Chemical Components in the PDB

pdbe.org/chem
spacer

YI3 : Summary

Code

YI3

One-letter code

X

Molecule name

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

Systematic names

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

Formula

C30 H52 O3

Formal charge

0

Molecular weight

460.732 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 OC3CC(=C/C=C1\C(CCCC)CCC2(C)C(C(C)CCCC(O)(C)C)CCC12)\CC(O)C3
SMILES CACTVS 3.370 CCCC[CH]1CC[C]2(C)[CH](CC[CH]2C1=C[CH]=[C]3C[CH](O)[CH2][CH](O)C3)[CH](C)CCCC(C)(C)O
SMILES OpenEye OEToolkits 1.7.6 CCCCC1CCC2(C(C1=CC=C3CC(CC(C3)O)O)CCC2C(C)CCCC(C)(C)O)C
Canonical SMILES CACTVS 3.370 CCCC[C@@H]1CC[C@]2(C)[C@H](CC[C@H]2/C1=C/[CH]=[C@@]3C[C@@H](O)[CH2][C@H](O)C3)[C@H](C)CCCC(C)(C)O
Canonical SMILES OpenEye OEToolkits 1.7.6 CCCC[C@@H]\1CC[C@]2([C@H](/C1=C/C=C3C[C@H](C[C@@H](C3)O)O)CC[C@@H]2[C@H](C)CCCC(C)(C)O)C

IUPAC InChI

InChI=1S/C30H52O3/c1-6-7-10-23-15-17-30(5)27(21(2)9-8-16-29(3,4)33)13-14-28(30)26(23)12-11-22-18-24(31)20-25(32)19-22/h11-12,21,23-25,27-28,31-33H,6-10,13-20H2,1-5H3/b26-12+/t21-,23-,24-,25-,27-,28+,30-/m1/s1

