Structure of PDB 4rdn Chain A Binding Site BS01

Receptor Information
>4rdn Chain A (length=149) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ENLYFQHMKHGRVFIIKSYSEDDIHRSIKYNIWCSTEHGNKRLDAAYRSM
NGKGPVYLLFSVNGSGHFCGVAEMKSAVDYNTCAGVWSQDKWKGRFDVRW
IFVKDVPNSQLRHIRLENNENKPVTNSRDTQEVPLEKAKQVLKIIASYK
Ligand information
Ligand ID6MD
InChIInChI=1S/C11H15N5O4/c1-12-9-6-10(14-3-13-9)16(4-15-6)11-8(19)7(18)5(2-17)20-11/h3-5,7-8,11,17-19H,2H2,1H3,(H,12,13,14)/t5-,7-,8-,11-/m1/s1
InChIKeyVQAYFKKCNSOZKM-IOSLPCCCSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01n2c1c(ncnc1n(c2)C3OC(C(O)C3O)CO)NC
CACTVS 3.385CNc1ncnc2n(cnc12)[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.7.6CNc1c2c(ncn1)n(cn2)C3C(C(C(O3)CO)O)O
OpenEye OEToolkits 1.7.6CNc1c2c(ncn1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O
CACTVS 3.385CNc1ncnc2n(cnc12)[CH]3O[CH](CO)[CH](O)[CH]3O
FormulaC11 H15 N5 O4
NameN-methyladenosine
ChEMBLCHEMBL383144
DrugBank
ZINCZINC000004245632
PDB chain4rdn Chain A Residue 601 [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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PDB4rdn Structure of the YTH domain of human YTHDF2 in complex with an m(6)A mononucleotide reveals an aromatic cage for m(6)A recognition.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		K416 S417 Y418 D422 W432 C433 W486 W491 D528
Binding residue
(residue number reindexed from 1)		K17 S18 Y19 D23 W33 C34 W87 W92 D129
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.92,Kd=1.2uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology

View graph for
Molecular Function
External links
PDB RCSB:4rdn, PDBe:4rdn, PDBj:4rdn
PDBsum4rdn
PubMed25412658
UniProtQ9Y5A9|YTHD2_HUMAN YTH domain-containing family protein 2 (Gene Name=YTHDF2)

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