Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

DSR : Summary

Code

DSR

One-letter code

X

Molecule name

2,6-dideoxy-4-thio-beta-D-allopyranose

Systematic names

ProgramVersionName
ACDLabs 10.04 2,6-dideoxy-4-thio-beta-D-ribo-hexopyranose
OpenEye OEToolkits 1.5.0 (2R,4S,5S,6R)-6-methyl-5-sulfanyl-oxane-2,4-diol

Formula

C6 H12 O3 S

Formal charge

0

Molecular weight

164.223 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 SC1C(OC(O)CC1O)C
SMILES CACTVS 3.341 C[CH]1O[CH](O)C[CH](O)[CH]1S
SMILES OpenEye OEToolkits 1.5.0 CC1C(C(CC(O1)O)O)S
Canonical SMILES CACTVS 3.341 C[C@H]1O[C@@H](O)C[C@H](O)[C@@H]1S
Canonical SMILES OpenEye OEToolkits 1.5.0 C[C@@H]1[C@H]([C@H](C[C@@H](O1)O)O)S

IUPAC InChI

InChI=1S/C6H12O3S/c1-3-6(10)4(7)2-5(8)9-3/h3-8,10H,2H2,1H3/t3-,4+,5-,6-/m1/s1

IUPAC InChI key

PYIPBDQDMFBTIQ-JGWLITMVSA-N
DSR

wwPDB Information

Atom count

22 (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



DSR : Atoms of Molecule

Total Number of Atoms: 22
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 R N N 0 -0.028 -0.219 1.885
2 C2 C C2 N N N 0 -1.158 0.662 1.348
3 C3 C C3 S N N 0 -1.341 0.383 -0.147
4 C4 C C4 S N N 0 0.011 0.558 -0.846
5 C5 C C5 R N N 0 1.052 -0.316 -0.144
6 C6 C C6 N N N 0 2.398 -0.176 -0.857
7 O1 O O1 N N Y 0 0.127 0.012 3.287
8 O3 O O3 N N N 0 -1.812 -0.953 -0.331
9 O5 O O5 N N N 0 1.189 0.094 1.214
10 S4 S S4 N N N 0 -0.133 0.053 -2.583
11 H1 H H1 N N N 0 -0.275 -1.267 1.717
12 H2 H H21 N N N 0 -2.083 0.432 1.878
13 H22 H H22 N N N 0 -0.903 1.711 1.495
14 H3 H H3 N N N 0 -2.062 1.085 -0.564
15 H4 H H4 N N N 0 0.316 1.603 -0.794
16 H5 H H5 N N N 0 0.731 -1.358 -0.177
17 H61 H H61 N N N 0 3.14 -0.801 -0.359
18 H62 H H62 N N N 0 2.295 -0.492 -1.895
19 H63 H H63 N N N 0 2.72 0.864 -0.825
20 HO1 H HO1 N N Y 0 0.843 -0.563 3.587
21 HO3 H HO3 N N Y 0 -2.657 -1.018 0.134
22 H4S H H4S N N N 0 -1.078 0.915 -2.998



DSR : Chemical Bonds

Total Number of Bonds: 22
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 C2 C C sing 1.53 N N
2 C1 O1 C O sing 1.43 N N
3 C1 O5 C O sing 1.42 N N
4 C1 H1 C H sing 1.09 N N
5 C2 C3 C C sing 1.53 N N
6 C2 H2 C H sing 1.09 N N
7 C2 H22 C H sing 1.09 N N
8 C3 C4 C C sing 1.53 N N
9 C3 O3 C O sing 1.43 N N
10 C3 H3 C H sing 1.09 N N
11 C4 C5 C C sing 1.53 N N
12 C4 S4 C S sing 1.81 N N
13 C4 H4 C H sing 1.09 N N
14 C5 C6 C C sing 1.53 N N
15 C5 O5 C O sing 1.43 N N
16 C5 H5 C H sing 1.09 N N
17 C6 H61 C H sing 1.09 N N
18 C6 H62 C H sing 1.09 N N
19 C6 H63 C H sing 1.09 N N
20 O1 HO1 O H sing 0.97 N N
21 O3 HO3 O H sing 0.97 N N
22 S4 H4S S H sing 1.34 N N



DSR : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
DSR 2l65 Open in New Window Bound ligand 1 1
DSR 2pik Open in New Window Bound ligand 1 1