Structure of PDB 6l5m Chain E Binding Site BS01

Receptor Information

>6l5m Chain E (length=366) Species: 9606 (Homo sapiens)

FSNFPISEETIKLLKGRGVTFLFPIQAKTFHHVYSGKDLIAQARTGTGKT
FSFAIPLIEKLHGELQDRKRGRAPQVLVLAPTRELANQVSKDFSDITKKL
SVACFYGGTPYGGQFERMRNGIDILVGTPGRIKDHIQNGKLDLTKLKHVV
LDEVDQMLDMGFADQVEEILSVAYKKDSEDNPQTLLFSATCPHWVFNVAK
KYMKSTYEQVDLTVEHLAIKCHWTQRAAVIGDVIRVYSGHQGRTIIFCET
KKEAQELSQNSAIKQDAQSLHGDIPQKQREITLKGFRNGSFGVLVATNVA
ARGLDIPEVDLVIQSSPPKDVESYIHRSGRTGRAGRTGVCICFYQHKEEY
QLVQVEQKAGIKFKRI

Ligand information

• Ligand ID: AMP
• InChI: InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: UDMBCSSLTHHNCD-KQYNXXCUSA-N
• SMILES:
  CACTVS 3.370: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
  CACTVS 3.370: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.7.6: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
  ACDLabs 12.01: O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.7.6: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
• Formula: C10 H14 N5 O7 P
• Name: ADENOSINE MONOPHOSPHATE
• ChEMBL: CHEMBL752
• DrugBank: DB00131
• ZINC: ZINC000003860156
• PDB chain: 6l5m Chain E Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6l5m Structural Basis of Human Helicase DDX21 in RNA Binding, Unwinding, and Antiviral Signal Activation.
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): V206 F210 Q213 G233 G235 K236 T237
• Binding residue (residue number reindexed from 1): V19 F23 Q26 G46 G48 K49 T50
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 3.6.4.13: RNA helicase.

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003724 RNA helicase activity
• GO:0005524 ATP binding

External links

• PDB: RCSB:6l5m, PDBe:6l5m, PDBj:6l5m
• PDBsum: 6l5m
• PubMed: 32714761
• UniProt: Q9NR30|DDX21_HUMAN Nucleolar RNA helicase 2 (Gene Name=DDX21)