Chemical Components in the PDB

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5YI : Summary

Code

5YI

One-letter code

X

Molecule name

(1R,2Z,3R,5E,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethylidene)-9,10-secoestra-5,7,16-triene-1,3-diol

Systematic names

ProgramVersionName
ACDLabs 12.01 (1R,2Z,3R,5E,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethylidene)-9,10-secoestra-5,7,16-triene-1,3-diol
OpenEye OEToolkits 1.7.6 (1R,3R)-5-[(2E)-2-[(3aS,7aS)-1-[(1S)-1-(2-ethyl-2-oxidanyl-butyl)sulfanylethyl]-7a-methyl-3a,5,6,7-tetrahydro-3H-inden-4-ylidene]ethylidene]-2-(2-oxidanylethylidene)cyclohexane-1,3-diol

Formula

C28 H44 O4 S

Formal charge

0

Molecular weight

476.712 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 OC3C(=C\CO)\C(O)C\C(=C\C=C1/CCCC2(C(=CCC12)C(SCC(O)(CC)CC)C)C)C3
SMILES CACTVS 3.370 CCC(O)(CC)CS[CH](C)C1=CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)C(=CCO)[CH](O)C3
SMILES OpenEye OEToolkits 1.7.6 CCC(CC)(CSC(C)C1=CCC2C1(CCCC2=CC=C3CC(C(=CCO)C(C3)O)O)C)O
Canonical SMILES CACTVS 3.370 CCC(O)(CC)CS[C@@H](C)C1=CC[C@H]2/C(CCC[C@]12C)=C/C=C3C[C@@H](O)C(=CCO)[C@H](O)C3
Canonical SMILES OpenEye OEToolkits 1.7.6 CCC(CC)(CS[C@@H](C)C1=CC[C@@H]\2[C@@]1(CCC/C2=C\C=C3C[C@H](C(=CCO)[C@@H](C3)O)O)C)O

IUPAC InChI

InChI=1S/C28H44O4S/c1-5-28(32,6-2)18-33-19(3)23-11-12-24-21(8-7-14-27(23,24)4)10-9-20-16-25(30)22(13-15-29)26(31)17-20/h9-11,13,19,24-26,29-32H,5-8,12,14-18H2,1-4H3/b20-9-,21-10+,22-13+/t19-,24-,25+,26+,27+/m0/s1

