MolNFT v1 · #146820 · protein
The structure of NTMT1 in complex with compound DC100-1
6DTN · N-terminal xaa-pro-lys N-methyltransferase 1: “The structure of NTMT1 in complex with compound DC100-1”. X-ray diffraction, 2 ligands (6D6, NH2), 2 pockets (best druggability 0.79). MolNFT v1 #146820 on GenesisL1: 3D structure…
- PDB
- 6DTN
- Type
- protein
- Length
- 239 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-terminal xaa-pro-lys N-methyltransferase 1; (6D6)PPKRIA(NH2), DC100-1
- EC
- 2.1.1.244
- UniProt
- Q9BV86
- Ligands
- 6D6, NH2
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | N-terminal xaa-pro-lys N-methyltransferase 1 (EC 2.1.1.244) | protein | 233 | 38% helix, 26% strand | Q9BV86 |
| A | (6D6)PPKRIA(NH2), DC100-1 | protein | 6 | 0% helix, 17% strand | — |
Ligands and binding sites
- 6D6 · 5'-{[(3S)-3-amino-3-carboxypropyl](3-aminopropyl) amino}-5'-deoxyadenosine · ligand · chains B, A
- NH2 · Amino group · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 173 | 0.79 | 0.94 | 30 | 6D6 |
| 2 | 53 | 0.35 | 0.79 | 13 | empty |
Interfaces
1 interface between chains.
- B–A · 503 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6DTN · The structure of NTMT1 in complex with compound DC100-1 · the same entry in another collection · chain B against B, TM-score 1.00
- Q9BV86 · AlphaFold monomer V2.0 prediction for N-terminal xaa-pro-lys N-methyltransferase 1… · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q9BV86
- Elsewhere: RCSB PDB 6DTN · PDBe 6DTN · UniProt Q9BV86
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