Structure of PDB 2pvc Chain B Binding Site BS03

Receptor Information
>2pvc Chain B (length=347) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GRDLIAYEVKANQRNIEDICICCGSLQVHTQHPLFEGGICAPCKDKFLDA
LFLYDDDGYQSYCSICCSGETLLICGNPDCTRCYCFECVDSLVGPGTSGK
VHAMSNWVCYLCLPSSRSGLLQRRRKWRSQLKAFYDRESENPLEMFETVP
VWRRQPVRVLSLFEDIKKELTSLGFLESGSDPGQLKHVVDVTDTVRKDVE
EWGPFDLVYGATPPLGHTCDRPPSWYLFQFHRLLQYARPKPGSPGPFFWM
FVDNLVLNKEDLDVASRFLEMEPVTIPDVHGGSLQNAVRVWSNIPAIRSR
HWALVSEEELSLLAQNKQSSKLAAKWPTKLVKNCFLPLREYFKYFST
Ligand information
Ligand IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain2pvc Chain B Residue 606 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2pvc DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA.
Resolution3.69 Å
Binding residue
(original residue number in PDB)		C108 C113 C142 C145
Binding residue
(residue number reindexed from 1)		C75 C80 C109 C112
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0005515 protein binding
GO:0008047 enzyme activator activity
GO:0019899 enzyme binding
GO:0046872 metal ion binding
GO:0051718 DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates
Biological Process
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0001890 placenta development
GO:0006346 DNA methylation-dependent heterochromatin formation
GO:0007141 male meiosis I
GO:0007283 spermatogenesis
GO:0010468 regulation of gene expression
GO:0010558 negative regulation of macromolecule biosynthetic process
GO:0030154 cell differentiation
GO:0032259 methylation
GO:0044726 epigenetic programing of female pronucleus
GO:0045814 negative regulation of gene expression, epigenetic
GO:0048863 stem cell differentiation
GO:0060718 chorionic trophoblast cell differentiation
GO:0071514 genomic imprinting
GO:0090310 negative regulation of DNA methylation-dependent heterochromatin formation
GO:0141005 retrotransposon silencing by heterochromatin formation
GO:0141068 autosome genomic imprinting
GO:0141196 retrotransposon silencing by piRNA-directed DNA methylation
Cellular Component
GO:0000792 heterochromatin
GO:0000794 condensed nuclear chromosome
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0035098 ESC/E(Z) complex
GO:1902494 catalytic complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2pvc, PDBe:2pvc, PDBj:2pvc
PDBsum2pvc
PubMed17687327
UniProtQ9UJW3|DNM3L_HUMAN DNA (cytosine-5)-methyltransferase 3-like (Gene Name=DNMT3L)

[Back to BioLiP]