Chemical Components in the PDB

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DS8 : Summary

Code

DS8

One-letter code

X

Molecule name

(2~{S},3~{S},4~{R},5~{S},6~{S})-2-[[(2~{S},4~{R},6~{R})-2-(hydroxymethyl)-6-oxidanyl-oxan-4-yl]methyl]-6-methyl-oxane-3,4,5-triol

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 (2~{S},3~{S},4~{R},5~{S},6~{S})-2-[[(2~{S},4~{R},6~{R})-2-(hydroxymethyl)-6-oxidanyl-oxan-4-yl]methyl]-6-methyl-oxane-3,4,5-triol

Formula

C13 H24 O7

Formal charge

0

Molecular weight

292.325 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 C[CH]1O[CH](C[CH]2C[CH](O)O[CH](CO)C2)[CH](O)[CH](O)[CH]1O
SMILES OpenEye OEToolkits 2.0.6 CC1C(C(C(C(O1)CC2CC(OC(C2)O)CO)O)O)O
Canonical SMILES CACTVS 3.385 C[C@@H]1O[C@@H](C[C@@H]2C[C@H](O)O[C@H](CO)C2)[C@@H](O)[C@H](O)[C@@H]1O
Canonical SMILES OpenEye OEToolkits 2.0.6 C[C@H]1[C@H]([C@H]([C@@H]([C@@H](O1)C[C@H]2C[C@H](O[C@H](C2)O)CO)O)O)O

IUPAC InChI

InChI=1S/C13H24O7/c1-6-11(16)13(18)12(17)9(19-6)3-7-2-8(5-14)20-10(15)4-7/h6-18H,2-5H2,1H3/t6-,7+,8-,9-,10+,11+,12+,13+/m0/s1

IUPAC InChI key

ROOQANRWEBNDFF-VBFQFBHJSA-N
DS8

wwPDB Information

Atom count

44 (20 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2018-01-29

Last modified at

2019-01-25

Status

Released

Obsoleted

Not Assigned



DS8 : Atoms of Molecule

Total Number of Atoms: 44
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 S N N 0 -1.245 -0.395 -0.347
2 C2 C C2 S N N 0 -2.41 -1.077 -1.07
3 C3 C C3 R N N 0 -3.702 -0.306 -0.78
4 C4 C C4 S N N 0 -3.916 -0.243 0.736
5 C5 C C5 S N N 0 -2.693 0.407 1.389
6 C6 C C6 N N N 0 -2.544 1.842 0.88
7 C7 C C7 N N N 0 0.039 -1.193 -0.583
8 C8 C C8 R N N 0 2.666 1.583 -0.129
9 O2 O O1 N N N 0 -2.54 -2.421 -0.603
10 O3 O O2 N N N 0 -3.596 1.019 -1.304
11 C11 C C11 N N N 0 2.491 -1.297 -0.101
12 C9 C C9 N N N 0 1.432 0.881 -0.701
13 O4 O O3 N N N 0 -5.079 0.536 1.021
14 C10 C C10 R N N 0 1.224 -0.447 0.034
15 C12 C C12 S N N 0 3.684 -0.51 0.447
16 C13 C C13 N N N 0 4.964 -1.328 0.262
17 O5 O O4 N N N 0 -1.522 -0.341 1.054
18 O8 O O5 N N N 0 2.899 2.797 -0.847
19 O12 O O6 N N N 0 3.803 0.727 -0.258
20 O13 O O7 N N N 0 6.059 -0.647 0.877
21 H1 H H1 N N N 0 -1.12 0.617 -0.732
22 H2 H H2 N N N 0 -2.22 -1.081 -2.143
23 H3 H H3 N N N 0 -4.543 -0.817 -1.247
24 H4 H H4 N N N 0 -4.047 -1.251 1.128
25 H5 H H5 N N N 0 -2.821 0.416 2.472
26 H6 H H6 N N N 0 -3.494 2.365 0.987
27 H7 H H7 N N N 0 -1.779 2.356 1.462
28 H8 H H8 N N N 0 -2.253 1.827 -0.17
29 H9 H H9 N N N 0 -0.053 -2.175 -0.119
30 H10 H H10 N N N 0 0.202 -1.311 -1.654
31 H11 H H11 N N N 0 2.5 1.811 0.924
32 H12 H H12 N N N 0 -3.261 -2.914 -1.02
33 H13 H H13 N N N 0 -4.38 1.564 -1.155
34 H14 H H14 N N N 0 0.555 1.515 -0.563
35 H15 H H15 N N N 0 1.581 0.69 -1.763
36 H16 H H16 N N N 0 -5.275 0.619 1.965
37 H17 H H17 N N N 0 1.024 -0.253 1.088
38 H18 H H18 N N N 0 2.372 -2.22 0.465
39 H19 H H19 N N N 0 2.661 -1.532 -1.151
40 H20 H H20 N N N 0 3.532 -0.31 1.508
41 H21 H H21 N N N 0 4.839 -2.307 0.724
42 H24 H H24 N N N 0 6.904 -1.109 0.798
43 H22 H H22 N N N 0 5.164 -1.452 -0.803
44 H23 H H23 N N N 0 3.668 3.295 -0.538



DS8 : Chemical Bonds

Total Number of Bonds: 45
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C6 C5 C C sing 1.53 N N
2 C5 C4 C C sing 1.53 N N
3 C5 O5 C O sing 1.43 N N
4 C4 O4 C O sing 1.43 N N
5 C4 C3 C C sing 1.53 N N
6 O5 C1 O C sing 1.43 N N
7 O8 C8 O C sing 1.43 N N
8 C9 C8 C C sing 1.53 N N
9 C9 C10 C C sing 1.53 N N
10 C7 C10 C C sing 1.53 N N
11 C7 C1 C C sing 1.53 N N
12 C3 O3 C O sing 1.43 N N
13 C3 C2 C C sing 1.53 N N
14 O12 C8 O C sing 1.43 N N
15 O12 C12 O C sing 1.43 N N
16 C11 C10 C C sing 1.53 N N
17 C11 C12 C C sing 1.53 N N
18 C1 C2 C C sing 1.53 N N
19 C13 C12 C C sing 1.53 N N
20 C13 O13 C O sing 1.43 N N
21 C2 O2 C O sing 1.43 N N
22 C1 H1 C H sing 1.09 N N
23 C2 H2 C H sing 1.09 N N
24 C3 H3 C H sing 1.09 N N
25 C4 H4 C H sing 1.09 N N
26 C5 H5 C H sing 1.09 N N
27 C6 H6 C H sing 1.09 N N
28 C6 H7 C H sing 1.09 N N
29 C6 H8 C H sing 1.09 N N
30 C7 H9 C H sing 1.09 N N
31 C7 H10 C H sing 1.09 N N
32 C8 H11 C H sing 1.09 N N
33 O2 H12 O H sing 0.97 N N
34 O3 H13 O H sing 0.97 N N
35 C9 H14 C H sing 1.09 N N
36 C9 H15 C H sing 1.09 N N
37 O4 H16 O H sing 0.97 N N
38 C10 H17 C H sing 1.09 N N
39 C11 H18 C H sing 1.09 N N
40 C11 H19 C H sing 1.09 N N
41 C12 H20 C H sing 1.09 N N
42 C13 H21 C H sing 1.09 N N
43 C13 H22 C H sing 1.09 N N
44 O8 H23 O H sing 0.97 N N
45 O13 H24 O H sing 0.97 N N



DS8 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
DS8 6fhy Open in New Window Bound ligand 12 1