Structure of PDB 6kda Chain A Binding Site BS03
Receptor Information
>6kda Chain A (length=284) Species:
9606
(Homo sapiens) [
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MRRRPIRVLSLFDGIATGYLVLKELGIKVGKYVASEVCEESIAVGTVKHE
GNIKYVNDVRNITKKNIEEWGPFDLVIGGSPCNDLSNVNPARKGLYEGTG
RLFFEFYHLLNYSRPKEGDDRPFFWMFENVVAMKVGDKRDISRFLECNPV
MIDAIKVSAAHRARYFWGNLPGMNRPVIASKNDKLELQDCLEYNRIAKLK
KVQTITTKSNSIKQGKNQLFPVVMNGKEDVLWCTELERIFGFPVHYTDVS
NMGRGARQKLLGRSWSVPVIRHLFAPLKDYFACE
Ligand information
Ligand ID
SAH
InChI
InChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
InChIKey
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
SMILES
Software
SMILES
CACTVS 3.341
N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O
OpenEye OEToolkits 1.5.0
c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
CACTVS 3.341
N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
ACDLabs 10.04
O=C(O)C(N)CCSCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0
c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CSCC[C@@H](C(=O)O)N)O)O)N
Formula
C14 H20 N6 O5 S
Name
S-ADENOSYL-L-HOMOCYSTEINE
ChEMBL
CHEMBL418052
DrugBank
DB01752
ZINC
ZINC000004228232
PDB chain
6kda Chain A Residue 901 [
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Receptor-Ligand Complex Structure
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PDB
6kda
Structural insights into CpG-specific DNA methylation by human DNA methyltransferase 3B.
Resolution
2.909 Å
Binding residue
(original residue number in PDB)
F581 D582 G583 T586 S604 E605 V606 D627 V628 R832 S833 W834
Binding residue
(residue number reindexed from 1)
F12 D13 G14 T17 S35 E36 V37 D58 V59 R263 S264 W265
Annotation score
5
Binding affinity
BindingDB: IC50=300nM
Enzymatic activity
Enzyme Commision number
2.1.1.37
: DNA (cytosine-5-)-methyltransferase.
Gene Ontology
Molecular Function
GO:0008168
methyltransferase activity
View graph for
Molecular Function
External links
PDB
RCSB:6kda
,
PDBe:6kda
,
PDBj:6kda
PDBsum
6kda
PubMed
32083663
UniProt
Q9UBC3
|DNM3B_HUMAN DNA (cytosine-5)-methyltransferase 3B (Gene Name=DNMT3B)
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