Structure of PDB 5vsc Chain B

Receptor sequence

>5vscB (length=272) Species: 9606 (Homo sapiens)

IRTEKIICRDVARGYENVPIPCVNGVDGEPCPEDYKYISENCETSTMNID
RNITHLQHCTCVDDCSSSNCLCGQLSIRCWYDKDGRLLQEFNKIEPPLIF
ECNQACSCWRNCKNRVVQSGIKVRLQLYRTAKMGWGVRALQTIPQGTFIC
EYVGELISDAEADVREDDSYLFDLDGEVYCIDARYYGNISRFINHLCDPN
IIPVRVFMLHQDLRFPRIAFFSSRDIRTGEELGFDYGDRFWDIKSKYFTC
QCGSEKCKHSAEAIALEQSRLA

3D structure

• PDB: 5vsc Structure-activity relationship studies of G9a-like protein (GLP) inhibitors.
• Chain: B
• Resolution: 1.4 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): Y1067 Y1154
• Catalytic site (residue number reindexed from 1): Y152 Y236
• Enzyme Commision number: 2.1.1.-
  2.1.1.367: [histone H3]-lysine(9) N-methyltransferase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	ZN	B	C980 C1017 C1023 C1027	C65 C102 C108 C112
BS02	ZN	B	C974 C987 C1017 C1021	C59 C72 C102 C106
BS03	ZN	B	C974 C976 C980 C985	C59 C61 C65 C70
BS04	ZN	B	C1115 C1168 C1170 C1175	C197 C250 C252 C257
BS05	SAM	B	M1048 W1050 S1084 Y1085 R1109 F1110 N1112 H1113 Y1154 F1166 C1168	M133 W135 S169 Y170 R191 F192 N194 H195 Y236 F248 C250
BS06	9HJ	B	D1074 A1077 D1078 D1083 L1086 D1088 Y1097 C1098 R1157 F1158 I1161	D159 A162 D163 D168 L171 D173 Y179 C180 R239 F240 I243	MOAD: Kd=510nM BindingDB: Kd=510nM,IC50=295nM

Gene Ontology

Molecular Function

• GO:0002039 p53 binding
• GO:0008270 zinc ion binding
• GO:0016279 protein-lysine N-methyltransferase activity
• GO:0042054 histone methyltransferase activity

Cellular Component

• GO:0005634 nucleus

External links

• PDB: RCSB:5vsc, PDBe:5vsc, PDBj:5vsc
• PDBsum: 5vsc
• PubMed: 28662962
• UniProt: Q96KQ7|EHMT2_HUMAN Histone-lysine N-methyltransferase EHMT2 (Gene Name=EHMT2)