Chemical Components in the PDB

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YI4 : Summary

Code

YI4

One-letter code

X

Molecule name

(1R,2Z,3R,5E,7E,9beta,17beta)-2-(2-hydroxyethylidene)-17-[(2R)-6-hydroxy-6-methylheptan-2-yl]-9-(prop-2-en-1-yl)-9,10-secoestra-5,7-diene-1,3-diol

Systematic names

ProgramVersionName
ACDLabs 12.01 (1R,2Z,3R,5E,7E,9beta,17beta)-2-(2-hydroxyethylidene)-17-[(2R)-6-hydroxy-6-methylheptan-2-yl]-9-(prop-2-en-1-yl)-9,10-secoestra-5,7-diene-1,3-diol
OpenEye OEToolkits 1.7.6 (1R,3R)-5-[(2E)-2-[(1R,3aR,5S,7aR)-7a-methyl-1-[(2R)-6-methyl-6-oxidanyl-heptan-2-yl]-5-prop-2-enyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-2-(2-oxidanylethylidene)cyclohexane-1,3-diol

Formula

C31 H50 O4

Formal charge

0

Molecular weight

486.726 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 OC3C(=C\CO)\C(O)C\C(=C\C=C1/C(C/C=C)CCC2(C)C(C(C)CCCC(O)(C)C)CCC12)C3
SMILES CACTVS 3.370 C[CH](CCCC(C)(C)O)[CH]1CC[CH]2C(=CC=C3C[CH](O)C(=CCO)[CH](O)C3)[CH](CC[C]12C)CC=C
SMILES OpenEye OEToolkits 1.7.6 CC(CCCC(C)(C)O)C1CCC2C1(CCC(C2=CC=C3CC(C(=CCO)C(C3)O)O)CC=C)C
Canonical SMILES CACTVS 3.370 C[C@H](CCCC(C)(C)O)[C@H]1CC[C@H]2/C(=C/C=C3C[C@@H](O)C(=CCO)[C@H](O)C3)[C@@H](CC[C@]12C)CC=C
Canonical SMILES OpenEye OEToolkits 1.7.6 C[C@H](CCCC(C)(C)O)[C@H]1CC[C@@H]\2[C@@]1(CC[C@H](/C2=C\C=C3C[C@H](C(=CCO)[C@@H](C3)O)O)CC=C)C

IUPAC InChI

InChI=1S/C31H50O4/c1-6-8-23-14-17-31(5)26(21(2)9-7-16-30(3,4)35)12-13-27(31)24(23)11-10-22-19-28(33)25(15-18-32)29(34)20-22/h6,10-11,15,21,23,26-29,32-35H,1,7-9,12-14,16-20H2,2-5H3/b22-10-,24-11+,25-15+/t21-,23-,26-,27+,28-,29-,31-/m1/s1