IUPAC InChI key

HGPWGYLACPHOSW-ZOBUFXTASA-N
YI3

wwPDB Information

Atom count

85 (33 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-06-06

Last modified at

2013-05-17

Status

Released

Obsoleted

Not Assigned



YI3 : 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 6.569 2.233 0.688
2 C02 C C02 N N N 0 6.069 3.629 0.329
3 C03 C C03 R N N 0 4.803 3.521 -0.523
4 C04 C C04 N N N 0 3.69 2.864 0.301
5 C05 C C05 N N N 0 4.199 1.543 0.831
6 C06 C C06 N N N 0 3.503 0.425 0.658
7 C07 C C07 N N N 0 2.283 0.438 -0.165
8 C08 C C08 N N N 0 1.53 -0.652 -0.253
9 C09 C C09 R N N 0 1.876 -1.944 0.474
10 C10 C C10 N N N 0 5.525 1.525 1.559
11 C11 C C11 N N N 0 0.67 -2.468 1.251
12 C12 C C12 N N N 0 -0.6 -2.494 0.385
13 C13 C C13 R N N 0 -0.86 -1.082 -0.085
14 C14 C C14 R N N 0 0.277 -0.699 -1.077
15 C15 C C15 N N N 0 -0.237 0.636 -1.622
16 C16 C C16 N N N 0 -1.751 0.357 -1.842
17 C17 C C17 R N N 0 -2.124 -0.804 -0.883
18 C18 C C18 N N N 0 -0.812 -0.143 1.123
19 C20 C C20 R N N 0 -3.26 -0.379 0.049
20 C21 C C21 N N N 0 -3.564 -1.511 1.032
21 C22 C C22 N N N 0 -4.51 -0.07 -0.777
22 C23 C C23 N N N 0 -5.606 0.474 0.141
23 C24 C C24 N N N 0 -6.857 0.782 -0.685
24 C25 C C25 N N N 0 -7.953 1.327 0.233
25 C26 C C26 N N N 0 -9.203 1.635 -0.593
26 C27 C C27 N N N 0 -7.461 2.607 0.911
27 C28 C C28 N N N 0 2.312 -2.995 -0.549
28 C29 C C29 N N N 0 2.81 -4.243 0.183
29 C30 C C30 N N N 0 3.246 -5.294 -0.84
30 C31 C C31 N N N 0 3.744 -6.542 -0.109
31 H1 H H1 N N N 0 -8.587 -0.488 0.87
32 H10 H H10 N N N 0 -5.256 1.386 0.624
33 H11 H H11 N N N 0 -5.847 -0.27 0.901
34 H12 H H12 N N N 0 -4.86 -0.982 -1.26
35 H13 H H13 N N N 0 -4.269 0.674 -1.536
36 H14 H H14 N N N 0 -2.961 0.512 0.603
37 H15 H H15 N N N 0 -2.673 -1.731 1.621
38 H16 H H16 N N N 0 -4.373 -1.208 1.697
39 H17 H H17 N N N 0 -3.863 -2.401 0.479
40 H18 H H18 N N N 0 -2.414 -1.687 -1.453
41 H19 H H19 N N N 0 -1.93 0.061 -2.876
42 H2 H H2 N N N 0 -9.984 2.023 0.061
43 H20 H H20 N N N 0 -2.335 1.244 -1.601
44 H21 H H21 N N N 0 0.252 0.882 -2.564
45 H22 H H22 N N N 0 -0.095 1.432 -0.891
46 H23 H H23 N N N 0 0.359 -1.436 -1.875
47 H24 H H24 N N N 0 -1.081 0.866 0.809
48 H25 H H25 N N N 0 -1.515 -0.488 1.88
49 H26 H H26 N N N 0 0.196 -0.138 1.539
50 H27 H H27 N N N 0 -1.444 -2.848 0.976
51 H28 H H28 N N N 0 -0.45 -3.148 -0.474
52 H29 H H29 N N N 0 0.498 -1.826 2.115
53 H3 H H3 N N N 0 -8.963 2.379 -1.352
54 H30 H H30 N N N 0 0.885 -3.479 1.597
55 H31 H H31 N N N 0 2.696 -1.756 1.167
56 H32 H H32 N N N 0 1.465 -3.259 -1.182
57 H33 H H33 N N N 0 3.115 -2.591 -1.166
58 H34 H H34 N N N 0 3.657 -3.979 0.816
59 H35 H H35 N N N 0 2.007 -4.647 0.799
60 H36 H H36 N N N 0 2.399 -5.558 -1.474
61 H37 H H37 N N N 0 4.049 -4.89 -1.457
62 H38 H H38 N N N 0 4.055 -7.291 -0.837
63 H39 H H39 N N N 0 4.591 -6.278 0.525
64 H4 H H4 N N N 0 -9.554 0.723 -1.076
65 H40 H H40 N N N 0 2.941 -6.946 0.508
66 H41 H H41 N N N 0 2.001 1.334 -0.698
67 H42 H H42 N N N 0 3.831 -0.494 1.121
68 H43 H H43 N N N 0 5.428 2.048 2.51
69 H44 H H44 N N N 0 5.832 0.495 1.738
70 H45 H H45 N N N 0 2.819 2.694 -0.332
71 H46 H H46 N N N 0 3.416 3.512 1.133
72 H47 H H47 N N N 0 5.009 2.914 -1.404
73 H48 H H48 N N N 0 3.59 4.833 -1.474
74 H49 H H49 N N N 0 6.838 4.156 -0.235
75 H5 H H5 N N N 0 -8.243 2.995 1.565
76 H50 H H50 N N N 0 5.85 4.181 1.244
77 H51 H H51 N N N 0 7.505 2.312 1.241
78 H52 H H52 N N N 0 7.103 0.582 -0.357
79 H6 H H6 N N N 0 -6.571 2.387 1.5
80 H7 H H7 N N N 0 -7.221 3.351 0.152
81 H8 H H8 N N N 0 -7.207 -0.13 -1.168
82 H9 H H9 N N N 0 -6.616 1.526 -1.444
83 O01 O O01 N N N 0 6.784 1.482 -0.509
84 O02 O O02 N N N 0 4.389 4.826 -0.929
85 O03 O O03 N N N 0 -8.269 0.351 1.229



