Structure of PDB 3fpd Chain A

Receptor sequence

>3fpdA (length=261) Species: 9606 (Homo sapiens)

VERIVSRDIARGYERIPIPCVNAVDSEPCPSNYKYVSQNCVTSPMNIDRN
ITHLQYCVCIDDCSSSNCMCGQLSMRCWYDKDGRLLPEFNMAEPPLIFEC
NHACSCWRNCRNRVVQNGLRARLQLYRTRDMGWGVRSLQDIPPGTFVCEY
VGELISDSEADVREEDSYLFDLDNKDGEVYCIDARFYGNVSRFINHHCEP
NLVPVRVFMAHQDLRFPRIAFFSTRLIEAGEQLGFDYGERFWDIKGKLFS
CRCGSPKCRHS

3D structure

• PDB: 3fpd Structural basis for G9a-like protein lysine methyltransferase inhibition by BIX-01294.
• Chain: A
• Resolution: 2.4 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): Y1124 Y1211
• Catalytic site (residue number reindexed from 1): Y150 Y237
• 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	SAH	A	M1105 W1107 S1141 Y1142 R1166 N1169 H1170 Y1211 R1226	M131 W133 S167 Y168 R192 N195 H196 Y237 R252	BindingDB: IC50=230nM
BS02	Q4A	A	D1131 A1134 D1135 R1137 D1140 L1143 D1145 R1214 F1215	D157 A160 D161 R163 D166 L169 D171 R240 F241	MOAD: ic50=0.7uM PDBbind-CN: -logKd/Ki=6.15,IC50=0.7uM BindingDB: IC50=700nM
BS03	ZN	A	C1031 C1044 C1074 C1078	C57 C70 C100 C104
BS04	ZN	A	C1037 C1074 C1080 C1084	C63 C100 C106 C110
BS05	ZN	A	C1031 C1033 C1037 C1042	C57 C59 C63 C68
BS06	ZN	A	C1227 C1232	C253 C258

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:3fpd, PDBe:3fpd, PDBj:3fpd
• PDBsum: 3fpd
• PubMed: 19219047
• UniProt: Q9H9B1|EHMT1_HUMAN Histone-lysine N-methyltransferase EHMT1 (Gene Name=EHMT1)