Structure of PDB 8jnr Chain D Binding Site BS02

Receptor Information
>8jnr Chain D (length=210) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RVIDREGVYEISLSPTGVSRVCLYPGFVDVKEADWILEQLSQDVPWKQRT
GIREDITYQQPRLTAWYGELPYTYSRITMEPNPHWHPVLRTLKNRIEENT
GHTFNSLLCNLYRNEKDSVCWHSDDEPSLGRSPIIASLSFGATRTFEMRK
KPPPEENGDYTYVERVKIPLDHGTLLIMEGATQADWQHRVPKEYHSREPR
VNLTFRTVYP
Ligand information
Ligand IDME6
InChIInChI=1S/C10H16N3O7P/c1-12-8(11)2-3-13(10(12)15)9-4-6(14)7(20-9)5-19-21(16,17)18/h2-3,6-7,9,11,14H,4-5H2,1H3,(H2,16,17,18)/p+1/t6-,7+,9+/m0/s1
InChIKeySXDBYGVVLMSJDZ-LKEWCRSYSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.6.1C[N+]1=C(C=CN(C1=O)C2CC(C(O2)COP(=O)(O)O)O)N
CACTVS 3.352C[N+]1=C(N)C=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C1=O
OpenEye OEToolkits 1.6.1C[N+]1=C(C=CN(C1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O)N
CACTVS 3.352C[N+]1=C(N)C=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C1=O
FormulaC10 H17 N3 O7 P
Name[(2R,3S,5R)-5-(4-azanyl-3-methyl-2-oxo-pyrimidin-3-ium-1-yl)-3-hydroxy-oxolan-2-yl]methyl dihydrogen phosphate
ChEMBL
DrugBank
ZINCZINC000103549611
PDB chain8jnr Chain D Residue 1003 [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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PDB8jnr The Molecular Basis of Human ALKBH3 Mediated RNA N1-methyladenosine (m1A) Demethylation
Resolution3.66 Å
Binding residue
(original residue number in PDB)		R131 Y143 S144 C189 H191
Binding residue
(residue number reindexed from 1)		R62 Y74 S75 C120 H122
Annotation score1
Enzymatic activity
Enzyme Commision number 1.14.11.33: DNA oxidative demethylase.
1.14.11.54: mRNA N(1)-methyladenine demethylase.
Gene Ontology
Molecular Function
GO:0051213 dioxygenase activity
Biological Process
GO:0006281 DNA repair
GO:0006307 DNA alkylation repair

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:8jnr, PDBe:8jnr, PDBj:8jnr
PDBsum8jnr
PubMed38158383
UniProtQ96Q83|ALKB3_HUMAN Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3 (Gene Name=ALKBH3)

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