Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

C30 : Summary

Code

C30

One-letter code

X

Molecule name

2-(acetylamino)-2-deoxy-1-O-[(S)-{[(R)-{[(2Z,6Z,10E,14E,18E)-3,7,11,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaen-1-yl]oxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-D-glucopyranose

Systematic names

ProgramVersionName
ACDLabs 12.01 2-(acetylamino)-2-deoxy-1-O-[(S)-{[(R)-{[(2Z,6Z,10E,14E,18E)-3,7,11,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaen-1-yl]oxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-D-glucopyranose
OpenEye OEToolkits 2.0.6 [(2~{R},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl] [[(2~{Z},6~{Z},10~{E},14~{E},18~{E})-3,7,11,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaenoxy]-oxidanyl-phosphoryl] hydrogen phosphate

Formula

C38 H65 N O12 P2

Formal charge

0

Molecular weight

789.87 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 C\C(=C\CC/C(C)=C/CCC(C)=[C@H]CC/C(C)=C/CCC(=[C@H]CC\C(=C/COP(O)(=O)OP(=O)(O)OC1C(C(C(C(CO)O1)O)O)NC(C)=O)C)C)C
SMILES CACTVS 3.385 CC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCO[P](O)(=O)O[P](O)(=O)O[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1NC(C)=O
SMILES OpenEye OEToolkits 2.0.6 CC(=CCCC(=CCCC(=CCCC(=CCCC(=CCCC(=CCOP(=O)(O)OP(=O)(O)OC1C(C(C(C(O1)CO)O)O)NC(=O)C)C)C)C)C)C)C
Canonical SMILES CACTVS 3.385 CC(C)=CCC\C(C)=C\CC/C(C)=C/CC\C(C)=C\CC\C(C)=C/CC\C(C)=C/CO[P](O)(=O)O[P](O)(=O)O[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1NC(C)=O
Canonical SMILES OpenEye OEToolkits 2.0.6 CC(=CCC/C(=C/CC/C(=C/CC/C(=C/CC/C(=C\CC/C(=C\COP(=O)(O)OP(=O)(O)O[C@@H]1[C@@H]([C@H]([C@@H]([C@H](O1)CO)O)O)NC(=O)C)/C)/C)/C)/C)/C)C

IUPAC InChI

InChI=1S/C38H65NO12P2/c1-27(2)14-9-15-28(3)16-10-17-29(4)18-11-19-30(5)20-12-21-31(6)22-13-23-32(7)24-25-48-52(44,45)51-53(46,47)50-38-35(39-33(8)41)37(43)36(42)34(26-40)49-38/h14,16,18,20,22,24,34-38,40,42-43H,9-13,15,17,19,21,23,25-26H2,1-8H3,(H,39,41)(H,44,45)(H,46,47)/b28-16+,29-18+,30-20+,31-22-,32-24-/t34-,35-,36-,37-,38-/m1/s1

