ChemComp-RP3: 3-deoxy-5-O-phosphono-beta-D-ribofuranose

Basic information

• Entry: Database: PDB chemical components / ID: RP3
• Name: Name: 3-deoxy-5-O-phosphono-beta-D-ribofuranose; Synonyms: 3'-deoxy-D-ribofuranose-5'-phosphate; 3-deoxy-5-O-phosphono-beta-D-ribose; 3-deoxy-5-O-phosphono-D-ribose

Chemical information

Composition

Formula: C₅H₁₁O₇P / Number of atoms: 24 / Formula weight: 214.11 / Formal charge: 0

Others

5cx8

Type: D-saccharide, beta linking / PDB classification: ATOMS / Three letter code: RP3 / Ideal coordinates details: Corina / Model coordinates PDB-ID: 5CX8

History

Create component	Jul 28, 2015
Initial release	Oct 21, 2015
Other modification	Jul 3, 2020
Modify name	Jul 17, 2020
Modify synonyms	Jul 17, 2020
Modify internal type	Jul 17, 2020
Modify linking type	Jul 17, 2020
Modify atom id	Jul 17, 2020
Modify component atom id	Jul 17, 2020
Modify leaving atom flag	Jul 17, 2020

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

Details

SMILES

• ACDLabs 12.01: OP(O)(=O)OCC1OC(C(C1)O)O
• CACTVS 3.385: O[CH]1C[CH](CO[P](O)(O)=O)O[CH]1O
• OpenEye OEToolkits 1.9.2: C1C(OC(C1O)O)COP(=O)(O)O

SMILES CANONICAL

• CACTVS 3.385: O[C@@H]1C[C@@H](CO[P](O)(O)=O)O[C@H]1O
• OpenEye OEToolkits 1.9.2: C1[C@H](O[C@H]([C@@H]1O)O)COP(=O)(O)O

InChI

• InChI 1.03: InChI=1S/C5H11O7P/c6-4-1-3(12-5(4)7)2-11-13(8,9)10/h3-7H,1-2H2,(H2,8,9,10)/t3-,4+,5+/m0/s1

InChIKey

• InChI 1.03: OOLHLHJSMUTTHE-VPENINKCSA-N

SYSTEMATIC NAME

• ACDLabs 12.01: 3-deoxy-5-O-phosphono-beta-D-erythro-pentofuranose
• OpenEye OEToolkits 1.9.2: [(2S,4R,5R)-4,5-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate

IUPAC CARBOHYDRATE SYMBOL

• PDB-CARE 1.0: b-D-3-deoxy-Ribf5PO3

PDB entries

Showing all 1 items

PDB-5cx8:
Structure of RagB, a major immunodominant virulence factor of Porphyromonas gingivalis.