Chemical Components in the PDB

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BKC : Summary

Code

BKC

One-letter code

X

Molecule name

Bongkrekic acid

Synonyms

Bongkrek acid

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 (2~{E},4~{Z},6~{R},8~{Z},10~{E},14~{E},17~{S},18~{E},20~{Z})-20-(2-hydroxy-2-oxoethyl)-6-methoxy-2,5,17-trimethyl-docosa-2,4,8,10,14,18,20-heptaenedioic acid

Formula

C28 H38 O7

Formal charge

0

Molecular weight

486.597 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CO[CH](CC=CC=CCCC=CC[CH](C)C=CC(CC(O)=O)=CC(O)=O)C(C)=CC=C(C)C(O)=O
SMILES OpenEye OEToolkits 2.0.6 CC(CC=CCCC=CC=CCC(C(=CC=C(C)C(=O)O)C)OC)C=CC(=CC(=O)O)CC(=O)O
Canonical SMILES CACTVS 3.385 CO[C@H](C/C=C\C=C\CC/C=C/C[C@H](C)/C=C/C(CC(O)=O)=C\C(O)=O)\C(C)=C/C=C(\C)C(O)=O
Canonical SMILES OpenEye OEToolkits 2.0.6 C[C@@H](C/C=C/CC/C=C/C=C\C[C@H](/C(=C\C=C(/C)\C(=O)O)/C)OC)/C=C/C(=C\C(=O)O)/CC(=O)O

IUPAC InChI

InChI=1S/C28H38O7/c1-21(15-18-24(19-26(29)30)20-27(31)32)13-11-9-7-5-6-8-10-12-14-25(35-4)22(2)16-17-23(3)28(33)34/h6,8-12,15-19,21,25H,5,7,13-14,20H2,1-4H3,(H,29,30)(H,31,32)(H,33,34)/b8-6+,11-9+,12-10-,18-15+,22-16-,23-17+,24-19+/t21-,25+/m0/s1

IUPAC InChI key

SHCXABJSXUACKU-WUTQZGRKSA-N
BKC

wwPDB Information

Atom count

73 (35 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2018-04-17

Last modified at

2021-03-01

Status

Released

Obsoleted

Not Assigned



BKC : Atoms of Molecule

Total Number of Atoms: 73
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O3 O O1 N N N 0 4.643 -0.129 1.764
2 C3 C C1 N N N 0 -4.263 1.692 0.135
3 C2 C C2 S N N 0 -4.281 0.206 -0.227
4 C1 C C3 N N N 0 -3.275 -0.057 -1.349
5 O1 O O2 N N N 0 11.266 -1.739 -0.981
6 O2 O O3 N N N 0 10.186 -0.332 0.36
7 C4 C C4 N N N 0 -2.919 2.053 0.712
8 C5 C C5 N N N 0 -2.221 3.029 0.187
9 C6 C C6 N N N 0 -0.876 3.39 0.763
10 C7 C C7 N N N 0 0.182 3.343 -0.341
11 C8 C C8 N N N 0 1.526 3.703 0.236
12 C9 C C9 N N N 0 2.556 2.876 0.088
13 C10 C C10 N N N 0 3.869 3.229 0.651
14 C11 C C11 N N N 0 4.921 2.451 0.42
15 C12 C C12 N N N 0 4.744 1.135 -0.293
16 C13 C C13 R N N 0 5.369 0.015 0.542
17 C14 C C14 N N N 0 5.314 -1.277 -0.231
18 C15 C C15 N N N 0 6.44 -1.836 -0.678
19 C16 C C16 N N N 0 7.736 -1.281 -0.288
20 C17 C C17 N N N 0 8.874 -1.779 -0.825
21 C18 C C18 N N N 0 8.806 -2.905 -1.823
22 C19 C C19 N N N 0 10.131 -1.242 -0.447
23 C20 C C20 N N N 0 3.987 -1.939 -0.498
24 C21 C C21 N N N 0 5.258 0.511 2.884
25 C25 C C25 N N N 0 -8.432 -2.349 0.261
26 C22 C C22 N N N 0 -5.662 -0.182 -0.688
27 C23 C C23 N N N 0 -6.344 -1.124 -0.033
28 C24 C C24 N N N 0 -7.685 -1.501 -0.481
29 C26 C C26 N N N 0 -8.043 -2.662 1.588
30 O4 O O4 N N N 0 -7.106 -2.079 2.1
31 O5 O O5 N N N 0 -8.711 -3.606 2.283
32 C27 C C27 N N N 0 -8.233 -0.944 -1.77
33 C28 C C28 N N N 0 -8.856 0.404 -1.51
34 O6 O O6 N N N 0 -8.855 0.864 -0.393
35 O7 O O7 N N N 0 -9.412 1.092 -2.519
36 H1 H H1 N N N 0 -4.446 2.287 -0.76
37 H2 H H2 N N N 0 -5.041 1.896 0.872
38 H3 H H3 N N N 0 -4.011 -0.385 0.649
39 H4 H H4 N N N 0 -2.276 0.224 -1.015
40 H5 H H5 N N N 0 -3.288 -1.116 -1.607
41 H6 H H6 N N N 0 -3.545 0.533 -2.225
42 H7 H H7 N N N 0 12.071 -1.309 -0.663
43 H8 H H8 N N N 0 -2.53 1.507 1.559
44 H9 H H9 N N N 0 -2.609 3.575 -0.66
45 H13 H H13 N N N 0 -0.08 4.053 -1.125
46 H10 H H10 N N N 0 -0.919 4.395 1.183
47 H11 H H11 N N N 0 -0.615 2.679 1.548
48 H12 H H12 N N N 0 0.224 2.338 -0.761
49 H14 H H14 N N N 0 1.653 4.634 0.769
50 H15 H H15 N N N 0 2.429 1.946 -0.445
51 H16 H H16 N N N 0 3.977 4.119 1.253
52 H17 H H17 N N N 0 5.904 2.763 0.742
53 H18 H H18 N N N 0 3.681 0.937 -0.429
54 H19 H H19 N N N 0 5.233 1.18 -1.266
55 H20 H H20 N N N 0 6.407 0.263 0.762
56 H21 H H21 N N N 0 6.395 -2.697 -1.328
57 H22 H H22 N N N 0 7.785 -0.474 0.427
58 H23 H H23 N N N 0 8.728 -2.494 -2.83
59 H24 H H24 N N N 0 9.708 -3.513 -1.748
60 H25 H H25 N N N 0 7.933 -3.524 -1.615
61 H26 H H26 N N N 0 3.58 -1.571 -1.44
62 H27 H H27 N N N 0 4.125 -3.019 -0.56
63 H35 H H35 N N N 0 -8.373 -3.75 3.177
64 H28 H H28 N N N 0 3.295 -1.707 0.312
65 H29 H H29 N N N 0 4.7 0.273 3.79
66 H30 H H30 N N N 0 6.284 0.157 2.986
67 H31 H H31 N N N 0 5.26 1.59 2.731
68 H32 H H32 N N N 0 -6.099 0.301 -1.549
69 H33 H H33 N N N 0 -5.907 -1.607 0.828
70 H34 H H34 N N N 0 -9.326 -2.789 -0.157
71 H36 H H36 N N N 0 -7.424 -0.837 -2.493
72 H37 H H37 N N N 0 -8.988 -1.622 -2.167
73 H38 H H38 N N N 0 -9.799 1.952 -2.304