IUPAC InChI key

DOEXPFXURIPLFY-QTFKUDQZSA-N
C30

wwPDB Information

Atom count

118 (53 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2018-10-09

Last modified at

2018-10-12

Status

Released

Obsoleted

Not Assigned



C30 : Atoms of Molecule

Total Number of Atoms: 118
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C01 C C1 N N N 0 -14.73 -3.727 1.098
2 C02 C C2 N N N 0 -14.872 -4.472 -0.204
3 C03 C C3 N N N 0 -15.895 -5.571 -0.336
4 C04 C C4 N N N 0 -14.106 -4.165 -1.221
5 C05 C C5 N N N 0 -13.0 -3.156 -1.054
6 C06 C C6 N N N 0 -11.656 -3.814 -1.374
7 C07 C C7 N N N 0 -10.55 -2.805 -1.207
8 C08 C C8 N N N 0 -10.2 -1.875 -2.34
9 C09 C C9 N N N 0 -9.892 -2.736 -0.076
10 C10 C C10 N N N 0 -8.872 -1.646 0.137
11 C11 C C11 N N N 0 -9.28 -0.795 1.342
12 C12 C C12 N N N 0 -8.261 0.294 1.555
13 C13 C C13 N N N 0 -7.016 0.014 2.357
14 C14 C C14 N N N 0 -8.457 1.484 1.043
15 C15 C C15 N N N 0 -7.387 2.539 1.157
16 C16 C C16 N N N 0 -6.948 2.973 -0.243
17 C17 C C17 N N N 0 -5.878 4.028 -0.129
18 C18 C C18 N N N 0 -6.262 5.476 0.043
19 C19 C C19 N N N 0 -4.614 3.687 -0.179
20 C20 C C20 N N N 0 -3.544 4.724 0.048
21 C21 C C21 N N N 0 -2.653 4.29 1.213
22 C22 C C22 N N N 0 -1.583 5.327 1.441
23 C23 C C23 N N N 0 -1.865 6.521 2.316
24 C24 C C24 N N N 0 -0.408 5.19 0.878
25 C25 C C25 N N N 0 -0.172 4.078 -0.112
26 C26 C C26 N N N 0 0.385 4.663 -1.412
27 C27 C C27 N N N 0 0.621 3.551 -2.401
28 C28 C C28 N N N 0 -0.505 3.074 -3.282
29 C29 C C29 N N N 0 1.805 2.999 -2.495
30 C30 C C30 N N N 0 2.896 3.385 -1.529
31 C40 C C31 R N N 0 8.187 -2.064 0.492
32 C42 C C32 R N N 0 6.888 -3.747 1.602
33 C43 C C33 N N N 0 6.751 -4.493 2.931
34 C45 C C34 S N N 0 7.14 -4.753 0.475
35 C47 C C35 R N N 0 7.336 -3.994 -0.841
36 C49 C C36 R N N 0 8.491 -3.002 -0.679
37 C51 C C37 N N N 0 9.829 -1.663 -2.213
38 C52 C C38 N N N 0 9.982 -0.857 -3.477
39 N50 N N1 N N N 0 8.64 -2.218 -1.908
40 O31 O O1 N N N 0 3.57 2.208 -1.077
41 O33 O O2 N N N 0 4.27 2.791 1.389
42 O34 O O3 N N N 0 5.852 3.145 -0.545
43 O35 O O4 N N N 0 5.391 0.762 0.149
44 O37 O O5 N N N 0 7.887 1.046 0.397
45 O38 O O6 N N N 0 6.627 0.12 2.378
46 O39 O O7 N N N 0 7.006 -1.312 0.206
47 O41 O O8 N N N 0 7.985 -2.835 1.679
48 O44 O O9 N N N 0 6.401 -3.568 3.962
49 O46 O O10 N N N 0 6.018 -5.63 0.359
50 O48 O O11 N N N 0 7.642 -4.921 -1.885
51 O53 O O12 N N N 0 10.776 -1.811 -1.47
52 P32 P P1 N N N 0 4.794 2.247 -0.032
53 P36 P P2 N N N 0 6.753 0.173 0.774
54 H013 H H1 N N N 0 -14.835 -2.657 0.918
55 H012 H H2 N N N 0 -15.503 -4.056 1.792
56 H011 H H3 N N N 0 -13.748 -3.929 1.527
57 H033 H H4 N N N 0 -16.838 -5.149 -0.684
58 H032 H H5 N N N 0 -15.542 -6.312 -1.052
59 H031 H H6 N N N 0 -16.046 -6.045 0.634
60 H041 H H7 N N N 0 -14.268 -4.635 -2.18
61 H051 H H8 N N N 0 -13.165 -2.319 -1.733
62 H052 H H9 N N N 0 -12.991 -2.793 -0.026
63 H061 H H10 N N N 0 -11.491 -4.651 -0.695
64 H062 H H11 N N N 0 -11.665 -4.177 -2.402
65 H081 H H12 N N N 0 -10.787 -2.138 -3.22
66 H083 H H13 N N N 0 -10.422 -0.848 -2.049
67 H082 H H14 N N N 0 -9.139 -1.966 -2.57
68 H091 H H15 N N N 0 -10.08 -3.459 0.703
69 H101 H H16 N N N 0 -7.896 -2.094 0.322
70 H102 H H17 N N N 0 -8.821 -1.018 -0.751
71 H111 H H18 N N N 0 -10.256 -0.348 1.157
72 H112 H H19 N N N 0 -9.331 -1.424 2.23
73 H133 H H20 N N N 0 -7.003 -1.034 2.654
74 H132 H H21 N N N 0 -6.136 0.231 1.75
75 H131 H H22 N N N 0 -7.007 0.645 3.246
76 H141 H H23 N N N 0 -9.386 1.709 0.54
77 H152 H H24 N N N 0 -7.781 3.399 1.698
78 H151 H H25 N N N 0 -6.531 2.132 1.696
79 H162 H H26 N N N 0 -6.554 2.113 -0.784
80 H161 H H27 N N N 0 -7.804 3.38 -0.782
81 H183 H H28 N N N 0 -7.346 5.557 0.118
82 H181 H H29 N N N 0 -5.803 5.868 0.95
83 H182 H H30 N N N 0 -5.913 6.048 -0.817
84 H191 H H31 N N N 0 -4.339 2.663 -0.384
85 H202 H H32 N N N 0 -2.94 4.826 -0.853
86 H201 H H33 N N N 0 -4.01 5.681 0.283
87 H211 H H34 N N N 0 -3.257 4.188 2.115
88 H212 H H35 N N N 0 -2.187 3.333 0.978
89 H231 H H36 N N N 0 -1.601 6.286 3.347
90 H233 H H37 N N N 0 -1.273 7.37 1.974
91 H232 H H38 N N N 0 -2.925 6.77 2.26
92 H241 H H39 N N N 0 0.391 5.874 1.122
93 H252 H H40 N N N 0 0.544 3.369 0.303
94 H251 H H41 N N N 0 -1.113 3.568 -0.316
95 H261 H H42 N N N 0 -0.331 5.372 -1.827
96 H262 H H43 N N N 0 1.326 5.173 -1.207
97 H282 H H44 N N N 0 -0.511 3.65 -4.208
98 H281 H H45 N N N 0 -0.364 2.018 -3.513
99 H283 H H46 N N N 0 -1.454 3.209 -2.764
100 H291 H H47 N N N 0 2.0 2.267 -3.265
101 H301 H H48 N N N 0 3.607 4.042 -2.028
102 H302 H H49 N N N 0 2.458 3.903 -0.676
103 H401 H H50 N N N 0 9.025 -1.383 0.64
104 H421 H H51 N N N 0 5.97 -3.195 1.398
105 H431 H H52 N N N 0 5.972 -5.251 2.843
106 H432 H H53 N N N 0 7.698 -4.972 3.178
107 H451 H H54 N N N 0 8.035 -5.333 0.698
108 H471 H H55 N N N 0 6.423 -3.454 -1.09
109 H491 H H56 N N N 0 9.414 -3.546 -0.479
110 H522 H H57 N N N 0 9.032 -0.835 -4.011
111 H523 H H58 N N N 0 10.281 0.161 -3.225
112 H521 H H59 N N N 0 10.743 -1.314 -4.109
113 H501 H H60 N N N 0 7.882 -2.1 -2.502
114 H1 H H61 N N N 0 3.574 2.25 1.785
115 H2 H H62 N N N 0 5.903 -0.435 2.698
116 H441 H H63 N N N 0 6.297 -3.972 4.834
117 H461 H H64 N N N 0 5.835 -6.143 1.158
118 H481 H H65 N N N 0 6.955 -5.583 -2.038



