MolNFT v1 · #166692 · protein
PRMT5:MEP50 complexed with allosteric inhibitor compound 1A
6UXX · Protein arginine N-methyltransferase 5: “PRMT5:MEP50 complexed with allosteric inhibitor compound 1A”. X-ray diffraction, 1 ligand (QL1), 9 pockets (best druggability 0.84). MolNFT v1 #166692 on GenesisL1: 3D structure, binding…
- PDB
- 6UXX
- Type
- protein
- Length
- 920 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein arginine N-methyltransferase 5; Methylosome protein 50
- EC
- 2.1.1.320
- UniProt
- O14744, Q9BQA1
- Ligands
- QL1
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein arginine N-methyltransferase 5 (EC 2.1.1.320) | protein | 610 | 30% helix, 27% strand | O14744 |
| B | Methylosome protein 50 | protein | 310 | 2% helix, 51% strand | Q9BQA1 |
Ligands and binding sites
- QL1 · (5R)-2-amino-5-(4-methoxyphenyl)-3-methyl-5-[(3S,5S, 7S)-tricyclo[3.3.1.1~3,7~]decan-1-yl]-3,5-dihydro-4H-imidazol-4-one · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 551 | 0.84 | 0.90 | 54 | empty |
| 2 | 514 | 0.84 | 0.90 | 58 | empty |
| 3 | 420 | 0.76 | 0.85 | 46 | QL1 |
| 4 | 318 | 0.60 | 0.78 | 36 | empty |
| 5 | 84 | 0.60 | 0.88 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2222 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 6UXX · PRMT5:MEP50 Complexed with Allosteric Inhibitor Compound 1a · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BQA1 · AlphaFold monomer V2.0 prediction for methylosome protein 50 (Q9BQA1) · a predicted model of the same protein · chain B against A, TM-score 0.99
- O14744 · AlphaFold monomer V2.0 prediction for protein arginine N-methyltransferase 5 (O14744) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 O14744
- Every structure of UniProt Q9BQA1
- Elsewhere: RCSB PDB 6UXX · PDBe 6UXX · UniProt O14744 · UniProt Q9BQA1
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