MolNFT v1 · #101583 · protein

Human G9A in complex with inhibitor a-366

4NVQ · Histone-lysine N-methyltransferase EHMT2: “Human G9A in complex with inhibitor a-366”. X-ray diffraction, 3 ligands (2OD, SAH, ZN), 9 pockets (best druggability 0.81). MolNFT v1 #101583 on GenesisL1: 3D structure, binding sites and…

PDB: 4NVQ
Type: protein
Length: 530 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone-lysine N-methyltransferase EHMT2
EC: 2.1.1.-, 2.1.1.43
UniProt: Q96KQ7
Ligands: 2OD, SAH, ZN
Pockets: 9 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 13% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone-lysine N-methyltransferase EHMT2 (EC 2.1.1.-, 2.1.1.43)	protein	267	13% helix, 25% strand	Q96KQ7
B	Histone-lysine N-methyltransferase EHMT2 (EC 2.1.1.-, 2.1.1.43)	protein	263	13% helix, 26% strand	Q96KQ7

Ligands and binding sites

2OD · 5'-methoxy-6'-[3-(pyrrolidin-1-yl) propoxy]spiro[cyclobutane-1,3'-indol]-2'-amine · ligand · 2 copies · chains A, B
SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
ZN · Zinc ion · metal · 8 copies · chains A, B

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

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1042	0.81	0.83	72	empty
2	409	0.67	0.79	50	SAH, 2OD
3	183	0.56	0.80	31	2OD
4	186	0.54	0.79	22	SAH
5	71	0.44	0.82	20	empty

Interfaces

1 interface between chains.

A–B · 1130 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

4NVQ · Human G9a in Complex with Inhibitor A-366 · the same entry in another collection · chain A against A, TM-score 1.00
Q96KQ7 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase EHMT2 (Q96KQ7) · a predicted model of the same protein · chain B 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 Q96KQ7
Elsewhere: RCSB PDB 4NVQ · PDBe 4NVQ · UniProt Q96KQ7

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