Chemical Components in the PDB

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JDF : Summary

Code

JDF

One-letter code

X

Molecule name

steviol-19-o-glucoside

Systematic names

Not Assigned

Formula

C26 H40 O8

Formal charge

0

Molecular weight

480.591 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 C[C]12CCC[C](C)([CH]1CC[C]34CC(=C)[C](O)(CC[CH]23)C4)C(=O)O[CH]5O[CH](CO)[CH](O)[CH](O)[CH]5O
SMILES OpenEye OEToolkits 2.0.7 CC12CCCC(C1CCC34C2CCC(C3)(C(=C)C4)O)(C)C(=O)OC5C(C(C(C(O5)CO)O)O)O
Canonical SMILES CACTVS 3.385 C[C@@]12CCC[C@](C)([C@H]1CC[C@]34CC(=C)[C@](O)(CC[C@@H]23)C4)C(=O)O[C@@H]5O[C@H](CO)[C@@H](O)[C@H](O)[C@H]5O
Canonical SMILES OpenEye OEToolkits 2.0.7 C[C@@]12CCC[C@@]([C@H]1CC[C@]34[C@H]2CC[C@](C3)(C(=C)C4)O)(C)C(=O)O[C@H]5[C@@H]([C@H]([C@@H]([C@H](O5)CO)O)O)O

IUPAC InChI

InChI=1S/C26H40O8/c1-14-11-25-9-5-16-23(2,17(25)6-10-26(14,32)13-25)7-4-8-24(16,3)22(31)34-21-20(30)19(29)18(28)15(12-27)33-21/h15-21,27-30,32H,1,4-13H2,2-3H3/t15-,16+,17+,18-,19+,20-,21+,23-,24-,25-,26+/m1/s1

IUPAC InChI key

OQPOFZJZPYRNFF-CULFPKEHSA-N
JDF

wwPDB Information

Atom count

74 (34 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2021-05-21

Last modified at

2021-12-03

Status

Released

Obsoleted

Not Assigned



JDF : Atoms of Molecule

Total Number of Atoms: 74
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 3.283 -0.431 0.455
2 C2 C C2 R N N 0 4.716 -0.94 0.278
3 C5 C C5 R N N 0 3.958 1.835 0.052
4 C3 C C3 S N N 0 5.696 0.162 0.692
5 O3 O O1 N N N 0 7.036 -0.278 0.461
6 C4 C C4 S N N 0 5.418 1.417 -0.141
7 C6 C C6 N N N 0 3.656 3.052 -0.824
8 CAH C C7 S N N 0 -1.4 -1.77 0.04
9 CAI C C8 N N N 0 -1.615 -1.321 1.484
10 CAJ C C9 N N N 0 -3.125 -1.36 1.767
11 CAK C C10 R N N 0 -3.857 -0.44 0.811
12 CAN C C11 N N N 0 -3.711 1.026 1.26
13 CAL C C12 N N N 0 -5.39 -0.657 0.913
14 CAM C C13 N N N 0 -6.007 0.691 0.584
15 CAA C C14 N N N 0 -7.283 0.952 0.446
16 CAO C C15 S N N 0 -4.862 1.684 0.452
17 OAW O O2 N N N 0 -5.212 2.977 0.952
18 CAP C C16 N N N 0 -4.398 1.727 -1.007
19 CAQ C C17 N N N 0 -4.2 0.329 -1.571
20 CAR C C18 R N N 0 -3.483 -0.636 -0.645
21 CAS C C19 S N N 0 -1.986 -0.74 -0.919
22 CAT C C20 N N N 0 -1.323 0.627 -0.792
23 CAE C C24 R N N 0 0.017 -2.211 -0.241
24 CAU C C21 N N N 0 -1.793 -1.236 -2.361
25 CAV C C22 N N N 0 -0.309 -1.471 -2.632
26 CAF C C23 N N N 0 0.219 -2.566 -1.714
27 CAG C C25 N N N 0 0.291 -3.508 0.558
28 CAC C C26 N N N 0 1.043 -1.202 0.194
29 OAD O O3 N N N 0 0.692 -0.166 0.709
30 O1 O O4 N N N 0 2.349 -1.45 0.01
31 O5 O O5 N N N 0 3.101 0.754 -0.322
32 O6 O O6 N N N 0 2.329 3.513 -0.558
33 O4 O O7 N N N 0 6.278 2.475 0.287
34 O2 O O8 N N N 0 4.918 -2.093 1.098
35 H1 H H1 N N N 0 3.104 -0.207 1.506
36 H2 H H2 N N N 0 4.884 -1.203 -0.767
37 H3 H H3 N N N 0 5.563 0.39 1.75
38 H4 H H4 N N N 0 7.279 -1.074 0.953
39 H5 H H5 N N N 0 5.599 1.202 -1.194
40 H6 H H6 N N N 0 3.787 2.088 1.098
41 H7 H H7 N N N 0 4.368 3.846 -0.601
42 H8 H H8 N N N 0 3.739 2.774 -1.875
43 H9 H H9 N N N 0 -2.038 -2.685 -0.081
44 H10 H H10 N N N 0 -1.112 -1.996 2.174
45 H11 H H11 N N N 0 -1.247 -0.314 1.64
46 H12 H H12 N N N 0 -3.488 -2.381 1.644
47 H13 H H13 N N N 0 -3.308 -1.028 2.79
48 H14 H H14 N N N 0 -3.915 1.11 2.34
49 H15 H H15 N N N 0 -2.755 1.475 1.045
50 H16 H H16 N N N 0 -5.7 -1.405 0.19
51 H17 H H17 N N N 0 -5.641 -0.965 1.924
52 H18 H H18 N N N 0 -8.012 0.165 0.567
53 H19 H H19 N N N 0 -7.606 1.956 0.21
54 H20 H H20 N N N 0 -5.928 3.407 0.464
55 H21 H H21 N N N 0 -5.158 2.243 -1.605
56 H22 H H22 N N N 0 -3.473 2.297 -1.083
57 H26 H H26 N N N 0 -0.288 0.562 -1.129
58 H23 H H23 N N N 0 -5.187 -0.089 -1.811
59 H24 H H24 N N N 0 -3.65 0.399 -2.513
60 H25 H H25 N N N 0 -3.887 -1.646 -0.919
61 H27 H H27 N N N 0 -1.86 1.35 -1.406
62 H28 H H28 N N N 0 -1.346 0.948 0.25
63 H29 H H29 N N N 0 -2.343 -2.164 -2.493
64 H30 H H30 N N N 0 -2.168 -0.484 -3.054
65 H31 H H31 N N N 0 -0.194 -1.802 -3.675
66 H32 H H32 N N N 0 0.266 -0.558 -2.51
67 H33 H H33 N N N 0 -0.312 -3.5 -1.927
68 H34 H H34 N N N 0 1.282 -2.723 -1.909
69 H35 H H35 N N N 0 -0.41 -4.282 0.245
70 H36 H H36 N N N 0 1.311 -3.843 0.368
71 H37 H H37 N N N 0 0.165 -3.313 1.623
72 H38 H H38 N N N 0 2.069 4.285 -1.079
73 H39 H H39 N N N 0 7.22 2.276 0.197
74 H40 H H40 N N N 0 4.327 -2.83 0.893



