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CARM1 bound with compound 9

Analyse CARM1 bound with compound 9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7FAI
Type: protein
Length: 1,339 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: XJ3
Pockets: 8 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 28% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone-arginine methyltransferase CARM1 (EC 2.1.1.319)	protein	333	28% helix, 36% strand	Q86X55
B	Histone-arginine methyltransferase CARM1 (EC 2.1.1.319)	protein	334	28% helix, 37% strand	Q86X55
C, D	Histone-arginine methyltransferase CARM1 (EC 2.1.1.319)	protein	336	27% helix, 35% strand	Q86X55

Ligands and binding sites

XJ3 · N'-[[3-[4-(3,5-dimethyl-1,2-oxazol-4-yl)-5-methyl-6-(oxan-4-ylamino)pyrimidin-2-yl]phenyl]methyl]-N-methyl-ethane-1,2-diamine · ligand · 4 copies · chains A, D, B, C

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

Pockets

8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1007	0.82	0.83	103	XJ3
2	356	0.79	0.88	53	XJ3
3	452	0.78	0.87	60	XJ3
4	225	0.71	0.87	37	empty
5	259	0.63	0.81	31	empty

Interfaces

5 interfaces between chains.

B–C · 1885 Å² buried · 26 hydrogen bonds · protein-protein
A–D · 1858 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 706 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 186 Å² buried · 1 hydrogen bond · protein-protein
A–C · 173 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

7FAI · CARM1 bound with compound 9 · 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 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 Q86X55
Elsewhere: RCSB PDB 7FAI · PDBe 7FAI · UniProt Q86X55

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