ChemComp-VDF: 2-O-phosphono-beta-L-arabinopyranose

Basic information

• Entry: Database: PDB chemical components / ID: VDF
• Name: Name: 2-O-phosphono-beta-L-arabinopyranose; Synonyms: 2-O-phosphono-beta-L-arabinose; 2-O-phosphono-L-arabinose; 2-O-phosphono-arabinose; [(2S,3R,4S,5S)-2,4,5-tris(oxidanyl)oxan-3-yl] dihydrogen phosphate

Chemical information

Composition

Formula: C₅H₁₁O₈P / Number of atoms: 25 / Formula weight: 230.11 / Formal charge: 0

Others

8ch2

ARB

Type: L-saccharide, beta linking / PDB classification: ATOMS / Three letter code: VDF / Ideal coordinates details: Corina / Model coordinates PDB-ID: 8CH2 / Parent comp.: ARB

History

Create component	Mar 1, 2023
Modify internal type	May 17, 2023
Initial release	Jan 24, 2024

• External links: UniChem / ChemSpider / Wikipedia search / Google search

Details

SMILES

• CACTVS 3.385: O[CH]1CO[CH](O)[CH](O[P](O)(O)=O)[CH]1O
• OpenEye OEToolkits 2.0.7: C1C(C(C(C(O1)O)OP(=O)(O)O)O)O

SMILES CANONICAL

• CACTVS 3.385: O[C@H]1CO[C@H](O)[C@H](O[P](O)(O)=O)[C@H]1O
• OpenEye OEToolkits 2.0.7: C1[C@@H]([C@@H]([C@H]([C@H](O1)O)OP(=O)(O)O)O)O

InChI

• InChI 1.06: InChI=1S/C5H11O8P/c6-2-1-12-5(8)4(3(2)7)13-14(9,10)11/h2-8H,1H2,(H2,9,10,11)/t2-,3-,4+,5-/m0/s1

InChIKey

• InChI 1.06: QIAIUTJEZJIPSH-KLVWXMOXSA-N

PDB entries

Showing all 3 items

PDB-8ch1:
PBP AccA from A. vitis S4 in complex with Agrocinopine A

PDB-8ch2:
PBP AccA from A. vitis S4 in complex with L-arabinose-2-phosphate (A2P)

PDB-8cke:
PBP AccA from A.tumefaciens C58 in complex with agrocinopine A in space group I222