MolNFT v1 · #183468 · protein
X-ray structure of PRMT6 in complex with indazole type inhibitor
7NR4 · Protein arginine N-methyltransferase 6: “X-ray structure of PRMT6 in complex with indazole type inhibitor”. X-ray diffraction, 2 ligands (SAH, UO2), 12 pockets (best druggability 0.75). MolNFT v1 #183468 on GenesisL1: 3D structure…
- PDB
- 7NR4
- Type
- protein
- Length
- 1,342 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein arginine N-methyltransferase 6
- EC
- 2.1.1.-, 2.1.1.125
- UniProt
- Q96LA8
- Ligands
- SAH, UO2
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein arginine N-methyltransferase 6 (EC 2.1.1.-, 2.1.1.125) | protein | 334 | 32% helix, 35% strand | Q96LA8 |
| B | Protein arginine N-methyltransferase 6 (EC 2.1.1.-, 2.1.1.125) | protein | 338 | 31% helix, 35% strand | Q96LA8 |
| C | Protein arginine N-methyltransferase 6 (EC 2.1.1.-, 2.1.1.125) | protein | 335 | 31% helix, 36% strand | Q96LA8 |
| D | Protein arginine N-methyltransferase 6 (EC 2.1.1.-, 2.1.1.125) | protein | 335 | 31% helix, 35% strand | Q96LA8 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
- UO2 · (2~{S})-2-azanyl-~{N}-[3-[3-(dimethylsulfamoyl)phenyl]-2~{H}-indazol-5-yl]propanamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 492 | 0.75 | 0.83 | 63 | SAH, UO2 |
| 2 | 467 | 0.75 | 0.84 | 61 | SAH, UO2 |
| 3 | 488 | 0.74 | 0.83 | 63 | SAH, UO2 |
| 4 | 448 | 0.71 | 0.82 | 59 | SAH, UO2 |
| 5 | 868 | 0.70 | 0.76 | 81 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1863 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1831 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 570 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 555 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 173 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7NR4 · X-RAY STRUCTURE OF PRMT6 IN COMPLEX WITH indazole type inhibitor · the same entry in another collection · chain C against C, TM-score 1.00
- Q96LA8 · AlphaFold monomer V2.0 prediction for protein arginine N-methyltransferase 6 (Q96LA8) · a predicted model of the same protein · 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 Q96LA8
- Elsewhere: RCSB PDB 7NR4 · PDBe 7NR4 · UniProt Q96LA8
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