MolNFT v1 · #179866 · protein

PRMT5:MEP50 complexed with 5,5-bicyclic inhibitor compound 72

7KID · Protein arginine N-methyltransferase 5: “PRMT5:MEP50 complexed with 5,5-bicyclic inhibitor compound 72”. X-ray diffraction, 1 ligand (WFV), 7 pockets (best druggability 0.87). MolNFT v1 #179866 on GenesisL1: 3D structure, binding…

PDB: 7KID
Type: protein
Length: 936 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: WFV
Pockets: 7 · best druggability 0.87

Structure

x-ray diffraction · 2 distinct chains · 22% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein arginine N-methyltransferase 5 (EC 2.1.1.320)	protein	625	31% helix, 27% strand	O14744
B	Methylosome protein 50	protein	311	2% helix, 50% strand	Q9BQA1

Ligands and binding sites

WFV · (1S,2R,3aR,4S,6aR)-4-[(2-amino-3,5-difluoroquinolin-7-yl)methyl]-2-(4-amino-5-fluoro-7H-pyrrolo[2,3-d]pyrimidin-7-yl)hexahydropentalene-1,6a(1H)-diol · ligand · chains A
EDO · 1,2-ethanediol · additive · 4 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, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1198	0.87	0.89	107	empty
2	339	0.80	0.90	46	WFV
3	358	0.61	0.77	37	empty
4	200	0.57	0.80	28	empty
5	183	0.51	0.77	31	empty

Interfaces

1 interface between chains.

A–B · 2226 Å² buried · 38 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

7KID · PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 72 · 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 7KID · PDBe 7KID · UniProt O14744 · UniProt Q9BQA1

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