YI3 : 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 O01 C01 O C sing 1.43 N N
2 C02 C01 C C sing 1.53 N N
3 C02 C03 C C sing 1.53 N N
4 C01 C10 C C sing 1.53 N N
5 C03 O02 C O sing 1.43 N N
6 C03 C04 C C sing 1.53 N N
7 C10 C05 C C sing 1.51 N N
8 C04 C05 C C sing 1.51 N N
9 C05 C06 C C doub 1.33 N N
10 C06 C07 C C sing 1.47 N N
11 C07 C08 C C doub 1.33 E N
12 C15 C14 C C sing 1.53 N N
13 C15 C16 C C sing 1.56 N N
14 C08 C14 C C sing 1.5 N N
15 C08 C09 C C sing 1.52 N N
16 C18 C13 C C sing 1.53 N N
17 C14 C13 C C sing 1.56 N N
18 C16 C17 C C sing 1.55 N N
19 C09 C28 C C sing 1.53 N N
20 C09 C11 C C sing 1.53 N N
21 C29 C30 C C sing 1.53 N N
22 C29 C28 C C sing 1.53 N N
23 C30 C31 C C sing 1.53 N N
24 C13 C17 C C sing 1.52 N N
25 C13 C12 C C sing 1.51 N N
26 C27 C25 C C sing 1.53 N N
27 C24 C25 C C sing 1.53 N N
28 C24 C23 C C sing 1.53 N N
29 C11 C12 C C sing 1.54 N N
30 C17 C20 C C sing 1.53 N N
31 C22 C23 C C sing 1.53 N N
32 C22 C20 C C sing 1.53 N N
33 C25 C26 C C sing 1.53 N N
34 C25 O03 C O sing 1.43 N N
35 C20 C21 C C sing 1.53 N N
36 O03 H1 O H sing 0.97 N N
37 C26 H2 C H sing 1.09 N N
38 C26 H3 C H sing 1.09 N N
39 C26 H4 C H sing 1.09 N N
40 C27 H5 C H sing 1.09 N N
41 C27 H6 C H sing 1.09 N N
42 C27 H7 C H sing 1.09 N N
43 C24 H8 C H sing 1.09 N N
44 C24 H9 C H sing 1.09 N N
45 C23 H10 C H sing 1.09 N N
46 C23 H11 C H sing 1.09 N N
47 C22 H12 C H sing 1.09 N N
48 C22 H13 C H sing 1.09 N N
49 C20 H14 C H sing 1.09 N N
50 C21 H15 C H sing 1.09 N N
51 C21 H16 C H sing 1.09 N N
52 C21 H17 C H sing 1.09 N N
53 C17 H18 C H sing 1.09 N N
54 C16 H19 C H sing 1.09 N N
55 C16 H20 C H sing 1.09 N N
56 C15 H21 C H sing 1.09 N N
57 C15 H22 C H sing 1.09 N N
58 C14 H23 C H sing 1.09 N N
59 C18 H24 C H sing 1.09 N N
60 C18 H25 C H sing 1.09 N N
61 C18 H26 C H sing 1.09 N N
62 C12 H27 C H sing 1.09 N N
63 C12 H28 C H sing 1.09 N N
64 C11 H29 C H sing 1.09 N N
65 C11 H30 C H sing 1.09 N N
66 C09 H31 C H sing 1.09 N N
67 C28 H32 C H sing 1.09 N N
68 C28 H33 C H sing 1.09 N N
69 C29 H34 C H sing 1.09 N N
70 C29 H35 C H sing 1.09 N N
71 C30 H36 C H sing 1.09 N N
72 C30 H37 C H sing 1.09 N N
73 C31 H38 C H sing 1.09 N N
74 C31 H39 C H sing 1.09 N N
75 C31 H40 C H sing 1.09 N N
76 C07 H41 C H sing 1.08 N N
77 C06 H42 C H sing 1.08 N N
78 C10 H43 C H sing 1.09 N N
79 C10 H44 C H sing 1.09 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 C02 H49 C H sing 1.09 N N
85 C02 H50 C H sing 1.09 N N
86 C01 H51 C H sing 1.09 N N
87 O01 H52 O H sing 0.97 N N



YI3 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
YI3 3vt8 Open in New Window Bound ligand 1 1