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Ligand · 3DR

3DR · 1',2'-dideoxyribofuranose-5'-phosphate

3DR, 1',2'-dideoxyribofuranose-5'-phosphate (C5 H11 O6 P, 198.1 g/mol), in the MolNFT structures on GenesisL1: bound in 4 records (4 PDB entries). Every binding site with its residues within 4.5 Å, the residues it binds most and the…

Component
3DR
Formula
C5 H11 O6 P
Class
ligand
Structures
4
PDB entries
4

Binding sites

3DR in 4 structures; the first of them:

  • 8KA3 · Arabidopsis AP endonuclease ARP complex with 22bp THF-containing DNA · 3DR D101 · binds ASN282, GLU313, TYR389, ASN392, ASP429, ASN431, ALA449, GLY450 and 7 more
  • 8KA5 · Arabidopsis AP endonuclease ARP complex with 20bp THF-containing DNA · 3DR B101 · binds ASN282, GLU313, TYR389, ASN392, ASP429, ASN431, ALA449, TYR484 and 5 more
  • 8QHR · Crystal structure of the human DNPH1 glycosyl-enzyme intermediate · 3DR A201 · binds TYR24, CYS26, GLY27, SER28, ILE29, ARG30, GLY31, GLN55 and 9 more
  • 1M06 · Structural studies of bacteriophage ALPHA3 assembly, X-ray crystallography · 3DR X5 · binds TYR135, ARG217, SER221, THR227, ARG234, SER22

Residues it binds most

ASP 7, SER 3, GLY 3, TYR 5, ASN 2, HIS 5, ARG 3, DC 2, GLU 4, LEU 4 (residue and the binding sites it lines).

Found with

  • NI · Nickel (II) ion
  • B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol
  • EDO · 1,2-ethanediol

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