IUPAC InChI key

PIRFBNFXEQEXIT-XXUXJEHWSA-N
5YI

wwPDB Information

Atom count

77 (33 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-06-04

Last modified at

2013-05-17

Status

Released

Obsoleted

Not Assigned



5YI : Atoms of Molecule

Total Number of Atoms: 77
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C12 C C12 N N N 0 -1.249 3.01 -0.233
2 C13 C C13 S N N 0 -1.14 1.516 -0.154
3 C14 C C14 S N N 0 -0.102 1.155 0.946
4 C15 C C15 N N N 0 -0.357 -0.353 1.0
5 C16 C C16 N N N 0 -1.863 -0.441 0.771
6 C21 C C21 N N N 0 -4.254 2.081 0.637
7 C23 C C23 N N N 0 -6.371 -0.063 -0.561
8 C24 C C24 N N N 0 -7.352 -1.223 -0.383
9 C29 C C29 N N N 0 -7.873 -0.518 1.956
10 C27 C C27 N N N 0 -7.361 -1.664 1.082
11 C26 C C26 N N N 0 -8.757 -0.769 -0.788
12 C28 C C28 N N N 0 -9.759 -1.888 -0.493
13 O03 O O03 N N N 0 -6.95 -2.319 -1.208
14 S22 S S22 N N N 0 -4.74 -0.55 0.067
15 C20 C C20 S N N 0 -3.732 0.93 -0.226
16 C17 C C17 N N N 0 -2.298 0.641 0.137
17 C18 C C18 N N N 0 -0.534 1.036 -1.474
18 C11 C C11 N N N 0 0.087 3.542 -0.782
19 C09 C C09 N N N 0 1.273 3.11 0.077
20 C08 C C08 N N N 0 1.208 1.636 0.393
21 C07 C C07 N N N 0 2.239 0.827 0.175
22 C06 C C06 N N N 0 3.536 1.384 -0.24
23 C05 C C05 N N N 0 4.537 0.571 -0.56
24 C10 C C10 N N N 0 5.913 1.122 -0.853
25 C01 C C01 R N N 0 6.925 0.431 0.071
26 O01 O O01 N N N 0 6.731 0.878 1.414
27 C04 C C04 N N N 0 4.32 -0.924 -0.632
28 C03 C C03 R N N 0 5.335 -1.61 0.292
29 O02 O O02 N N N 0 5.322 -3.02 0.055
30 C02 C C02 N N N 0 6.706 -1.063 -0.007
31 C30 C C30 N N N 0 7.693 -1.865 -0.323
32 C31 C C31 N N N 0 9.093 -1.323 -0.452
33 O04 O O04 N N N 0 10.002 -2.181 0.241
34 H1 H H1 N N N 0 -2.062 3.287 -0.904
35 H2 H H2 N N N 0 -1.432 3.421 0.76
36 H3 H H3 N N N 0 -0.333 1.634 1.898
37 H4 H H4 N N N 0 0.186 -0.866 0.206
38 H5 H H5 N N N 0 -0.089 -0.757 1.976
39 H6 H H6 N N N 0 -2.487 -1.267 1.08
40 H8 H H8 N N N 0 -4.194 1.803 1.689
41 H9 H H9 N N N 0 -3.648 2.97 0.461
42 H10 H H10 N N N 0 -5.291 2.29 0.374
43 H11 H H11 N N N 0 -6.293 0.188 -1.619
44 H12 H H12 N N N 0 -6.729 0.804 -0.007
45 H13 H H13 N N N 0 -7.948 -0.856 2.99
46 H14 H H14 N N N 0 -7.181 0.321 1.897
47 H15 H H15 N N N 0 -8.856 -0.204 1.605
48 H16 H H16 N N N 0 -8.014 -2.529 1.197
49 H17 H H17 N N N 0 -6.349 -1.93 1.387
50 H18 H H18 N N N 0 -9.028 0.121 -0.22
51 H19 H H19 N N N 0 -8.772 -0.539 -1.853
52 H20 H H20 N N N 0 -9.487 -2.778 -1.06
53 H21 H H21 N N N 0 -9.744 -2.117 0.572
54 H22 H H22 N N N 0 -10.759 -1.564 -0.781
55 H23 H H23 N N N 0 -6.922 -2.11 -2.152
56 H24 H H24 N N N 0 -3.792 1.208 -1.278
57 H26 H H26 N N N 0 -1.214 1.269 -2.293
58 H27 H H27 N N N 0 0.42 1.538 -1.639
59 H28 H H28 N N N 0 -0.374 -0.042 -1.43
60 H29 H H29 N N N 0 0.229 3.167 -1.796
61 H30 H H30 N N N 0 0.05 4.631 -0.81
62 H31 H H31 N N N 0 2.199 3.328 -0.455
63 H32 H H32 N N N 0 1.259 3.667 1.014
64 H33 H H33 N N N 0 2.126 -0.239 0.303
65 H34 H H34 N N N 0 3.675 2.454 -0.284
66 H35 H H35 N N N 0 6.173 0.924 -1.893
67 H36 H H36 N N N 0 5.923 2.197 -0.671
68 H37 H H37 N N N 0 7.938 0.67 -0.252
69 H38 H H38 N N N 0 6.844 1.832 1.532
70 H39 H H39 N N N 0 3.308 -1.163 -0.305
71 H40 H H40 N N N 0 4.464 -1.266 -1.656
72 H41 H H41 N N N 0 5.076 -1.412 1.332
73 H42 H H42 N N N 0 4.465 -3.438 0.214
74 H43 H H43 N N N 0 7.503 -2.914 -0.491
75 H44 H H44 N N N 0 9.369 -1.276 -1.505
76 H45 H H45 N N N 0 9.137 -0.323 -0.02
77 H46 H H46 N N N 0 10.924 -1.892 0.2



