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Ligand · VDF

VDF · 2-O-phosphono-beta-L-arabinopyranose

VDF, 2-O-phosphono-beta-L-arabinopyranose (C5 H11 O8 P, 230.1 g/mol), in the MolNFT structures on GenesisL1: bound in 3 records (3 PDB entries). Every binding site with its residues within 4.5 Å, the residues it binds most and the ligands…

Component
VDF
Formula
C5 H11 O8 P
Class
sugar
Structures
3
PDB entries
3

Binding sites

VDF in 3 structures; the first of them:

  • 8CH1 · PBP AccA from A. vitis S4 in complex with Agrocinopine A · VDF A601 · binds ILE52, SER53, ASN54, TYR145, TRP178, ASN284, TYR375, TYR376 and 5 more
  • 8CH2 · PBP AccA from A. vitis S4 in complex with L-arabinose-2-phosphate (A2P) · VDF A602 · binds ILE52, SER53, ASN54, TYR145, TRP178, ASN284, TYR375, TYR376 and 5 more
  • 8CKE · PBP AccA from A.tumefaciens C58 in complex with agrocinopine A in space group I222 · VDF A601 · binds ILE52, SER53, ASN54, TYR145, TRP178, TYR375, TYR376, TRP418 and 5 more

Residues it binds most

TYR 3, ASN 3, SER 3, TRP 3, GLU 3, GLY 3, ILE 3 (residue and the binding sites it lines).

Found with

  • LAO · 2-O-phosphono-alpha-L-arabinopyranose
  • EDO · 1,2-ethanediol
  • FRU · beta-D-fructofuranose
  • GLC · alpha-D-glucopyranose
  • ACT · Acetate ion
  • PEG · Di(hydroxyethyl)ether

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