IUPAC InChI key

VQPYCEUJPLIUFQ-ZVOFGSMJSA-N
YI4

wwPDB Information

Atom count

85 (35 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-06-06

Last modified at

2013-05-17

Status

Released

Obsoleted

Not Assigned



YI4 : Atoms of Molecule

Total Number of Atoms: 85
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C01 C C01 R N N 0 -6.219 -0.335 0.477
2 C02 C C02 N N N 0 -5.932 -1.748 0.023
3 C03 C C03 R N N 0 -4.617 -2.037 -0.653
4 C04 C C04 N N N 0 -3.479 -1.584 0.271
5 C05 C C05 N N N 0 -3.764 -0.172 0.73
6 C06 C C06 N N N 0 -2.872 0.794 0.54
7 C07 C C07 N N N 0 -1.667 0.534 -0.264
8 C08 C C08 N N N 0 -0.712 1.455 -0.346
9 C09 C C09 S N N 0 -0.809 2.795 0.369
10 C10 C C10 N N N 0 -5.085 0.123 1.403
11 C11 C C11 N N N 0 0.465 3.079 1.163
12 C12 C C12 N N N 0 1.728 2.848 0.316
13 C13 C C13 R N N 0 1.712 1.408 -0.141
14 C14 C C14 R N N 0 0.537 1.247 -1.149
15 C15 C C15 N N N 0 0.787 -0.167 -1.679
16 C16 C C16 N N N 0 2.329 -0.192 -1.877
17 C17 C C17 R N N 0 2.909 0.881 -0.919
18 C18 C C18 N N N 0 1.463 0.507 1.07
19 C20 C C20 R N N 0 3.925 0.249 0.034
20 C21 C C21 N N N 0 4.432 1.308 1.015
21 C22 C C22 N N N 0 5.102 -0.306 -0.771
22 C23 C C23 N N N 0 6.057 -1.047 0.168
23 C24 C C24 N N N 0 7.234 -1.602 -0.637
24 C25 C C25 N N N 0 8.189 -2.343 0.301
25 C26 C C26 N N N 0 8.612 -1.411 1.438
26 C27 C C27 N N N 0 9.427 -2.79 -0.48
27 C28 C C28 N N N 0 -1.015 3.903 -0.666
28 C29 C C29 N N N 0 -1.265 5.21 0.04
29 C30 C C30 N N N 0 -0.515 6.252 -0.224
30 C32 C C32 N N N 0 -6.812 -2.7 0.21
31 C33 C C33 N N N 0 -8.184 -2.365 0.735
32 H1 H H1 N N N 0 8.077 -4.007 1.449
33 H10 H H10 N N N 0 5.527 -1.869 0.65
34 H11 H H11 N N N 0 6.428 -0.359 0.927
35 H12 H H12 N N N 0 5.632 0.516 -1.253
36 H13 H H13 N N N 0 4.731 -0.994 -1.53
37 H14 H H14 N N N 0 3.449 -0.561 0.587
38 H15 H H15 N N N 0 4.907 2.117 0.462
39 H16 H H16 N N N 0 3.593 1.702 1.589
40 H17 H H17 N N N 0 5.155 0.857 1.694
41 H18 H H18 N N N 0 3.374 1.686 -1.488
42 H19 H H19 N N N 0 2.577 0.055 -2.909
43 H2 H H2 N N N 0 9.292 -1.939 2.106
44 H20 H H20 N N N 0 2.724 -1.175 -1.622
45 H21 H H21 N N N 0 0.272 -0.32 -2.628
46 H22 H H22 N N N 0 0.48 -0.913 -0.947
47 H23 H H23 N N N 0 0.613 1.98 -1.953
48 H24 H H24 N N N 0 1.537 -0.538 0.767
49 H25 H H25 N N N 0 2.208 0.716 1.838
50 H26 H H26 N N N 0 0.467 0.701 1.468
51 H27 H H27 N N N 0 2.617 3.034 0.919
52 H28 H H28 N N N 0 1.722 3.511 -0.548
53 H29 H H29 N N N 0 0.495 2.423 2.033
54 H3 H H3 N N N 0 9.115 -0.538 1.024
55 H30 H H30 N N N 0 0.448 4.115 1.5
56 H31 H H31 N N N 0 -1.66 2.777 1.05
57 H32 H H32 N N N 0 -0.123 3.99 -1.287
58 H33 H H33 N N N 0 -1.872 3.659 -1.293
59 H35 H H35 N N N 0 -2.062 5.289 0.765
60 H36 H H36 N N N 0 0.282 6.173 -0.949
61 H37 H H37 N N N 0 -0.695 7.188 0.282
62 H39 H H39 N N N 0 -1.559 -0.404 -0.787
63 H4 H H4 N N N 0 7.731 -1.093 1.994
64 H40 H H40 N N N 0 -3.03 1.769 0.976
65 H41 H H41 N N N 0 -5.143 -0.419 2.347
66 H42 H H42 N N N 0 -5.17 1.193 1.589
67 H43 H H43 N N N 0 -7.166 -0.309 1.017
68 H44 H H44 N N N 0 -6.461 1.457 -0.436
69 H45 H H45 N N N 0 -2.534 -1.609 -0.273
70 H46 H H46 N N N 0 -3.421 -2.245 1.135
71 H47 H H47 N N N 0 -4.559 -1.496 -1.597
72 H48 H H48 N N N 0 -3.675 -3.702 -1.321
73 H49 H H49 N N N 0 -6.553 -3.725 -0.011
74 H5 H H5 N N N 0 9.125 -3.454 -1.29
75 H50 H H50 N N N 0 -8.248 -2.642 1.787
76 H51 H H51 N N N 0 -8.363 -1.295 0.628
77 H52 H H52 N N N 0 -10.076 -2.921 0.275
78 H6 H H6 N N N 0 9.93 -1.916 -0.894
79 H7 H H7 N N N 0 10.107 -3.318 0.188
80 H8 H H8 N N N 0 7.764 -0.78 -1.12
81 H9 H H9 N N N 0 6.863 -2.29 -1.396
82 O01 O O01 N N N 0 -6.291 0.532 -0.658
83 O02 O O02 N N N 0 -4.505 -3.441 -0.898
84 O03 O O03 N N N 0 7.529 -3.488 0.844
85 O04 O O04 N N N 0 -9.167 -3.089 -0.0090



