Chemical Components in the PDB

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

RIB : Summary

Code

RIB

One-letter code

X

Molecule name

alpha-D-ribofuranose

Synonyms

alpha-D-ribose
D-ribose
ribose

Systematic names

ProgramVersionName
ACDLabs 10.04 alpha-D-ribofuranose
OpenEye OEToolkits 1.5.0 (2S,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-AIHAYLRMSA-N
RIB

wwPDB Information

Atom count

20 (10 without Hydrogen)

Polymer type

Saccharide

Type description

D-saccharide, alpha 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



RIB : 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 O5 O O5' N N N 0 -0.774 -0.372 3.102
2 C5 C C5' N N N 0 0.124 0.364 2.271
3 C4 C C4' R N N 0 0.184 -0.281 0.885
4 O4 O O4' N N N 0 -1.11 -0.245 0.276
5 C3 C C3' S N N 0 1.151 0.511 -0.02
6 O3 O O3' N N N 0 2.419 -0.141 -0.116
7 C2 C C2' R N N 0 0.412 0.487 -1.387
8 O2 O O2' N N N 0 0.687 -0.72 -2.1
9 C1 C C1' S N N 0 -1.065 0.539 -0.925
10 O1 O O1' N N Y 0 -1.918 -0.028 -1.921
11 HO5 H HO5' N N Y 0 -0.783 0.067 3.963
12 H51 H H5'1 N N N 0 -0.225 1.392 2.178
13 H52 H H5'2 N N N 0 1.119 0.359 2.718
14 H4 H H4' N N N 0 0.523 -1.313 0.973
15 H3 H H3' N N N 0 1.269 1.533 0.339
16 HO3 H HO3' N N Y 0 2.94 0.354 -0.763
17 H2 H H2' N N N 0 0.667 1.361 -1.987
18 HO2 H HO2' N N Y 0 0.116 -0.72 -2.88
19 H1 H H1' N N N 0 -1.36 1.568 -0.717
20 HO1 H HO1' N N Y 0 -2.816 -0.0090 -1.563



RIB : 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 O5 C5 O C sing 1.43 N N
2 O5 HO5 O H sing 0.97 N N
3 C5 C4 C C sing 1.53 N N
4 C5 H51 C H sing 1.09 N N
5 C5 H52 C H sing 1.09 N N
6 C4 O4 C O sing 1.43 N N
7 C4 C3 C C sing 1.54 N N
8 C4 H4 C H sing 1.09 N N
9 O4 C1 O C sing 1.43 N N
10 C3 O3 C O sing 1.43 N N
11 C3 C2 C C sing 1.55 N N
12 C3 H3 C H sing 1.09 N N
13 O3 HO3 O H sing 0.97 N N
14 C2 O2 C O sing 1.43 N N
15 C2 C1 C C sing 1.55 N N
16 C2 H2 C H sing 1.09 N N
17 O2 HO2 O H sing 0.97 N N
18 C1 O1 C O sing 1.43 N N
19 C1 H1 C H sing 1.09 N N
20 O1 HO1 O H sing 0.97 N N



RIB : Used in PDB Entries

Total Number of PDB Entries: 26
Ligand Code PDB Entry ID Type Total Distinct
RIB 1gqt Open in New Window Bound ligand 4 1
RIB 1qd3 Open in New Window s 1 1
RIB 1rk2 Open in New Window Bound ligand 4 1
RIB 1rkd Open in New Window Bound ligand 1 1
RIB 1rks Open in New Window Bound ligand 1 1
RIB 1yoe Open in New Window Bound ligand 1 1
RIB 2c40 Open in New Window Bound ligand 2 1
RIB 2kqd Open in New Window Bound ligand 1 1
RIB 2kqe Open in New Window Bound ligand 1 1
RIB 3go6 Open in New Window Bound ligand 1 1
RIB 3go7 Open in New Window Bound ligand 1 1
RIB 3i3y Open in New Window Bound ligand 1 1
RIB 3rcy Open in New Window Bound ligand 8 1
RIB 4mav Open in New Window Bound ligand 1 1
RIB 4rhn Open in New Window Bound ligand 1 1
RIB 4rk0 Open in New Window Bound ligand 4 1
RIB 4rk1 Open in New Window Bound ligand 6 1
RIB 4xck Open in New Window Bound ligand 2 1
RIB 4xda Open in New Window Bound ligand 3 1
RIB 5bu2 Open in New Window Bound ligand 1 1
RIB 5m93 Open in New Window Bound ligand 2 1
RIB 5wv1 Open in New Window Bound ligand 1 1
RIB 6a89 Open in New Window Bound ligand 1 1
RIB 6egw Open in New Window Bound ligand 1 1
RIB 6ils Open in New Window Bound ligand 1 1
RIB 6wk0 Open in New Window Bound ligand 2 1