MolNFT v1 · #145316 · protein

Structure of PRMT5:MEP50 in complex with lly-283, a potent and selective inhibitor of PRMT5, with antitumor activity

6CKC · Protein arginine N-methyltransferase 5: “Structure of PRMT5:MEP50 in complex with lly-283, a potent and selective inhibitor of PRMT5, with antitumor…”. X-ray diffraction, 1 ligand (F5J), 7 pockets (best druggability 0.84). MolNFT v1…

PDB: 6CKC
Type: protein
Length: 928 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: F5J
Pockets: 7 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 23% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein arginine N-methyltransferase 5 (EC 2.1.1.320)	protein	625	33% helix, 27% strand	O14744
B	Methylosome protein 50	protein	303	2% helix, 51% strand	Q9BQA1

Ligands and binding sites

F5J · 7-[(5R)-5-C-phenyl-beta-D-ribofuranosyl]-7H-pyrrolo[2, 3-d]pyrimidin-4-amine · ligand · 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	564	0.84	0.90	55	empty
2	511	0.82	0.89	57	empty
3	148	0.79	0.96	33	F5J
4	369	0.62	0.77	44	empty
5	152	0.56	0.81	18	empty

Interfaces

1 interface between chains.

A–B · 2158 Å² buried · 36 hydrogen bonds · protein-protein

Compared structures

6CKC · Structure of PRMT5:MEP50 in complex with LLY-283, a potent and selective inhibitor of… · 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 1.00
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 6CKC · PDBe 6CKC · UniProt O14744 · UniProt Q9BQA1

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