Structure of PDB 1vd3 Chain A Binding Site BS01

Receptor Information

>1vd3 Chain A (length=204) Species: 35889 (Nicotiana glutinosa)

AQDFDFFYFVQQWPASYCDTRRSCCYPTTGKPDEDFSIHGLWPNYENGKW
PQNCDRESSLDESEISDLISTMEKNWPSLACPSSDGVRFWSHEWLKHGTC
SALGERAYFQAALDFRKKSNLLENLKNAEITPRNGEHYTLESIKKAIEEG
VGHSPYIECNVDTQGNHQIYQVYLCVDKTATDFIDCPIFPHGRGCGSKIE
FPPF

Ligand information

• Ligand ID: U2P
• InChI: InChI=1S/C9H13N2O9P/c12-3-4-6(14)7(20-21(16,17)18)8(19-4)11-2-1-5(13)10-9(11)15/h1-2,4,6-8,12,14H,3H2,(H,10,13,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
• InChIKey: HQIDPEYTETUCNF-XVFCMESISA-N
• SMILES:
  ACDLabs 10.04: O=C1NC(=O)N(C=C1)C2OC(C(O)C2OP(=O)(O)O)CO
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)NC1=O)C2C(C(C(O2)CO)O)OP(=O)(O)O
  CACTVS 3.341: OC[CH]1O[CH]([CH](O[P](O)(O)=O)[CH]1O)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)CO)O)OP(=O)(O)O
  CACTVS 3.341: OC[C@H]1O[C@H]([C@H](O[P](O)(O)=O)[C@@H]1O)N2C=CC(=O)NC2=O
• Formula: C9 H13 N2 O9 P
• Name: PHOSPHORIC ACID MONO-[2-(2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-4-HYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3-YL] ESTER;
  URIDINE-2'-PHOSPHATE;
  2'-URIDINEMONOPHOSPHATE
• ChEMBL: CHEMBL447360
• ZINC: ZINC000004095997
• PDB chain: 1vd3 Chain A Residue 214

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1vd3 Crystal Structure of the Nicotiana glutinosa Ribonuclease NT in Complex with Nucleotide Monophosphates
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): H39 W42 W50 H92 E93 K96 H97
• Binding residue (residue number reindexed from 1): H39 W42 W50 H92 E93 K96 H97
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): H39 W42 W50 E93 K96 H97
• Catalytic site (residue number reindexed from 1): H39 W42 W50 E93 K96 H97
• Enzyme Commision number: 3.1.27.1: Transferred entry: 4.6.1.19.

Gene Ontology

Molecular Function

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

External links

• PDB: RCSB:1vd3, PDBe:1vd3, PDBj:1vd3
• PDBsum: 1vd3
• UniProt: Q9SSV1