Structure of PDB 6qdx Chain A Binding Site BS01

Receptor Information
>6qdx Chain A (length=273) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SYRHSFHAGNHADVLKHTVQSLIIESLKEKDKPFLYLDTHAGAGRYQLGR
TGKYLEGIARIWQQDDLPAELEAYINVVKHFNRSGQLRYYPGSPLIARQL
LREQDSLQLTELHPSDYPLLRSEFQKDSRARVEKADGFQQLKAKLPPVSR
RGLILIDPPYEMKTDYQAVVSGIAEGYKRFATGTYALWYPVVLRQQIKRM
IHDLEATGIRKILQIELAVLPDSDRRGMTASGMIVINPPWKLEQQMNNVL
PWLHSKLVPAGTGHATVSWIVPE
Ligand information
Ligand IDHY8
InChIInChI=1S/C27H38N12O9/c28-12(27(45)46)2-5-37(6-13-17(41)19(43)25(47-13)38-10-35-15-21(29)31-8-33-23(15)38)4-1-3-30-22-16-24(34-9-32-22)39(11-36-16)26-20(44)18(42)14(7-40)48-26/h8-14,17-20,25-26,40-44H,1-7,28H2,(H,45,46)(H2,29,31,33)(H,30,32,34)/t12-,13-,14-,17+,18+,19+,20+,25+,26-/m0/s1
InChIKeyBNMNWGQODJWABC-JIDNCIPASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@@H](O3)CN(CCCNc4c5c(ncn4)n(cn5)[C@@H]6[C@@H]([C@@H]([C@@H](O6)CO)O)O)CC[C@@H](C(=O)O)N)O)O)N
CACTVS 3.385N[C@@H](CCN(CCCNc1ncnc2n(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
OpenEye OEToolkits 2.0.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CN(CCCNc4c5c(ncn4)n(cn5)C6C(C(C(O6)CO)O)O)CCC(C(=O)O)N)O)O)N
CACTVS 3.385N[CH](CCN(CCCNc1ncnc2n(cnc12)[CH]3O[CH](CO)[CH](O)[CH]3O)C[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)C(O)=O
FormulaC27 H38 N12 O9
Name(2~{S})-4-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[3-[[9-[(2~{S},3~{R},4~{S},5~{S})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]purin-6-yl]amino]propyl]amino]-2-azanyl-butanoic acid
ChEMBL
DrugBank
ZINC
PDB chain6qdx 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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PDB6qdx Bisubstrate analogues as structural tools to investigate m6A methyltransferase active sites.
Resolution2.1 Å
Binding residue
(original residue number in PDB)
H9 D15 K18 H42 A43 G44 S100 D164 P166 E168 M235
Binding residue
(residue number reindexed from 1)
H7 D13 K16 H40 A41 G42 S93 D157 P159 E161 M228
Annotation score3
Binding affinityMOAD: Kd=30uM
PDBbind-CN: -logKd/Ki=4.52,Kd=30uM
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:6qdx, PDBe:6qdx, PDBj:6qdx
PDBsum6qdx
PubMed30879411
UniProtP37634|RLMJ_ECOLI Ribosomal RNA large subunit methyltransferase J (Gene Name=rlmJ)

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