YI4 : Chemical Bonds

Total Number of Bonds: 87
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O04 C33 O C sing 1.43 N N
2 C33 C32 C C sing 1.51 N N
3 C32 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 C15 C14 C C sing 1.53 N N
16 C15 C16 C C sing 1.55 N N
17 C08 C14 C C sing 1.5 N N
18 C08 C09 C C sing 1.52 N N
19 C14 C13 C C sing 1.56 N N
20 C18 C13 C C sing 1.53 N N
21 C16 C17 C C sing 1.55 N N
22 C09 C28 C C sing 1.53 N N
23 C09 C11 C C sing 1.53 N N
24 C28 C29 C C sing 1.51 N N
25 C13 C17 C C sing 1.52 N N
26 C13 C12 C C sing 1.51 N N
27 C27 C25 C C sing 1.53 N N
28 C29 C30 C C doub 1.31 N N
29 C17 C20 C C sing 1.53 N N
30 C24 C25 C C sing 1.53 N N
31 C24 C23 C C sing 1.53 N N
32 C11 C12 C C sing 1.54 N N
33 C22 C23 C C sing 1.53 N N
34 C22 C20 C C sing 1.53 N N
35 C25 O03 C O sing 1.43 N N
36 C25 C26 C C sing 1.53 N N
37 C20 C21 C C sing 1.53 N N
38 O03 H1 O H sing 0.97 N N
39 C26 H2 C H sing 1.09 N N
40 C26 H3 C H sing 1.09 N N
41 C26 H4 C H sing 1.09 N N
42 C27 H5 C H sing 1.09 N N
43 C27 H6 C H sing 1.09 N N
44 C27 H7 C H sing 1.09 N N
45 C24 H8 C H sing 1.09 N N
46 C24 H9 C H sing 1.09 N N
47 C23 H10 C H sing 1.09 N N
48 C23 H11 C H sing 1.09 N N
49 C22 H12 C H sing 1.09 N N
50 C22 H13 C H sing 1.09 N N
51 C20 H14 C H sing 1.09 N N
52 C21 H15 C H sing 1.09 N N
53 C21 H16 C H sing 1.09 N N
54 C21 H17 C H sing 1.09 N N
55 C17 H18 C H sing 1.09 N N
56 C16 H19 C H sing 1.09 N N
57 C16 H20 C H sing 1.09 N N
58 C15 H21 C H sing 1.09 N N
59 C15 H22 C H sing 1.09 N N
60 C14 H23 C H sing 1.09 N N
61 C18 H24 C H sing 1.09 N N
62 C18 H25 C H sing 1.09 N N
63 C18 H26 C H sing 1.09 N N
64 C12 H27 C H sing 1.09 N N
65 C12 H28 C H sing 1.09 N N
66 C11 H29 C H sing 1.09 N N
67 C11 H30 C H sing 1.09 N N
68 C09 H31 C H sing 1.09 N N
69 C28 H32 C H sing 1.09 N N
70 C28 H33 C H sing 1.09 N N
71 C29 H35 C H sing 1.08 N N
72 C30 H36 C H sing 1.08 N N
73 C30 H37 C H sing 1.08 N N
74 C07 H39 C H sing 1.08 N N
75 C06 H40 C H sing 1.08 N N
76 C10 H41 C H sing 1.09 N N
77 C10 H42 C H sing 1.09 N N
78 C01 H43 C H sing 1.09 N N
79 O01 H44 O H sing 0.97 N N
80 C04 H45 C H sing 1.09 N N
81 C04 H46 C H sing 1.09 N N
82 C03 H47 C H sing 1.09 N N
83 O02 H48 O H sing 0.97 N N
84 C32 H49 C H sing 1.08 N N
85 C33 H50 C H sing 1.09 N N
86 C33 H51 C H sing 1.09 N N
87 O04 H52 O H sing 0.97 N N



YI4 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
YI4 3vt9 Open in New Window Bound ligand 1 1