Structure of PDB 6qe0 Chain A Binding Site BS01

Receptor Information
>6qe0 Chain A (length=278) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSHMLSYRHSFHAGNHADVLKHTVQSLIIESLKEKDKPFLYLDTHAGAGR
YQLGRTGKYLEGIARIWQQDDLPAELEAYINVVKHFNRSGQLRYYPGSPL
IARQLLREQDSLQLTELHPSDYPLLRSEFQKDSRARVEKADGFQQLKAKL
PPVSRRGLILIDPPYEMKTDYQAVVSGIAEGYKRFATGTYALWYPVVLRQ
QIKRMIHDLEATGIRKILQIELAVLPDSDRRGMTASGMIVINPPWKLEQQ
MNNVLPWLHSKLVPAGTGHATVSWIVPE
Ligand information
Ligand IDHZ2
InChIInChI=1S/C26H36N12O9/c27-11(26(44)45)1-3-36(5-12-16(40)18(42)24(46-12)37-9-34-14-20(28)30-7-32-22(14)37)4-2-29-21-15-23(33-8-31-21)38(10-35-15)25-19(43)17(41)13(6-39)47-25/h7-13,16-19,24-25,39-43H,1-6,27H2,(H,44,45)(H2,28,30,32)(H,29,31,33)/t11-,12+,13+,16+,17+,18+,19+,24+,25+/m0/s1
InChIKeyUAGVZMOWWSWEAM-CZUOOHDMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CN(CC[C@@H](C(=O)O)N)CCNc4c5c(ncn4)n(cn5)[C@H]6[C@@H]([C@@H]([C@H](O6)CO)O)O)O)O)N
OpenEye OEToolkits 2.0.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CN(CCC(C(=O)O)N)CCNc4c5c(ncn4)n(cn5)C6C(C(C(O6)CO)O)O)O)O)N
CACTVS 3.385N[CH](CCN(CCNc1ncnc2n(cnc12)[CH]3O[CH](CO)[CH](O)[CH]3O)C[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)C(O)=O
CACTVS 3.385N[C@@H](CCN(CCNc1ncnc2n(cnc12)[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)C[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)C(O)=O
FormulaC26 H36 N12 O9
Name(2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[2-[[9-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]purin-6-yl]amino]ethyl]amino]-2-azanyl-butanoic acid
ChEMBL
DrugBank
ZINC
PDB chain6qe0 Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6qe0 Bisubstrate analogues as structural tools to investigate m6A methyltransferase active sites.
Resolution1.394 Å
Binding residue
(original residue number in PDB)
H9 D15 K18 H19 H42 A43 S100 D164 P166 P197 M235
Binding residue
(residue number reindexed from 1)
H12 D18 K21 H22 H45 A46 S98 D162 P164 P195 M233
Annotation score3
Binding affinityMOAD: Kd=25uM
PDBbind-CN: -logKd/Ki=4.60,Kd=25uM
Enzymatic activity
Enzyme Commision number 2.1.1.266: 23S rRNA (adenine(2030)-N(6))-methyltransferase.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0008649 rRNA methyltransferase activity
GO:0008988 rRNA (adenine-N6-)-methyltransferase activity
GO:0036307 23S rRNA (adenine(2030)-N(6))-methyltransferase activity
Biological Process
GO:0006364 rRNA processing
GO:0015976 carbon utilization
GO:0032259 methylation
GO:0070475 rRNA base methylation
Cellular Component
GO:0005829 cytosol

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:6qe0, PDBe:6qe0, PDBj:6qe0
PDBsum6qe0
PubMed30879411
UniProtP37634|RLMJ_ECOLI Ribosomal RNA large subunit methyltransferase J (Gene Name=rlmJ)

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