Structure of PDB 4g0p Chain A Binding Site BS01

Receptor Information

>4g0p Chain A (length=147) Species: 3702 (Arabidopsis thaliana)

SNKKMINGGTVNNWICINFSRQVQDNLARTFCQELAQMCYVSGMAFNPEP
VLPPVSARPEQVEKVLKTRYHDATSKLSQGKEIDLLIVILPDNNGSLYGD
LKRICETELGIVSQCCLTKHVFKMSKQYMANVALKINVKVGGRNTVL

Ligand information

• Ligand ID: U5P
• InChI: InChI=1S/C9H13N2O9P/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
• InChIKey: DJJCXFVJDGTHFX-XVFCMESISA-N
• SMILES:
  ACDLabs 10.04: O=C1NC(=O)N(C=C1)C2OC(C(O)C2O)COP(=O)(O)O
  CACTVS 3.341: O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O
  CACTVS 3.341: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
• Formula: C9 H13 N2 O9 P
• Name: URIDINE-5'-MONOPHOSPHATE
• ChEMBL: CHEMBL214393
• DrugBank: DB03685
• ZINC: ZINC000002123545
• PDB chain: 4g0p Chain A Residue 801

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4g0p Arabidopsis Argonaute MID domains use their nucleotide specificity loop to sort small RNAs.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): Y691 K695 Q707 C708 K728 K732
• Binding residue (residue number reindexed from 1): Y98 K102 Q114 C115 K135 K139
• Annotation score: 4
• Binding affinity: MOAD: Kd=0.98mM
  PDBbind-CN: -logKd/Ki=3.01,Kd=0.98mM

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding

External links

• PDB: RCSB:4g0p, PDBe:4g0p, PDBj:4g0p
• PDBsum: 4g0p
• PubMed: 22850669
• UniProt: O04379|AGO1_ARATH Protein argonaute 1 (Gene Name=AGO1)