MolNFT v1 · #179864 · protein
PRMT5:MEP50 complexed with 5,5-bicyclic inhibitor compound 4
7KIB · Protein arginine N-methyltransferase 5: “PRMT5:MEP50 complexed with 5,5-bicyclic inhibitor compound 4”. X-ray diffraction, 2 ligands (WFM, CL), 7 pockets (best druggability 0.85). MolNFT v1 #179864 on GenesisL1: 3D structure…
- PDB
- 7KIB
- Type
- protein
- Length
- 935 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
- WFM, CL
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein arginine N-methyltransferase 5 (EC 2.1.1.320) | protein | 625 | 32% helix, 27% strand | O14744 |
| B | Methylosome protein 50 | protein | 310 | 1% helix, 51% strand | Q9BQA1 |
Ligands and binding sites
- WFM · (2r,3r,3as,6s,6ar)-6-[(2-amino-3-bromoquinolin-7-yl) oxy]-2-(4-amino-7H-pyrrolo[2,3-d]pyrimidin-7-yl) hexahydro-3AH-cyclopenta[b]furan-3,3A-diol · ligand · chains A
- CL · Chloride ion · ion · 3 copies · chains A
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 650 | 0.85 | 0.89 | 69 | empty |
| 2 | 546 | 0.84 | 0.89 | 59 | EDO |
| 3 | 343 | 0.79 | 0.89 | 50 | WFM, EDO, PEG |
| 4 | 354 | 0.60 | 0.77 | 43 | CL |
| 5 | 201 | 0.49 | 0.76 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 2165 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7KIB · PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 4 · 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 0.97
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 7KIB · PDBe 7KIB · UniProt O14744 · UniProt Q9BQA1
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