MolNFT v1 · #152985 · protein

PRMT4 bound with a bicyclic compound

6IZQ · Histone-arginine methyltransferase CARM1: “PRMT4 bound with a bicyclic compound”. X-ray diffraction, 1 ligand (XJ2), 10 pockets (best druggability 0.83). MolNFT v1 #152985 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6IZQ
Type: protein
Length: 1,324 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone-arginine methyltransferase CARM1
EC: 2.1.1.319
UniProt: Q86X55
Ligands: XJ2
Pockets: 10 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 27% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Histone-arginine methyltransferase CARM1 (EC 2.1.1.319)	protein	332	28% helix, 37% strand	Q86X55
B	Histone-arginine methyltransferase CARM1 (EC 2.1.1.319)	protein	330	27% helix, 38% strand	Q86X55
D	Histone-arginine methyltransferase CARM1 (EC 2.1.1.319)	protein	330	27% helix, 36% strand	Q86X55

Ligands and binding sites

XJ2 · (2R)-1-(methylamino)-3-(1,3,4,5-tetrahydro-2-benzazepin-2-yl)propan-2-ol · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	858	0.83	0.85	109	XJ2
2	260	0.73	0.87	41	empty
3	232	0.72	0.87	38	empty
4	1004	0.72	0.75	76	empty
5	207	0.60	0.81	29	empty

Interfaces

5 interfaces between chains.

A–C · 1860 Å² buried · 27 hydrogen bonds · protein-protein
B–D · 1858 Å² buried · 29 hydrogen bonds · protein-protein
C–D · 724 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 176 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 164 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6IZQ · PRMT4 bound with a bicyclic compound · the same entry in another collection · chain D against D, TM-score 1.00
Q86X55 · AlphaFold monomer V2.0 prediction for histone-arginine methyltransferase CARM1 (Q86X55) · 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 Q86X55
Elsewhere: RCSB PDB 6IZQ · PDBe 6IZQ · UniProt Q86X55

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