5VSC: Human G9a SET-domain

Structure of human G9a SET-domain (EHMT2) in complex with inhibitor 13. Determined by X-ray diffraction at 1.4 Å resolution. Released 12 Jul 2017.

Method: X-ray diffraction
Resolution: 1.4 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,888
Mol. weight: 65.53 kDa
Ligands: 9HJ, SAM, ZN
Released: 12 Jul 2017

Explore 5VSC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5VSC contains 28 α-helices and 42 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 14 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	920-923	4	1
β-strand	937-939	3	1
α-helix	944-947	4
β-strand	951-952	2	2
β-strand	957-958	2	2
β-strand	967	1	3
α-helix	968-970	3
α-helix	986-989	4
β-strand	996	1	4
α-helix	1001	1
β-strand	1002	1	4
α-helix	1003	1
α-helix	1011-1013	3
β-strand	1014-1015	2	5
α-helix	1032-1034	3
β-strand	1040-1044	5	1
β-strand	1050-1054	5	1
β-strand	1058	1	6
β-strand	1063-1067	5	5
β-strand	1069-1073	5	2
α-helix	1074-1077	4
β-strand	1086-1089	4	2
β-strand	1097-1105	9	2
α-helix	1107-1110	4
α-helix	1111	1
β-strand	1112-1113	2	7
β-strand	1119-1125	7	5
β-strand	1135-1140	6	5
β-strand	1144	1	6
α-helix	1148	1
β-strand	1149	1	1
α-helix	1150	1
β-strand	1151-1152	2	7
α-helix	1156-1162	7
α-helix	1179-1189	11

Chain B: 14 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	917-919	3
β-strand	920-923	4	8
β-strand	937-939	3	8
β-strand	951-952	2	3
β-strand	957-958	2	3
β-strand	967	1	2
α-helix	968-970	3
α-helix	986-989	4
β-strand	996	1	9
α-helix	1001	1
β-strand	1002	1	9
α-helix	1003	1
α-helix	1011-1013	3
β-strand	1014-1015	2	10
α-helix	1032-1034	3
β-strand	1040-1044	5	8
β-strand	1050-1054	5	8
β-strand	1058	1	11
β-strand	1063-1067	5	10
β-strand	1069-1073	5	3
α-helix	1074-1077	4
β-strand	1086-1089	4	3
β-strand	1097-1105	9	3
α-helix	1107-1110	4
α-helix	1111	1
β-strand	1112-1113	2	12
β-strand	1119-1125	7	10
β-strand	1135-1140	6	10
β-strand	1144	1	11
α-helix	1148	1
β-strand	1149	1	8
α-helix	1150	1
β-strand	1151-1152	2	12
α-helix	1156-1162	7
α-helix	1179-1189	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase EHMT2	A, B	protein	275	Homo sapiens	Q96KQ7 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5VSC_1 Histone-lysine N-methyltransferase EHMT2 (chains A, B)
IRTEKIICRDVARGYENVPIPCVNGVDGEPCPEDYKYISENCETSTMNIDRNITHLQHCT
CVDDCSSSNCLCGQLSIRCWYDKDGRLLQEFNKIEPPLIFECNQACSCWRNCKNRVVQSG
IKVRLQLYRTAKMGWGVRALQTIPQGTFICEYVGELISDAEADVREDDSYLFDLDNKDGE
VYCIDARYYGNISRFINHLCDPNIIPVRVFMLHQDLRFPRIAFFSSRDIRTGEELGFDYG
DRFWDIKSKYFTCQCGSEKCKHSAEAIALEQSRLA

Ligands and cofactors

ID	Name	Formula	Copies
9HJ	6,7-dimethoxy-N~2~-methyl-N~4~-(1-methylpiperidin-4-yl)-N~2~-propylquinazoline-…	C20 H31 N5 O2	2
SAM	S-adenosylmethionine	C15 H22 N6 O5 S	2
ZN	Zinc ion	Zn	8

Primary citation

Structure-activity relationship studies of G9a-like protein (GLP) inhibitors. Xiong, Y., Li, F., Babault, N. et al. Bioorg Med Chem (2017) 25:4414-4423. DOI 10.1016/j.bmc.2017.06.021 · PubMed

Other PDB entries of the same protein (UniProt Q96KQ7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7XUD 1.45 Å, Structure of G9a in complex with compound 26a
5JIY 1.48 Å, Structure of G9a SET-domain with Histone H3K9norLeucine mutant peptide and bound…
7X73 1.49 Å, Structure of G9a in complex with RK-701
8Z7C 1.52 Å, Structure of G9a in complex with compound 7i
8Z7E 1.54 Å, Structure of G9a in complex with compound 9b
8Z7D 1.58 Å, Structure of G9a in complex with compound 9a
5VSE 1.6 Å, Structure of human G9a SET-domain (EHMT2) in complex with inhibitor 17:…
5JHN 1.67 Å, Structure of G9a SET-domain with Histone H3K9Ala mutant peptide and bound…
7XUC 1.67 Å, Structure of G9a in complex with compound 11a
3K5K 1.7 Å, Discovery of a 2,4-Diamino-7-aminoalkoxy-quinazoline as a Potent Inhibitor of Histone…
5T0K 1.7 Å, Structure of G9a SET-domain with H3K9M mutant peptide and SAM
5JJ0 1.72 Å, Structure of G9a SET-domain with Histone H3K9M peptide and excess SAH

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