Structure of PDB 1iyb Chain B Binding Site BS01

Receptor Information

>1iyb Chain B (length=208) Species: 35889 (Nicotiana glutinosa)

YVEFAQDFDFFYFVQQWPGSYCDTKQSCCYPKTGKPASDFGIHGLWPNNN
DGSYPSNCDSNSPYDQSQVSDLISRMQQNWPTLACPSGTGSAFWSHEWEK
HGTCAENVFDQHGYFKKALDLKNQINLLEILQGAGIHPDGGFYSLNSIKN
AIRSAIGYAPGIECNVDESGNSQLYQIYICVDGSGSNLIECPIFPRGKCG
SSIEFPTF

Ligand information

• Ligand ID: 5GP
• InChI: InChI=1S/C10H14N5O8P/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(23-9)1-22-24(19,20)21/h2-3,5-6,9,16-17H,1H2,(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
• InChIKey: RQFCJASXJCIDSX-UUOKFMHZSA-N
• SMILES:
  CACTVS 3.341: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
  CACTVS 3.341: NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=C1c2ncn(c2N=C(N)N1)C3OC(C(O)C3O)COP(=O)(O)O
  OpenEye OEToolkits 1.5.0: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)O)O)O)N=C(NC2=O)N
  OpenEye OEToolkits 1.5.0: c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N=C(NC2=O)N
• Formula: C10 H14 N5 O8 P
• Name: GUANOSINE-5'-MONOPHOSPHATE
• ChEMBL: CHEMBL283807
• DrugBank: DB01972
• ZINC: ZINC000002159505
• PDB chain: 1iyb Chain B Residue 1296

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1iyb Guanine binding site of the Nicotiana glutinosa ribonuclease NW revealed by X-ray crystallography
• Resolution: 1.5 Å
• Binding residue (original residue number in PDB): Q12 Y17 H39 W42 T78 L79 A80 F89 H92 E93 K96 H97
• Binding residue (residue number reindexed from 1): Q16 Y21 H43 W46 T82 L83 A84 F93 H96 E97 K100 H101
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): H39 W42 Y50 E93 K96 H97
• Catalytic site (residue number reindexed from 1): H43 W46 Y54 E97 K100 H101
• Enzyme Commision number: 3.1.-.-

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0033897 ribonuclease T2 activity

External links

• PDB: RCSB:1iyb, PDBe:1iyb, PDBj:1iyb
• PDBsum: 1iyb
• PubMed: 12484757
• UniProt: Q7XZV5