Chemical Components in the PDB

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XTG : Summary

Code

XTG

One-letter code

X

Molecule name

4-NITROPHENYL 6-THIO-6-S-ALPHA-D-XYLOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE

Systematic names

ProgramVersionName
ACDLabs 10.04 4-nitrophenyl 6-thio-6-S-alpha-D-xylopyranosyl-beta-D-glucopyranoside
OpenEye OEToolkits 1.5.0 (2S,3R,4S,5S,6S)-2-(4-nitrophenoxy)-6-[[(2R,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]sulfanylmethyl]oxane-3,4,5-triol

Formula

C17 H23 N O11 S

Formal charge

0

Molecular weight

449.43 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 [O-][N+](=O)c3ccc(OC2OC(CSC1OCC(O)C(O)C1O)C(O)C(O)C2O)cc3
SMILES CACTVS 3.341 O[CH]1CO[CH](SC[CH]2O[CH](Oc3ccc(cc3)[N+]([O-])=O)[CH](O)[CH](O)[CH]2O)[CH](O)[CH]1O
SMILES OpenEye OEToolkits 1.5.0 c1cc(ccc1[N+](=O)[O-])OC2C(C(C(C(O2)CSC3C(C(C(CO3)O)O)O)O)O)O
Canonical SMILES CACTVS 3.341 O[C@@H]1CO[C@H](SC[C@H]2O[C@@H](Oc3ccc(cc3)[N+]([O-])=O)[C@H](O)[C@@H](O)[C@@H]2O)[C@H](O)[C@H]1O
Canonical SMILES OpenEye OEToolkits 1.5.0 c1cc(ccc1[N+](=O)[O-])O[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CS[C@@H]3[C@@H]([C@H]([C@@H](CO3)O)O)O)O)O)O

IUPAC InChI

InChI=1S/C17H23NO11S/c19-9-5-27-17(15(24)11(9)20)30-6-10-12(21)13(22)14(23)16(29-10)28-8-3-1-7(2-4-8)18(25)26/h1-4,9-17,19-24H,5-6H2/t9-,10-,11+,12-,13+,14-,15-,16-,17-/m1/s1

IUPAC InChI key

HQYVHBCTLFPWRQ-ZMFOIVQCSA-N
XTG

wwPDB Information

Atom count

53 (30 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2005-11-17

Last modified at

2021-03-01

Status

Released

Obsoleted

Not Assigned



XTG : Atoms of Molecule

Total Number of Atoms: 53
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C14 C C14 N Y N 0 -2.968 2.858 -1.182
2 C13 C C13 N Y N 0 -2.192 3.937 -0.805
3 C12 C C12 N Y N 0 -1.217 3.784 0.164
4 N1 N N1 N N N 1 -0.386 4.941 0.566
5 O10 O O10 N N N -1 -0.561 6.027 0.043
6 O11 O O11 N N N 0 0.472 4.807 1.419
7 C17 C C17 N Y N 0 -1.017 2.551 0.758
8 C16 C C16 N Y N 0 -1.795 1.471 0.388
9 C15 C C15 N Y N 0 -2.769 1.621 -0.588
10 O1 O O1 N N N 0 -3.532 0.558 -0.957
11 C1 C C1 S N N 0 -3.093 -0.556 -0.177
12 O5 O O5 N N N 0 -1.749 -0.879 -0.526
13 C2 C C2 R N N 0 -4.003 -1.756 -0.45
14 O2 O O2 N N N 0 -5.352 -1.418 -0.125
15 C3 C C3 S N N 0 -3.545 -2.936 0.414
16 O3 O O3 N N N 0 -4.289 -4.105 0.063
17 C4 C C4 S N N 0 -2.053 -3.178 0.163
18 O4 O O4 N N N 0 -1.571 -4.176 1.065
19 C5 C C5 S N N 0 -1.291 -1.87 0.391
20 C6 C C6 N N N 0 0.205 -2.109 0.177
21 S6 S S6 N N N 0 1.124 -0.602 0.595
22 C7 C C7 R N N 0 2.816 -1.161 0.257
23 O9 O O9 N N N 0 2.99 -1.324 -1.15
24 C11 C C11 N N N 0 4.264 -1.931 -1.36
25 C10 C C10 R N N 0 5.374 -0.955 -0.964
26 O8 O O8 N N N 0 5.259 0.241 -1.738
27 C9 C C9 S N N 0 5.238 -0.618 0.525
28 O7 O O7 N N N 0 5.491 -1.785 1.31
29 C8 C C8 R N N 0 3.809 -0.123 0.785
30 O6 O O6 N N N 0 3.603 1.121 0.112
31 H14 H H14 N N N 0 -3.729 2.979 -1.939
32 H13 H H13 N N N 0 -2.346 4.901 -1.267
33 H17 H H17 N N N 0 -0.255 2.434 1.514
34 H16 H H16 N N N 0 -1.638 0.508 0.852
35 H1 H H1 N N N 0 -3.141 -0.299 0.881
36 H2 H H2 N N N 0 -3.939 -2.03 -1.504
37 HO2 H HO2 N N N 0 -5.595 -0.669 -0.687
38 H4 H H4 N N N 0 -1.905 -3.513 -0.864
39 H3 H H3 N N N 0 -3.707 -2.703 1.467
40 HO3 H HO3 N N N 0 -5.221 -3.903 0.225
41 HO4 H HO4 N N N 0 -2.082 -4.978 0.893
42 H7 H H7 N N N 0 2.99 -2.114 0.756
43 H5 H H5 N N N 0 -1.46 -1.526 1.412
44 H61 H 1H6 N N N 0 0.386 -2.368 -0.866
45 H62 H 2H6 N N N 0 0.538 -2.927 0.817
46 H111 H 1H11 N N N 0 4.37 -2.193 -2.412
47 H112 H 2H11 N N N 0 4.34 -2.832 -0.752
48 H10 H H10 N N N 0 6.346 -1.415 -1.146
49 HO8 H HO8 N N N 0 5.347 -0.017 -2.665
50 H9 H H9 N N N 0 5.95 0.164 0.792
51 HO7 H HO7 N N N 0 6.398 -2.061 1.116
52 H8 H H8 N N N 0 3.659 0.013 1.856
53 HO6 H HO6 N N N 0 2.693 1.392 0.297