5YI : Chemical Bonds

Total Number of Bonds: 79
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O04 C31 O C sing 1.43 N N
2 C31 C30 C C sing 1.51 N N
3 C30 C02 C C doub 1.31 Z N
4 O01 C01 O C sing 1.43 N N
5 C02 C01 C C sing 1.51 N N
6 C02 C03 C C sing 1.51 N N
7 C01 C10 C C sing 1.53 N N
8 C03 O02 C O sing 1.43 N N
9 C03 C04 C C sing 1.53 N N
10 C10 C05 C C sing 1.51 N N
11 C04 C05 C C sing 1.51 N N
12 C05 C06 C C doub 1.33 Z N
13 C06 C07 C C sing 1.47 N N
14 C07 C08 C C doub 1.33 E N
15 C08 C14 C C sing 1.5 N N
16 C08 C09 C C sing 1.51 N N
17 C15 C14 C C sing 1.53 N N
18 C15 C16 C C sing 1.53 N N
19 C28 C26 C C sing 1.53 N N
20 C14 C13 C C sing 1.55 N N
21 C18 C13 C C sing 1.53 N N
22 C09 C11 C C sing 1.53 N N
23 C16 C17 C C doub 1.33 N N
24 C26 C24 C C sing 1.53 N N
25 C13 C17 C C sing 1.48 N N
26 C13 C12 C C sing 1.5 N N
27 C11 C12 C C sing 1.54 N N
28 C17 C20 C C sing 1.51 N N
29 C23 C24 C C sing 1.53 N N
30 C23 S22 C S sing 1.81 N N
31 C24 O03 C O sing 1.43 N N
32 C24 C27 C C sing 1.53 N N
33 C29 C27 C C sing 1.53 N N
34 C20 S22 C S sing 1.81 N N
35 C20 C21 C C sing 1.53 N N
36 C12 H1 C H sing 1.09 N N
37 C12 H2 C H sing 1.09 N N
38 C14 H3 C H sing 1.09 N N
39 C15 H4 C H sing 1.09 N N
40 C15 H5 C H sing 1.09 N N
41 C16 H6 C H sing 1.08 N N
42 C21 H8 C H sing 1.09 N N
43 C21 H9 C H sing 1.09 N N
44 C21 H10 C H sing 1.09 N N
45 C23 H11 C H sing 1.09 N N
46 C23 H12 C H sing 1.09 N N
47 C29 H13 C H sing 1.09 N N
48 C29 H14 C H sing 1.09 N N
49 C29 H15 C H sing 1.09 N N
50 C27 H16 C H sing 1.09 N N
51 C27 H17 C H sing 1.09 N N
52 C26 H18 C H sing 1.09 N N
53 C26 H19 C H sing 1.09 N N
54 C28 H20 C H sing 1.09 N N
55 C28 H21 C H sing 1.09 N N
56 C28 H22 C H sing 1.09 N N
57 O03 H23 O H sing 0.97 N N
58 C20 H24 C H sing 1.09 N N
59 C18 H26 C H sing 1.09 N N
60 C18 H27 C H sing 1.09 N N
61 C18 H28 C H sing 1.09 N N
62 C11 H29 C H sing 1.09 N N
63 C11 H30 C H sing 1.09 N N
64 C09 H31 C H sing 1.09 N N
65 C09 H32 C H sing 1.09 N N
66 C07 H33 C H sing 1.08 N N
67 C06 H34 C H sing 1.08 N N
68 C10 H35 C H sing 1.09 N N
69 C10 H36 C H sing 1.09 N N
70 C01 H37 C H sing 1.09 N N
71 O01 H38 O H sing 0.97 N N
72 C04 H39 C H sing 1.09 N N
73 C04 H40 C H sing 1.09 N N
74 C03 H41 C H sing 1.09 N N
75 O02 H42 O H sing 0.97 N N
76 C30 H43 C H sing 1.08 N N
77 C31 H44 C H sing 1.09 N N
78 C31 H45 C H sing 1.09 N N
79 O04 H46 O H sing 0.97 N N



5YI : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
5YI 3vt4 Open in New Window Bound ligand 1 1
5YI 3vt6 Open in New Window Bound ligand 1 1