Chemical Components in the PDB

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O1U : Summary

Code

O1U

One-letter code

X

Molecule name

(2~{Z},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E},16~{E})-4,8,13,17-tetramethyl-3-oxidanyl-19-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]-1-[(1~{R},4~{S})-1,2,2-trimethyl-4-oxidanyl-cyclopentyl]nonadeca-2,4,6,8,10,12,14,16-octaen-18-yn-1-one

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 (2~{Z},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E},16~{E})-4,8,13,17-tetramethyl-3-oxidanyl-19-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]-1-[(1~{R},4~{S})-1,2,2-trimethyl-4-oxidanyl-cyclopentyl]nonadeca-2,4,6,8,10,12,14,16-octaen-18-yn-1-one

Formula

C40 H54 O4

Formal charge

0

Molecular weight

598.854 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CC(=CC=CC=C(C)C=CC=C(C)C(O)=CC(=O)[C]1(C)C[CH](O)CC1(C)C)C=CC=C(C)C#CC2=C(C)C[CH](O)CC2(C)C
SMILES OpenEye OEToolkits 2.0.7 CC1=C(C(CC(C1)O)(C)C)C#CC(=CC=CC(=CC=CC=C(C)C=CC=C(C)C(=CC(=O)C2(CC(CC2(C)C)O)C)O)C)C
Canonical SMILES CACTVS 3.385 CC(=C/C=C/C=C(C)/C=C/C=C(C)/C(O)=C/C(=O)[C@]1(C)C[C@@H](O)CC1(C)C)\C=C\C=C(C)\C#CC2=C(C)C[C@@H](O)CC2(C)C
Canonical SMILES OpenEye OEToolkits 2.0.7 CC1=C(C(C[C@@H](C1)O)(C)C)C#C/C(=C/C=C/C(=C/C=C/C=C(\C)/C=C/C=C(\C)/C(=C/C(=O)[C@@]2(C[C@H](CC2(C)C)O)C)/O)/C)/C

IUPAC InChI

InChI=1S/C40H54O4/c1-28(17-13-18-30(3)21-22-35-32(5)23-33(41)25-38(35,6)7)15-11-12-16-29(2)19-14-20-31(4)36(43)24-37(44)40(10)27-34(42)26-39(40,8)9/h11-20,24,33-34,41-43H,23,25-27H2,1-10H3/b12-11+,17-13+,19-14+,28-15+,29-16+,30-18+,31-20+,36-24-/t33-,34+,40+/m1/s1

