Chemical Components in the PDB

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8W5 : Summary

Code

8W5

One-letter code

X

Molecule name

(1~{S},2~{S},4~{R},6~{R},8~{S},9~{S},11~{S},12~{S},13~{R})-9,13-dimethyl-11-oxidanyl-8-(2-oxidanylethanoyl)-6-propyl-5,7-dioxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosa-14,17-dien-16-one

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 (1~{S},2~{S},4~{R},6~{R},8~{S},9~{S},11~{S},12~{S},13~{R})-9,13-dimethyl-11-oxidanyl-8-(2-oxidanylethanoyl)-6-propyl-5,7-dioxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosa-14,17-dien-16-one

Formula

C25 H34 O6

Formal charge

0

Molecular weight

430.534 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CCC[CH]1O[CH]2C[CH]3[CH]4CCC5=CC(=O)C=C[C]5(C)[CH]4[CH](O)C[C]3(C)[C]2(O1)C(=O)CO
SMILES OpenEye OEToolkits 2.0.6 CCCC1OC2CC3C4CCC5=CC(=O)C=CC5(C4C(CC3(C2(O1)C(=O)CO)C)O)C
Canonical SMILES CACTVS 3.385 CCC[C@@H]1O[C@@H]2C[C@H]3[C@@H]4CCC5=CC(=O)C=C[C@]5(C)[C@H]4[C@@H](O)C[C@]3(C)[C@@]2(O1)C(=O)CO
Canonical SMILES OpenEye OEToolkits 2.0.6 CCC[C@@H]1O[C@@H]2C[C@H]3[C@@H]4CCC5=CC(=O)C=C[C@@]5([C@H]4[C@H](C[C@@]3([C@@]2(O1)C(=O)CO)C)O)C

IUPAC InChI

InChI=1S/C25H34O6/c1-4-5-21-30-20-11-17-16-7-6-14-10-15(27)8-9-23(14,2)22(16)18(28)12-24(17,3)25(20,31-21)19(29)13-26/h8-10,16-18,20-22,26,28H,4-7,11-13H2,1-3H3/t16-,17-,18-,20+,21+,22+,23-,24-,25+/m0/s1

IUPAC InChI key

VOVIALXJUBGFJZ-VXKMTNQYSA-N
8W5

wwPDB Information

Atom count

65 (31 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2017-03-15

Last modified at

2017-09-29

Status

Released

Obsoleted

Not Assigned



8W5 : Atoms of Molecule

Total Number of Atoms: 65
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N N N 0 -5.031 4.701 -1.099
2 C2 C C2 N N N 0 -4.884 3.39 -0.324
3 C14 C C8 N N N 0 1.872 1.184 1.865
4 C3 C C3 N N N 0 -3.842 2.505 -1.011
5 C7 C C4 R N N 0 -2.533 0.168 1.449
6 C9 C C5 N N N 0 -1.113 0.431 2.021
7 C10 C C6 S N N 0 -0.221 0.375 0.776
8 C12 C C7 S N N 0 1.245 0.068 1.026
9 C15 C C9 N N N 0 3.34 0.853 2.149
10 C16 C C10 N N N 0 4.036 0.612 0.823
11 C20 C C11 N N N 0 5.243 0.174 -1.724
12 C21 C C12 N N N 0 4.126 -0.475 -1.434
13 C22 C C13 R N N 0 3.415 -0.368 -0.129
14 C27 C C14 N N N 0 -0.21 -0.849 -1.405
15 C4 C C18 R N N 0 -3.695 1.194 -0.235
16 C31 C C15 N N N 0 -3.105 -1.904 0.057
17 C33 C C16 N N N 0 -4.457 -1.952 -0.605
18 C35 C C17 N N N 0 -0.45 -2.136 0.73
19 O6 O O1 N N N 0 -3.093 1.437 1.054
20 C17 C C19 N N N 0 5.156 1.269 0.555
21 C18 C C20 N N N 0 5.847 1.076 -0.729
22 O19 O O2 N N N 0 6.895 1.648 -0.963
23 C23 C C21 S N N 0 1.938 -0.026 -0.342
24 C25 C C22 S N N 0 1.304 -1.07 -1.256
25 C28 C C23 S N N 0 -0.822 -0.836 0.014
26 C29 C C24 S N N 0 -2.338 -0.608 0.113
27 O30 O O3 N N N 0 -2.77 0.314 -0.907
28 O32 O O4 N N N 0 -2.634 -2.905 0.543
29 O34 O O5 N N N 0 -4.977 -3.281 -0.531
30 O36 O O6 N N N 0 1.534 -2.37 -0.71
31 C37 C C25 N N N 0 3.443 -1.746 0.535
32 H1 H H1 N N N 0 -4.072 5.219 -1.122
33 H2 H H2 N N N 0 -5.352 4.486 -2.119
34 H3 H H3 N N N 0 -5.773 5.331 -0.61
35 H4 H H4 N N N 0 -4.563 3.605 0.695
36 H5 H H5 N N N 0 -5.843 2.872 -0.301
37 H6 H H6 N N N 0 -4.163 2.29 -2.03
38 H7 H H7 N N N 0 -2.883 3.023 -1.033
39 H8 H H8 N N N 0 -3.171 -0.367 2.152
40 H9 H H9 N N N 0 -1.062 1.415 2.488
41 H10 H H10 N N N 0 -0.835 -0.346 2.733
42 H11 H H11 N N N 0 -0.333 1.288 0.191
43 H12 H H12 N N N 0 1.337 -0.883 1.551
44 H13 H H13 N N N 0 1.811 2.125 1.319
45 H14 H H14 N N N 0 1.332 1.275 2.808
46 H15 H H15 N N N 0 3.812 1.689 2.666
47 H16 H H16 N N N 0 3.403 -0.043 2.766
48 H17 H H17 N N N 0 5.709 0.043 -2.689
49 H18 H H18 N N N 0 3.705 -1.121 -2.189
50 H19 H H19 N N N 0 -0.372 0.114 -1.889
51 H20 H H20 N N N 0 -0.664 -1.643 -1.998
52 H21 H H21 N N N 0 -5.135 -1.267 -0.097
53 H22 H H22 N N N 0 -4.361 -1.658 -1.651
54 H23 H H23 N N N 0 -1.007 -2.208 1.664
55 H24 H H24 N N N 0 -0.697 -2.985 0.093
56 H25 H H25 N N N 0 0.619 -2.14 0.943
57 H26 H H26 N N N 0 -4.666 0.713 -0.116
58 H27 H H27 N N N 0 5.564 1.951 1.286
59 H28 H H28 N N N 0 1.861 0.948 -0.826
60 H29 H H29 N N N 0 1.77 -1.012 -2.24
61 H30 H H30 N N N 0 -5.848 -3.386 -0.938
62 H31 H H31 N N N 0 1.16 -3.09 -1.236
63 H32 H H32 N N N 0 2.614 -1.828 1.238
64 H33 H H33 N N N 0 3.349 -2.519 -0.228
65 H34 H H34 N N N 0 4.385 -1.874 1.067



