MolNFT v1 · #186368 · protein
Co-crystal structure of human PRMT9 in complex with MT556 inhibitor
7RBQ · Protein arginine N-methyltransferase 9: “Co-crystal structure of human PRMT9 in complex with MT556 inhibitor”. X-ray diffraction, 2 ligands (44T, UNX), 8 pockets (best druggability 0.73). MolNFT v1 #186368 on GenesisL1: 3D…
- PDB
- 7RBQ
- Type
- protein
- Length
- 614 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein arginine N-methyltransferase 9
- EC
- 2.1.1.320
- UniProt
- Q6P2P2
- Ligands
- 44T, UNX
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein arginine N-methyltransferase 9 (EC 2.1.1.320) | protein | 614 | 26% helix, 34% strand | Q6P2P2 |
Ligands and binding sites
- 44T · 7-[5-S-(4-{[(4-ethylpyridin-3-yl)methyl]amino}butyl)-5-thio-beta-D-ribofuranosyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine · ligand · chains A
- UNX · Unknown atom or ion · ion · 5 copies · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 349 | 0.73 | 0.84 | 42 | 44T |
| 2 | 453 | 0.68 | 0.80 | 49 | UNX |
| 3 | 117 | 0.63 | 0.87 | 25 | empty |
| 4 | 124 | 0.42 | 0.76 | 18 | empty |
| 5 | 76 | 0.40 | 0.79 | 15 | empty |
Compared structures
- 7RBQ · Co-crystal structure of human PRMT9 in complex with MT556 inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- Q6P2P2 · AlphaFold monomer V2.0 prediction for protein arginine N-methyltransferase 9 (Q6P2P2) · a predicted model of the same protein · chain A 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 Q6P2P2
- Elsewhere: RCSB PDB 7RBQ · PDBe 7RBQ · UniProt Q6P2P2
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