JDF : Chemical Bonds

Total Number of Bonds: 78
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O2 C2 O C sing 1.43 N N
2 O3 C3 O C sing 1.43 N N
3 C3 C2 C C sing 1.53 N N
4 C3 C4 C C sing 1.53 N N
5 O4 C4 O C sing 1.43 N N
6 C2 C1 C C sing 1.53 N N
7 OAD CAC O C doub 1.21 N N
8 C1 O1 C O sing 1.45 N N
9 C1 O5 C O sing 1.43 N N
10 C4 C5 C C sing 1.53 N N
11 C5 O5 C O sing 1.43 N N
12 C5 C6 C C sing 1.53 N N
13 CAG CAE C C sing 1.55 N N
14 CAC O1 C O sing 1.34 N N
15 CAC CAE C C sing 1.5 N N
16 C6 O6 C O sing 1.43 N N
17 CAE CAH C C sing 1.51 N N
18 CAE CAF C C sing 1.53 N N
19 CAI CAH C C sing 1.53 N N
20 CAI CAJ C C sing 1.54 N N
21 CAH CAS C C sing 1.52 N N
22 CAJ CAK C C sing 1.52 N N
23 CAF CAV C C sing 1.52 N N
24 CAT CAS C C sing 1.52 N N
25 CAN CAK C C sing 1.54 N N
26 CAN CAO C C sing 1.55 N N
27 CAS CAU C C sing 1.54 N N
28 CAS CAR C C sing 1.53 N N
29 CAV CAU C C sing 1.53 N N
30 CAK CAR C C sing 1.52 N N
31 CAK CAL C C sing 1.55 N N
32 CAR CAQ C C sing 1.52 N N
33 CAL CAM C C sing 1.52 N N
34 OAW CAO O C sing 1.43 N N
35 CAO CAM C C sing 1.52 N N
36 CAO CAP C C sing 1.53 N N
37 CAM CAA C C doub 1.31 N N
38 CAP CAQ C C sing 1.52 N N
39 C1 H1 C H sing 1.09 N N
40 C2 H2 C H sing 1.09 N N
41 C3 H3 C H sing 1.09 N N
42 O3 H4 O H sing 0.97 N N
43 C4 H5 C H sing 1.09 N N
44 C5 H6 C H sing 1.09 N N
45 C6 H7 C H sing 1.09 N N
46 C6 H8 C H sing 1.09 N N
47 CAH H9 C H sing 1.12 N N
48 CAI H10 C H sing 1.09 N N
49 CAI H11 C H sing 1.08 N N
50 CAJ H12 C H sing 1.09 N N
51 CAJ H13 C H sing 1.09 N N
52 CAN H14 C H sing 1.1 N N
53 CAN H15 C H sing 1.08 N N
54 CAL H16 C H sing 1.09 N N
55 CAL H17 C H sing 1.09 N N
56 CAA H18 C H sing 1.08 N N
57 CAA H19 C H sing 1.08 N N
58 OAW H20 O H sing 0.97 N N
59 CAP H21 C H sing 1.1 N N
60 CAP H22 C H sing 1.09 N N
61 CAQ H23 C H sing 1.1 N N
62 CAQ H24 C H sing 1.09 N N
63 CAR H25 C H sing 1.12 N N
64 CAT H26 C H sing 1.09 N N
65 CAT H27 C H sing 1.09 N N
66 CAT H28 C H sing 1.09 N N
67 CAU H29 C H sing 1.09 N N
68 CAU H30 C H sing 1.09 N N
69 CAV H31 C H sing 1.1 N N
70 CAV H32 C H sing 1.09 N N
71 CAF H33 C H sing 1.1 N N
72 CAF H34 C H sing 1.09 N N
73 CAG H35 C H sing 1.09 N N
74 CAG H36 C H sing 1.09 N N
75 CAG H37 C H sing 1.09 N N
76 O6 H38 O H sing 0.97 N N
77 O4 H39 O H sing 0.97 N N
78 O2 H40 O H sing 0.97 N N



JDF : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
JDF 7es1 Open in New Window Bound ligand 1 1