Structure of PDB 6kdt Chain A Binding Site BS01

Receptor Information
>6kdt Chain A (length=272) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMRRRPIRVLSLFDGIATGYLVLKELGIKVGKYVASEVCEESIAVGTVKH
EGNIKYVNDVRNITKKNIEEWGPFDLVIGGSPCNDLSNVNPARKGLYEGT
GRLFFEFYHLLNYSRPKEGDDRPFFWMFENVVAMKVGDKRDISRFLECNP
VMIDAIKVSAAHRARYFWGNLPGMNRPVIASKNDKLELQDCLEYNRIAKL
KKVRTQLFPVVMNGKEDVLWCTELERIFGFPVHYTDVSNMGRGARQKLLG
RSWSVPVIRHLFAPLKDYFACE
Ligand information
Ligand IDSAH
InChIInChI=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
InChIKeyZJUKTBDSGOFHSH-WFMPWKQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
CACTVS 3.341N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
ACDLabs 10.04O=C(O)C(N)CCSCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CSCC[C@@H](C(=O)O)N)O)O)N
FormulaC14 H20 N6 O5 S
NameS-ADENOSYL-L-HOMOCYSTEINE
ChEMBLCHEMBL418052
DrugBankDB01752
ZINCZINC000004228232
PDB chain6kdt Chain A Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6kdt Structural insights into CpG-specific DNA methylation by human DNA methyltransferase 3B.
Resolution2.87 Å
Binding residue
(original residue number in PDB)		F581 D582 T586 E605 V606 D627 V628 G648 P650 R832 W834
Binding residue
(residue number reindexed from 1)		F13 D14 T18 E37 V38 D59 V60 G80 P82 R251 W253
Annotation score5
Binding affinityBindingDB: 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:6kdt, PDBe:6kdt, PDBj:6kdt
PDBsum6kdt
PubMed32083663
UniProtQ9UBC3|DNM3B_HUMAN DNA (cytosine-5)-methyltransferase 3B (Gene Name=DNMT3B)

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