS2756
Analyse Structure of human nnmt in complex with bisubstrate inhibitor MS2756 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CHH
- 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
- F0P
- Pockets
- 14 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicotinamide N-methyltransferase (EC 2.1.1.1) | protein | 269 | 36% helix, 24% strand | P40261 |
| B | Nicotinamide N-methyltransferase (EC 2.1.1.1) | protein | 267 | 37% helix, 25% strand | P40261 |
| C | Nicotinamide N-methyltransferase (EC 2.1.1.1) | protein | 244 | 37% helix, 27% strand | P40261 |
| D | Nicotinamide N-methyltransferase (EC 2.1.1.1) | protein | 243 | 38% helix, 27% strand | P40261 |
Ligands and binding sites
- F0P · (2~{S})-5-[2-(3-aminocarbonylphenyl)ethyl-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl]amino]-2-azanyl-pentanoic acid · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.82 | 0.94 | 44 | F0P |
| 2 | 231 | 0.82 | 0.94 | 40 | F0P |
| 3 | 777 | 0.74 | 0.79 | 100 | empty |
| 4 | 282 | 0.70 | 0.84 | 39 | F0P |
| 5 | 360 | 0.69 | 0.82 | 53 | F0P |
Interfaces
4 interfaces between chains.
- A–D · 695 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 599 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 449 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 434 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6CHH · Structure of human NNMT in complex with bisubstrate inhibitor MS2756 · 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 6CHH · PDBe 6CHH · UniProt P40261
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