IUPAC InChI key

WSLGBPCJDUQFND-BBPSKTQQSA-N
O1U

wwPDB Information

Atom count

98 (44 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2023-01-20

Last modified at

2023-08-11

Status

Released

Obsoleted

Not Assigned



O1U : Atoms of Molecule

Total Number of Atoms: 98
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C14 C C1 N N N 0 -2.579 0.413 0.097
2 C21 C C2 N N N 0 12.031 -1.172 -1.021
3 C22 C C3 N N N 0 13.34 -0.59 -1.594
4 C23 C C4 S N N 0 13.609 0.665 -0.727
5 C24 C C5 N N N 0 13.168 0.206 0.685
6 C29 C C10 N N N 0 7.01 -0.28 0.461
7 C25 C C6 R N N 0 11.922 -0.666 0.428
8 C26 C C7 N N N 0 10.672 0.159 0.594
9 C27 C C8 N N N 0 9.424 -0.445 0.507
10 C28 C C9 N N N 0 8.271 0.331 0.548
11 C11 C C11 N N N 0 -6.113 1.36 -0.098
12 C12 C C12 N N N 0 -4.977 0.585 0.006
13 C3 C C16 R N N 0 -14.66 -1.385 0.285
14 C13 C C13 N N N 0 -3.716 1.188 -0.007
15 C1 C C14 N N N 0 -12.214 -1.712 -0.019
16 C2 C C15 N N N 0 -13.595 -2.214 -0.443
17 O3 O O1 N N N 0 -15.952 -1.95 0.051
18 C4 C C17 N N N 0 -14.619 0.045 -0.258
19 C5 C C18 N N N 0 -13.209 0.56 -0.251
20 C6 C C19 N N N 0 -12.144 -0.218 -0.149
21 C7 C C20 N N N 0 -10.852 0.399 -0.163
22 C8 C C21 N N N 0 -9.793 0.905 -0.174
23 C9 C C22 N N N 0 -8.501 1.523 -0.188
24 C10 C C23 N N N 0 -7.376 0.755 -0.084
25 C15 C C24 N N N 0 -1.318 1.015 0.083
26 C17 C C25 N N N 0 -11.149 -2.349 -0.913
27 C16 C C26 N N N 0 -11.956 -2.107 1.437
28 C18 C C27 N N N 0 -12.995 2.047 -0.366
29 C19 C C28 N N N 0 -8.383 3.02 -0.317
30 C20 C C29 N N N 0 -3.597 2.685 -0.136
31 O23 O O2 N N N 0 14.998 1.001 -0.739
32 O26 O O3 N N N 0 10.755 1.356 0.803
33 O28 O O4 N N N 0 8.365 1.676 0.671
34 C30 C C30 N N N 0 5.875 0.495 0.356
35 C31 C C31 N N N 0 4.614 -0.108 0.37
36 C35 C C35 N N N 0 -0.181 0.239 0.188
37 C32 C C32 N N N 0 3.477 0.668 0.266
38 C33 C C33 N N N 0 2.216 0.066 0.279
39 C34 C C34 N N N 0 1.079 0.842 0.175
40 C37 C C36 N N N 0 12.085 -2.701 -1.04
41 C36 C C37 N N N 0 10.836 -0.68 -1.84
42 C38 C C38 N N N 0 11.901 -1.85 1.396
43 C39 C C39 N N N 0 6.898 -1.782 0.482
44 C40 C C40 N N N 0 2.098 -1.431 0.408
45 H1 H H1 N N N 0 -2.664 -0.66 0.194
46 H2 H H2 N N N 0 14.154 -1.308 -1.49
47 H3 H H3 N N N 0 13.209 -0.313 -2.64
48 H4 H H4 N N N 0 13.004 1.506 -1.066
49 H5 H H5 N N N 0 13.955 -0.384 1.158
50 H6 H H6 N N N 0 12.911 1.066 1.303
51 H7 H H7 N N N 0 9.349 -1.518 0.41
52 H8 H H8 N N N 0 -6.028 2.432 -0.191
53 H9 H H9 N N N 0 -5.062 -0.488 0.098
54 H10 H H10 N N N 0 -13.713 -2.095 -1.521
55 H11 H H11 N N N 0 -13.702 -3.265 -0.174
56 H12 H H12 N N N 0 -14.45 -1.377 1.354
57 H13 H H13 N N N 0 -16.674 -1.474 0.484
58 H14 H H14 N N N 0 -15.002 0.055 -1.278
59 H15 H H15 N N N 0 -15.241 0.686 0.366
60 H16 H H16 N N N 0 -7.461 -0.317 0.008
61 H17 H H17 N N N 0 -1.234 2.088 -0.009
62 H18 H H18 N N N 0 -11.195 -3.434 -0.816
63 H19 H H19 N N N 0 -11.331 -2.069 -1.951
64 H20 H H20 N N N 0 -10.162 -1.999 -0.61
65 H21 H H21 N N N 0 -12.712 -1.65 2.076
66 H22 H H22 N N N 0 -12.007 -3.192 1.533
67 H23 H H23 N N N 0 -10.968 -1.761 1.738
68 H24 H H24 N N N 0 -13.96 2.548 -0.442
69 H25 H H25 N N N 0 -12.466 2.407 0.516
70 H26 H H26 N N N 0 -12.403 2.261 -1.257
71 H27 H H27 N N N 0 -8.387 3.471 0.675
72 H28 H H28 N N N 0 -7.452 3.268 -0.826
73 H29 H H29 N N N 0 -9.225 3.402 -0.893
74 H30 H H30 N N N 0 -3.537 2.955 -1.19
75 H31 H H31 N N N 0 -4.472 3.158 0.31
76 H32 H H32 N N N 0 -2.698 3.024 0.378
77 H33 H H33 N N N 0 15.219 1.78 -0.211
78 H34 H H34 N N N 0 7.516 2.136 0.613
79 H35 H H35 N N N 0 5.96 1.568 0.264
80 H36 H H36 N N N 0 4.529 -1.18 0.462
81 H37 H H37 N N N 0 3.562 1.741 0.173
82 H38 H H38 N N N 0 1.164 1.914 0.082
83 H39 H H39 N N N 0 -0.266 -0.833 0.28
84 H40 H H40 N N N 0 11.177 -3.102 -0.588
85 H41 H H41 N N N 0 12.162 -3.049 -2.07
86 H42 H H42 N N N 0 12.953 -3.041 -0.476
87 H43 H H43 N N N 0 10.737 0.4 -1.725
88 H44 H H44 N N N 0 10.991 -0.921 -2.891
89 H45 H H45 N N N 0 9.927 -1.167 -1.486
90 H46 H H46 N N N 0 12.82 -2.426 1.286
91 H47 H H47 N N N 0 11.823 -1.482 2.419
92 H48 H H48 N N N 0 11.045 -2.487 1.173
93 H49 H H49 N N N 0 6.951 -2.165 -0.538
94 H50 H H50 N N N 0 7.715 -2.2 1.07
95 H51 H H51 N N N 0 5.946 -2.069 0.928
96 H52 H H52 N N N 0 2.037 -1.701 1.462
97 H53 H H53 N N N 0 1.199 -1.77 -0.107
98 H54 H H54 N N N 0 2.973 -1.904 -0.039



