Structure of PDB 5vsd Chain B

Receptor sequence

>5vsdB (length=258) Species: 9606 (Homo sapiens)

VERIVSRDIARGYERIPIPCVNAVDSEPCPSNYKYVSQNCVTSPMNIDRN
ITHLQYCVCIDDCSSSNCMCGQLSMRCWYDKDGRLLPEFNMAEPPLIFEC
NHACSCWRNCRNRVVQNGLRARLQLYRTRDMGWGVRSLQDIPPGTFVCEY
VGELISDSEADVREEDSYLFDLDGEVYCIDARFYGNVSRFINHHCEPNLV
PVRVFMAHQDLRFPRIAFFSTRLIEAGEQLGFDYGERFWDIKGKLFSCRC
GSPKCRHS

3D structure

• PDB: 5vsd Structure-activity relationship studies of G9a-like protein (GLP) inhibitors.
• Chain: B
• Resolution: 1.85 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): Y1155 Y1242
• Catalytic site (residue number reindexed from 1): Y150 Y234
• 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	SAM	B	M1136 G1137 W1138 S1172 Y1173 R1197 F1198 N1200 H1201 Y1242 F1246 C1256 R1257	M131 G132 W133 S167 Y168 R189 F190 N192 H193 Y234 F238 C248 R249
BS02	ZN	B	C1062 C1075 C1105 C1109	C57 C70 C100 C104
BS03	ZN	B	C1068 C1105 C1111 C1115	C63 C100 C106 C110
BS04	ZN	B	C1062 C1064 C1068 C1073	C57 C59 C63 C68
BS05	ZN	B	C1203 C1256 C1258 C1263	C195 C248 C250 C255
BS06	9HJ	B	A1165 D1171 L1174 D1176 R1245 F1246 I1249 K1250	A160 D166 L169 D171 R237 F238 I241 K242	MOAD: Kd=57nM BindingDB: Kd=57nM,IC50=5.0nM

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:5vsd, PDBe:5vsd, PDBj:5vsd
• PDBsum: 5vsd
• PubMed: 28662962
• UniProt: Q9H9B1|EHMT1_HUMAN Histone-lysine N-methyltransferase EHMT1 (Gene Name=EHMT1)