8W5 : Chemical Bonds

Total Number of Bonds: 69
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O19 C18 O C doub 1.22 N N
2 C18 C20 C C sing 1.47 N N
3 C18 C17 C C sing 1.47 N N
4 C20 C21 C C doub 1.32 N N
5 C17 C16 C C doub 1.33 N N
6 C21 C22 C C sing 1.49 N N
7 C16 C15 C C sing 1.52 N N
8 C16 C22 C C sing 1.5 N N
9 C37 C22 C C sing 1.53 N N
10 C15 C14 C C sing 1.53 N N
11 C22 C23 C C sing 1.53 N N
12 C23 C12 C C sing 1.54 N N
13 C23 C25 C C sing 1.53 N N
14 C14 C12 C C sing 1.53 N N
15 O36 C25 O C sing 1.43 N N
16 C12 C10 C C sing 1.52 N N
17 C25 C27 C C sing 1.54 N N
18 C10 C28 C C sing 1.55 N N
19 C10 C9 C C sing 1.53 N N
20 C27 C28 C C sing 1.55 N N
21 C28 C35 C C sing 1.53 N N
22 C28 C29 C C sing 1.54 N N
23 C9 C7 C C sing 1.55 N N
24 C1 C2 C C sing 1.53 N N
25 C3 C2 C C sing 1.53 N N
26 C3 C4 C C sing 1.53 N N
27 C29 O30 C O sing 1.44 N N
28 C29 C7 C C sing 1.56 N N
29 C29 C31 C C sing 1.51 N N
30 O30 C4 O C sing 1.44 N N
31 C7 O6 C O sing 1.44 N N
32 O6 C4 O C sing 1.44 N N
33 C31 C33 C C sing 1.51 N N
34 C31 O32 C O doub 1.21 N N
35 C33 O34 C O sing 1.43 N N
36 C1 H1 C H sing 1.09 N N
37 C1 H2 C H sing 1.09 N N
38 C1 H3 C H sing 1.09 N N
39 C2 H4 C H sing 1.09 N N
40 C2 H5 C H sing 1.09 N N
41 C3 H6 C H sing 1.09 N N
42 C3 H7 C H sing 1.09 N N
43 C7 H8 C H sing 1.09 N N
44 C9 H9 C H sing 1.09 N N
45 C9 H10 C H sing 1.09 N N
46 C10 H11 C H sing 1.09 N N
47 C12 H12 C H sing 1.09 N N
48 C14 H13 C H sing 1.09 N N
49 C14 H14 C H sing 1.09 N N
50 C15 H15 C H sing 1.09 N N
51 C15 H16 C H sing 1.09 N N
52 C20 H17 C H sing 1.08 N N
53 C21 H18 C H sing 1.08 N N
54 C27 H19 C H sing 1.09 N N
55 C27 H20 C H sing 1.09 N N
56 C33 H21 C H sing 1.09 N N
57 C33 H22 C H sing 1.09 N N
58 C35 H23 C H sing 1.09 N N
59 C35 H24 C H sing 1.09 N N
60 C35 H25 C H sing 1.09 N N
61 C4 H26 C H sing 1.09 N N
62 C17 H27 C H sing 1.08 N N
63 C23 H28 C H sing 1.09 N N
64 C25 H29 C H sing 1.09 N N
65 O34 H30 O H sing 0.97 N N
66 O36 H31 O H sing 0.97 N N
67 C37 H32 C H sing 1.09 N N
68 C37 H33 C H sing 1.09 N N
69 C37 H34 C H sing 1.09 N N



8W5 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
8W5 5nfp Open in New Window Bound ligand 1 1