O1U : Chemical Bonds

Total Number of Bonds: 99
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C17 C1 C C sing 1.53 N N
2 C36 C21 C C sing 1.53 N N
3 C23 C22 C C sing 1.55 N N
4 C23 C24 C C sing 1.55 N N
5 C23 O23 C O sing 1.43 N N
6 C2 C1 C C sing 1.53 N N
7 C2 C3 C C sing 1.53 N N
8 C22 C21 C C sing 1.54 N N
9 C39 C29 C C sing 1.51 N N
10 C1 C16 C C sing 1.53 N N
11 C1 C6 C C sing 1.5 N N
12 C24 C25 C C sing 1.54 N N
13 C40 C33 C C sing 1.51 N N
14 O3 C3 O C sing 1.43 N N
15 C21 C25 C C sing 1.54 N N
16 C21 C37 C C sing 1.53 N N
17 C3 C4 C C sing 1.53 N N
18 C6 C7 C C sing 1.43 N N
19 C6 C5 C C doub 1.32 N N
20 C29 C30 C C doub 1.38 E N
21 C29 C28 C C sing 1.4 N N
22 C27 C28 C C doub 1.39 Z N
23 C27 C26 C C sing 1.39 N N
24 C7 C8 C C trip 1.17 N N
25 C31 C30 C C sing 1.4 N N
26 C31 C32 C C doub 1.38 E N
27 C8 C9 C C sing 1.43 N N
28 C33 C32 C C sing 1.4 N N
29 C33 C34 C C doub 1.38 E N
30 C25 C26 C C sing 1.51 N N
31 C25 C38 C C sing 1.53 N N
32 C9 C19 C C sing 1.51 N N
33 C9 C10 C C doub 1.37 E N
34 C28 O28 C O sing 1.35 N N
35 C10 C11 C C sing 1.4 N N
36 C35 C34 C C sing 1.4 N N
37 C35 C15 C C doub 1.38 E N
38 C4 C5 C C sing 1.5 N N
39 C26 O26 C O doub 1.22 N N
40 C12 C11 C C doub 1.38 E N
41 C12 C13 C C sing 1.4 N N
42 C5 C18 C C sing 1.51 N N
43 C14 C13 C C doub 1.38 E N
44 C14 C15 C C sing 1.4 N N
45 C13 C20 C C sing 1.51 N N
46 C14 H1 C H sing 1.08 N N
47 C22 H2 C H sing 1.09 N N
48 C22 H3 C H sing 1.09 N N
49 C23 H4 C H sing 1.09 N N
50 C24 H5 C H sing 1.09 N N
51 C24 H6 C H sing 1.09 N N
52 C27 H7 C H sing 1.08 N N
53 C11 H8 C H sing 1.08 N N
54 C12 H9 C H sing 1.08 N N
55 C2 H10 C H sing 1.09 N N
56 C2 H11 C H sing 1.09 N N
57 C3 H12 C H sing 1.09 N N
58 O3 H13 O H sing 0.97 N N
59 C4 H14 C H sing 1.09 N N
60 C4 H15 C H sing 1.09 N N
61 C10 H16 C H sing 1.08 N N
62 C15 H17 C H sing 1.08 N N
63 C17 H18 C H sing 1.09 N N
64 C17 H19 C H sing 1.09 N N
65 C17 H20 C H sing 1.09 N N
66 C16 H21 C H sing 1.09 N N
67 C16 H22 C H sing 1.09 N N
68 C16 H23 C H sing 1.09 N N
69 C18 H24 C H sing 1.09 N N
70 C18 H25 C H sing 1.09 N N
71 C18 H26 C H sing 1.09 N N
72 C19 H27 C H sing 1.09 N N
73 C19 H28 C H sing 1.09 N N
74 C19 H29 C H sing 1.09 N N
75 C20 H30 C H sing 1.09 N N
76 C20 H31 C H sing 1.09 N N
77 C20 H32 C H sing 1.09 N N
78 O23 H33 O H sing 0.97 N N
79 O28 H34 O H sing 0.97 N N
80 C30 H35 C H sing 1.08 N N
81 C31 H36 C H sing 1.08 N N
82 C32 H37 C H sing 1.08 N N
83 C34 H38 C H sing 1.08 N N
84 C35 H39 C H sing 1.08 N N
85 C37 H40 C H sing 1.09 N N
86 C37 H41 C H sing 1.09 N N
87 C37 H42 C H sing 1.09 N N
88 C36 H43 C H sing 1.09 N N
89 C36 H44 C H sing 1.09 N N
90 C36 H45 C H sing 1.09 N N
91 C38 H46 C H sing 1.09 N N
92 C38 H47 C H sing 1.09 N N
93 C38 H48 C H sing 1.09 N N
94 C39 H49 C H sing 1.09 N N
95 C39 H50 C H sing 1.09 N N
96 C39 H51 C H sing 1.09 N N
97 C40 H52 C H sing 1.09 N N
98 C40 H53 C H sing 1.09 N N
99 C40 H54 C H sing 1.09 N N



O1U : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
O1U 8i34 Open in New Window Bound ligand 4 1