BKC : Chemical Bonds

Total Number of Bonds: 72
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O4 C26 O C doub 1.22 N N
2 C26 O5 C O sing 1.35 N N
3 C26 C25 C C sing 1.42 N N
4 C21 O3 C O sing 1.43 N N
5 O3 C13 O C sing 1.43 N N
6 C20 C14 C C sing 1.51 N N
7 C25 C24 C C doub 1.35 Z N
8 C13 C12 C C sing 1.53 N N
9 C13 C14 C C sing 1.51 N N
10 C12 C11 C C sing 1.51 N N
11 C14 C15 C C doub 1.33 Z N
12 C24 C23 C C sing 1.46 N N
13 C24 C27 C C sing 1.51 N N
14 C15 C16 C C sing 1.46 N N
15 C23 C22 C C doub 1.33 E N
16 C11 C10 C C doub 1.33 Z N
17 C1 C2 C C sing 1.53 N N
18 C27 C28 C C sing 1.51 N N
19 C16 C17 C C doub 1.35 E N
20 C22 C2 C C sing 1.51 N N
21 C10 C9 C C sing 1.47 N N
22 C9 C8 C C doub 1.33 E N
23 C2 C3 C C sing 1.53 N N
24 O6 C28 O C doub 1.21 N N
25 C17 C18 C C sing 1.51 N N
26 C17 C19 C C sing 1.42 N N
27 C3 C4 C C sing 1.51 N N
28 C28 O7 C O sing 1.34 N N
29 O2 C19 O C doub 1.22 N N
30 C19 O1 C O sing 1.35 N N
31 C8 C7 C C sing 1.51 N N
32 C4 C5 C C doub 1.31 E N
33 C5 C6 C C sing 1.51 N N
34 C7 C6 C C sing 1.53 N N
35 C3 H1 C H sing 1.09 N N
36 C3 H2 C H sing 1.09 N N
37 C2 H3 C H sing 1.09 N N
38 C1 H4 C H sing 1.09 N N
39 C1 H5 C H sing 1.09 N N
40 C1 H6 C H sing 1.09 N N
41 O1 H7 O H sing 0.97 N N
42 C4 H8 C H sing 1.08 N N
43 C5 H9 C H sing 1.08 N N
44 C6 H10 C H sing 1.09 N N
45 C6 H11 C H sing 1.09 N N
46 C7 H12 C H sing 1.09 N N
47 C7 H13 C H sing 1.09 N N
48 C8 H14 C H sing 1.08 N N
49 C9 H15 C H sing 1.08 N N
50 C10 H16 C H sing 1.08 N N
51 C11 H17 C H sing 1.08 N N
52 C12 H18 C H sing 1.09 N N
53 C12 H19 C H sing 1.09 N N
54 C13 H20 C H sing 1.09 N N
55 C15 H21 C H sing 1.08 N N
56 C16 H22 C H sing 1.08 N N
57 C18 H23 C H sing 1.09 N N
58 C18 H24 C H sing 1.09 N N
59 C18 H25 C H sing 1.09 N N
60 C20 H26 C H sing 1.09 N N
61 C20 H27 C H sing 1.09 N N
62 C20 H28 C H sing 1.09 N N
63 C21 H29 C H sing 1.09 N N
64 C21 H30 C H sing 1.09 N N
65 C21 H31 C H sing 1.09 N N
66 C22 H32 C H sing 1.08 N N
67 C23 H33 C H sing 1.08 N N
68 C25 H34 C H sing 1.08 N N
69 O5 H35 O H sing 0.97 N N
70 C27 H36 C H sing 1.09 N N
71 C27 H37 C H sing 1.09 N N
72 O7 H38 O H sing 0.97 N N



BKC : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
BKC 6gci Open in New Window Bound ligand 1 1