XTG : Chemical Bonds

Total Number of Bonds: 55
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C14 C13 C C doub 1.38 N Y
2 C14 C15 C C sing 1.39 N Y
3 C14 H14 C H sing 1.08 N N
4 C13 C12 C C sing 1.38 N Y
5 C13 H13 C H sing 1.08 N N
6 C12 N1 C N sing 1.48 N N
7 C12 C17 C C doub 1.38 N Y
8 N1 O10 N O sing 1.22 N N
9 N1 O11 N O doub 1.22 N N
10 C17 C16 C C sing 1.38 N Y
11 C17 H17 C H sing 1.08 N N
12 C16 C15 C C doub 1.39 N Y
13 C16 H16 C H sing 1.08 N N
14 C15 O1 C O sing 1.36 N N
15 O1 C1 O C sing 1.43 N N
16 C1 O5 C O sing 1.43 N N
17 C1 C2 C C sing 1.53 N N
18 C1 H1 C H sing 1.09 N N
19 O5 C5 O C sing 1.43 N N
20 C2 O2 C O sing 1.43 N N
21 C2 C3 C C sing 1.53 N N
22 C2 H2 C H sing 1.09 N N
23 O2 HO2 O H sing 0.97 N N
24 C3 O3 C O sing 1.43 N N
25 C3 C4 C C sing 1.53 N N
26 C3 H3 C H sing 1.09 N N
27 O3 HO3 O H sing 0.97 N N
28 C4 O4 C O sing 1.43 N N
29 C4 C5 C C sing 1.53 N N
30 C4 H4 C H sing 1.09 N N
31 O4 HO4 O H sing 0.97 N N
32 C5 C6 C C sing 1.53 N N
33 C5 H5 C H sing 1.09 N N
34 C6 S6 C S sing 1.81 N N
35 C6 H61 C H sing 1.09 N N
36 C6 H62 C H sing 1.09 N N
37 S6 C7 S C sing 1.81 N N
38 C7 O9 C O sing 1.43 N N
39 C7 C8 C C sing 1.53 N N
40 C7 H7 C H sing 1.09 N N
41 O9 C11 O C sing 1.43 N N
42 C11 C10 C C sing 1.53 N N
43 C11 H111 C H sing 1.09 N N
44 C11 H112 C H sing 1.09 N N
45 C10 O8 C O sing 1.43 N N
46 C10 C9 C C sing 1.53 N N
47 C10 H10 C H sing 1.09 N N
48 O8 HO8 O H sing 0.97 N N
49 C9 O7 C O sing 1.43 N N
50 C9 C8 C C sing 1.53 N N
51 C9 H9 C H sing 1.09 N N
52 O7 HO7 O H sing 0.97 N N
53 C8 O6 C O sing 1.43 N N
54 C8 H8 C H sing 1.09 N N
55 O6 HO6 O H sing 0.97 N N



XTG : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
XTG 2f2h Open in New Window Bound ligand 7 1