Chemical Components in the PDB

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  • Z6J (Stereoisomer)
  • BXY (Stereoisomer)
  • BXX (Stereoisomer)
  • 32O (Stereoisomer)
  • AHR (Stereoisomer)
  • FUB (Stereoisomer)
  • XYZ (Stereoisomer)
  • RIB (Stereoisomer)

BDR : Summary

Code

BDR

One-letter code

X

Molecule name

beta-D-ribofuranose

Synonyms

beta-D-ribose
D-ribose
ribose
BETA-D-RIBOFURANOSYL

Systematic names

ProgramVersionName
ACDLabs 10.04 beta-D-ribofuranose
OpenEye OEToolkits 1.5.0 (2R,3R,4S,5R)-5-(hydroxymethyl)oxolane-2,3,4-triol

Formula

C5 H10 O5

Formal charge

0

Molecular weight

150.13 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 OC1C(OC(O)C1O)CO
SMILES CACTVS 3.341 OC[CH]1O[CH](O)[CH](O)[CH]1O
SMILES OpenEye OEToolkits 1.5.0 C(C1C(C(C(O1)O)O)O)O
Canonical SMILES CACTVS 3.341 OC[C@H]1O[C@@H](O)[C@H](O)[C@@H]1O
Canonical SMILES OpenEye OEToolkits 1.5.0 C([C@@H]1[C@H]([C@H]([C@@H](O1)O)O)O)O

IUPAC InChI

InChI=1S/C5H10O5/c6-1-2-3(7)4(8)5(9)10-2/h2-9H,1H2/t2-,3-,4-,5-/m1/s1

IUPAC InChI key

HMFHBZSHGGEWLO-TXICZTDVSA-N

Is part of

ON0 , M5Z , RPO
BDR

wwPDB Information

Atom count

20 (10 without Hydrogen)

Polymer type

Saccharide

Type description

D-saccharide, beta linking

Type code

ATOMS

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2020-07-17

Status

Released

Obsoleted

Not Assigned



BDR : Atoms of Molecule

Total Number of Atoms: 20
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C4 C C4 R N N 0 0.289 -0.315 0.986
2 O4 O O N N N 0 -1.069 -0.337 0.516
3 C1 C C1 R N N 0 -1.015 -0.388 -0.925
4 O1 O O1 N N Y 0 -2.244 0.072 -1.491
5 C2 C C2 R N N 0 0.147 0.573 -1.279
6 O2 O O2 N N N 0 0.718 0.238 -2.545
7 C3 C C3 S N N 0 1.153 0.302 -0.13
8 O3 O O3 N N N 0 2.163 -0.615 -0.555
9 C5 C C5 N N N 0 0.387 0.536 2.252
10 O5 O O5 N N N 0 -0.422 -0.039 3.279
11 H4 H H4 N N N 0 0.624 -1.331 1.195
12 H1 H H1 N N N 0 -0.793 -1.4 -1.265
13 HO1 H HO1 N N Y 0 -2.937 -0.525 -1.18
14 H2 H H2 N N N 0 -0.188 1.609 -1.267
15 HO2 H HO2 N N Y 0 0.017 0.339 -3.203
16 H3 H H3 N N N 0 1.604 1.234 0.209
17 HO3 H HO3 N N Y 0 2.629 -0.196 -1.291
18 H51 H H51 N N N 0 0.039 1.547 2.039
19 H52 H H52 N N N 0 1.425 0.573 2.586
20 HO5 H H5 N N Y 0 -0.331 0.526 4.057



BDR : Chemical Bonds

Total Number of Bonds: 20
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C4 O4 C O sing 1.44 N N
2 C4 C3 C C sing 1.54 N N
3 C4 C5 C C sing 1.53 N N
4 C4 H4 C H sing 1.09 N N
5 O4 C1 O C sing 1.44 N N
6 C1 O1 C O sing 1.43 N N
7 C1 C2 C C sing 1.55 N N
8 C1 H1 C H sing 1.09 N N
9 O1 HO1 O H sing 0.97 N N
10 C2 O2 C O sing 1.43 N N
11 C2 C3 C C sing 1.55 N N
12 C2 H2 C H sing 1.09 N N
13 O2 HO2 O H sing 0.97 N N
14 C3 O3 C O sing 1.43 N N
15 C3 H3 C H sing 1.09 N N
16 O3 HO3 O H sing 0.97 N N
17 C5 O5 C O sing 1.43 N N
18 C5 H51 C H sing 1.09 N N
19 C5 H52 C H sing 1.09 N N
20 O5 HO5 O H sing 0.97 N N



BDR : Used in PDB Entries

Total Number of PDB Entries: 7
Ligand Code PDB Entry ID Type Total Distinct
BDR 1nem Open in New Window s 1 1
BDR 1pbr Open in New Window s 1 1
BDR 1qxb Open in New Window Bound ligand 2 1
BDR 3ksm Open in New Window Bound ligand 2 1
BDR 4h55 Open in New Window Bound ligand 1 1
BDR 5tsq Open in New Window Bound ligand 1 1
BDR 6o0q Open in New Window Bound ligand 2 1
BDR 4b3m Open in New Window Sub-component 1 1
BDR 4b3r Open in New Window Sub-component 1 1
BDR 4b3s Open in New Window Sub-component 1 1