Structure of PDB 5vse Chain A

Receptor sequence

>5vseA (length=269) Species: 9606 (Homo sapiens)

EKIICRDVARGYENVPIPCVNGVDGEPCPEDYKYISENCETSTMNIDRNI
THLQHCTCVDDCSSSNCLCGQLSIRCWYDKDGRLLQEFNKIEPPLIFECN
QACSCWRNCKNRVVQSGIKVRLQLYRTAKMGWGVRALQTIPQGTFICEYV
GELISDAEADVREDDSYLFDLDNEVYCIDARYYGNISRFINHLCDPNIIP
VRVFMLHQDLRFPRIAFFSSRDIRTGEELGFDYGDRFWDIKSKYFTCQCG
SEKCKHSAEAIALEQSRLA

3D structure

• PDB: 5vse Structure-activity relationship studies of G9a-like protein (GLP) inhibitors.
• Chain: A
• Resolution: 1.6 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): Y1067 Y1154
• Catalytic site (residue number reindexed from 1): Y149 Y233
• 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	A	C980 C1017 C1023 C1027	C62 C99 C105 C109
BS02	ZN	A	C974 C987 C1017 C1021	C56 C69 C99 C103
BS03	ZN	A	C974 C976 C980 C985	C56 C58 C62 C67
BS04	ZN	A	C1115 C1168 C1170 C1175	C194 C247 C249 C254
BS05	SAM	A	M1048 W1050 S1084 Y1085 R1109 F1110 N1112 H1113 Y1154 F1166 C1168 Q1169	M130 W132 S166 Y167 R188 F189 N191 H192 Y233 F245 C247 Q248
BS06	9HG	A	D1074 A1077 D1078 R1080 D1083 L1086 D1088 C1098 R1157 F1158 I1161	D156 A159 D160 R162 D165 L168 D170 C177 R236 F237 I240	MOAD: Kd=1070nM PDBbind-CN: -logKd/Ki=5.97,Kd=1070nM BindingDB: IC50=259nM,Kd=1070nM

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