Chemical Components in the PDB

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VCW : Summary

Code

VCW

One-letter code

X

Molecule name

[(2S,3S,4S,5R,6S)-6-[(2R)-2,3-bis(oxidanyl)propoxy]-3,4,5-tris(oxidanyl)oxan-2-yl]methanesulfonic acid

Synonyms

sulfoquinovosyl glycerol
SQGro

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 [(2~{S},3~{S},4~{S},5~{R},6~{S})-6-[(2~{R})-2,3-bis(oxidanyl)propoxy]-3,4,5-tris(oxidanyl)oxan-2-yl]methanesulfonic acid

Formula

C9 H18 O10 S

Formal charge

0

Molecular weight

318.298 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 OC[CH](O)CO[CH]1O[CH](C[S](O)(=O)=O)[CH](O)[CH](O)[CH]1O
SMILES OpenEye OEToolkits 2.0.7 C(C1C(C(C(C(O1)OCC(CO)O)O)O)O)S(=O)(=O)O
Canonical SMILES CACTVS 3.385 OC[C@@H](O)CO[C@H]1O[C@H](C[S](O)(=O)=O)[C@@H](O)[C@H](O)[C@H]1O
Canonical SMILES OpenEye OEToolkits 2.0.7 C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)OC[C@@H](CO)O)O)O)O)S(=O)(=O)O

IUPAC InChI

InChI=1S/C9H18O10S/c10-1-4(11)2-18-9-8(14)7(13)6(12)5(19-9)3-20(15,16)17/h4-14H,1-3H2,(H,15,16,17)/t4-,5-,6-,7+,8-,9+/m1/s1

IUPAC InChI key

JTXHNMDHGMNPEG-NZJLWHDDSA-N
VCW

wwPDB Information

Atom count

38 (20 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2021-05-05

Last modified at

2022-01-14

Status

Released

Obsoleted

Not Assigned



VCW : Atoms of Molecule

Total Number of Atoms: 38
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C4 C C1 N N N 0 -2.046 -0.067 -0.666
2 C5 C C2 R N N 0 -3.152 0.061 0.383
3 C6 C C3 N N N 0 -4.008 1.291 0.074
4 C7 C C4 R N N 0 0.607 -2.667 -0.903
5 C8 C C5 S N N 0 1.212 -2.573 0.501
6 C1 C C6 N N N 0 2.34 1.092 0.169
7 C2 C C7 S N N 0 1.387 -0.105 0.172
8 C3 C C8 S N N 0 -0.104 -1.352 -1.234
9 C9 C C9 S N N 0 2.158 -1.37 0.558
10 O1 O O1 N N N 0 0.555 2.91 0.959
11 S1 S S1 N N N 0 1.401 2.612 -0.143
12 O2 O O2 N N N 0 2.447 3.717 -0.123
13 O3 O O3 N N N 0 0.902 2.626 -1.474
14 O4 O O4 N N N 0 0.825 -0.271 -1.133
15 O5 O O5 N N N 0 -1.178 -1.145 -0.314
16 O6 O O6 N N N 0 -3.972 -1.109 0.356
17 O7 O O7 N N N 0 -4.967 1.478 1.117
18 O8 O O8 N N N 0 -0.333 -3.742 -0.947
19 O9 O O9 N N N 0 1.94 -3.769 0.789
20 O10 O O10 N N N 0 2.672 -1.23 1.884
21 H1 H H1 N N N 0 -2.492 -0.263 -1.642
22 H2 H H2 N N N 0 -1.475 0.861 -0.708
23 H3 H H3 N N N 0 -2.705 0.169 1.371
24 H4 H H4 N N N 0 -3.369 2.171 0.007
25 H5 H H5 N N N 0 -4.526 1.145 -0.874
26 H6 H H6 N N N 0 1.399 -2.845 -1.63
27 H7 H H7 N N N 0 0.414 -2.447 1.234
28 H8 H H8 N N N 0 2.837 1.164 1.136
29 H9 H H9 N N N 0 3.087 0.959 -0.614
30 H10 H H10 N N N 0 0.589 0.068 0.894
31 H11 H H11 N N N 0 -0.499 -1.397 -2.249
32 H12 H H12 N N N 0 2.983 -1.521 -0.139
33 H13 H H13 N N N 0 -4.403 -1.267 -0.495
34 H14 H H14 N N N 0 -5.546 2.242 0.987
35 H15 H H15 N N N 0 -0.758 -3.858 -1.809
36 H16 H H16 N N N 0 1.402 -4.572 0.763
37 H17 H H17 N N N 0 3.173 -1.997 2.195
38 H18 H H18 N N N 0 2.089 4.601 -0.278



VCW : Chemical Bonds

Total Number of Bonds: 38
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O1 S1 O S doub 1.42 N N
2 S1 O3 S O doub 1.42 N N
3 S1 O2 S O sing 1.52 N N
4 S1 C1 S C sing 1.81 N N
5 C6 O7 C O sing 1.43 N N
6 C6 C5 C C sing 1.53 N N
7 C5 C4 C C sing 1.53 N N
8 C5 O6 C O sing 1.43 N N
9 O10 C9 O C sing 1.43 N N
10 C1 C2 C C sing 1.53 N N
11 C4 O5 C O sing 1.43 N N
12 C2 C9 C C sing 1.53 N N
13 C2 O4 C O sing 1.43 N N
14 O5 C3 O C sing 1.43 N N
15 C9 C8 C C sing 1.53 N N
16 C8 O9 C O sing 1.43 N N
17 C8 C7 C C sing 1.53 N N
18 O4 C3 O C sing 1.43 N N
19 C3 C7 C C sing 1.53 N N
20 C7 O8 C O sing 1.43 N N
21 C4 H1 C H sing 1.09 N N
22 C4 H2 C H sing 1.09 N N
23 C5 H3 C H sing 1.09 N N
24 C6 H4 C H sing 1.09 N N
25 C6 H5 C H sing 1.09 N N
26 C7 H6 C H sing 1.09 N N
27 C8 H7 C H sing 1.09 N N
28 C1 H8 C H sing 1.09 N N
29 C1 H9 C H sing 1.09 N N
30 C2 H10 C H sing 1.09 N N
31 C3 H11 C H sing 1.09 N N
32 C9 H12 C H sing 1.09 N N
33 O6 H13 O H sing 0.97 N N
34 O7 H14 O H sing 0.97 N N
35 O8 H15 O H sing 0.97 N N
36 O9 H16 O H sing 0.97 N N
37 O10 H17 O H sing 0.97 N N
38 O2 H18 O H sing 0.97 N N



VCW : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
VCW 7ofx Open in New Window Bound ligand 4 1
VCW 7ofy Open in New Window Bound ligand 2 1