Structure of PDB 3k5k Chain A

Receptor sequence

>3k5kA (length=272) Species: 9606 (Homo sapiens)

RTEKIICRDVARGYENVPIPCVNGVDGEPCPEDYKYISENCETSTMNIDR
NITHLQHCTCVDDCSSSNCLCGQLSIRCWYDKDGRLLQEFNKIEPPLIFE
CNQACSCWRNCKNRVVQSGIKVRLQLYRTAKMGWGVRALQTIPQGTFICE
YVGELISDAEADVREDDSYLFDLDNKEVYCIDARYYGNISRFINHLCDPN
IIPVRVFMLHQDLRFPRIAFFSSRDIRTGEELGFDYGDRFWDIKSKYFTC
QCGSEKCKHSAEAIALEQSRLA

3D structure

• PDB: 3k5k Discovery of a 2,4-diamino-7-aminoalkoxyquinazoline as a potent and selective inhibitor of histone lysine methyltransferase G9a.
• Chain: A
• Resolution: 1.7 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): Y1067 Y1154
• Catalytic site (residue number reindexed from 1): Y151 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	A	C974 C987 C1017 C1021	C58 C71 C101 C105
BS02	ZN	A	C980 C1017 C1023 C1027	C64 C101 C107 C111
BS03	ZN	A	C974 C976 C980 C985	C58 C60 C64 C69
BS04	ZN	A	C1115 C1168 C1170 C1175	C197 C250 C252 C257
BS05	SAH	A	M1048 W1050 Y1085 R1109 F1110 N1112 H1113 Y1154 F1158 F1166 C1168 Q1169	M132 W134 Y169 R191 F192 N194 H195 Y236 F240 F248 C250 Q251	BindingDB: Ki=570nM,IC50=2000nM
BS06	DXQ	A	D1074 A1077 D1078 D1083 L1086 D1088 F1152 Y1154 R1157 F1158	D158 A161 D162 D167 L170 D172 F234 Y236 R239 F240	MOAD: Kd=23nM PDBbind-CN: -logKd/Ki=7.64,Kd=23nM BindingDB: IC50=15nM,Ki=2.6nM,Kd=23nM

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:3k5k, PDBe:3k5k, PDBj:3k5k
• PDBsum: 3k5k
• PubMed: 19891491
• UniProt: Q96KQ7|EHMT2_HUMAN Histone-lysine N-methyltransferase EHMT2 (Gene Name=EHMT2)