C30 : Chemical Bonds

Total Number of Bonds: 118
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C01 C02 C C sing 1.51 N N
2 C03 C02 C C sing 1.51 N N
3 C02 C04 C C doub 1.31 N N
4 C04 C05 C C sing 1.51 N N
5 C05 C06 C C sing 1.53 N N
6 C06 C07 C C sing 1.51 N N
7 C16 C15 C C sing 1.53 N N
8 C16 C17 C C sing 1.51 N N
9 C15 C14 C C sing 1.51 N N
10 C07 C08 C C sing 1.51 N N
11 C07 C09 C C doub 1.31 E N
12 C17 C18 C C sing 1.51 N N
13 C17 C19 C C doub 1.31 E N
14 C13 C12 C C sing 1.51 N N
15 C14 C12 C C doub 1.31 E N
16 C19 C20 C C sing 1.51 N N
17 C09 C10 C C sing 1.51 N N
18 C12 C11 C C sing 1.51 N N
19 C28 C27 C C sing 1.51 N N
20 C20 C21 C C sing 1.53 N N
21 C10 C11 C C sing 1.53 N N
22 O37 P36 O P doub 1.48 N N
23 C27 C26 C C sing 1.51 N N
24 C27 C29 C C doub 1.31 Z N
25 C26 C25 C C sing 1.53 N N
26 O38 P36 O P sing 1.61 N N
27 C21 C22 C C sing 1.51 N N
28 C29 C30 C C sing 1.51 N N
29 C25 C24 C C sing 1.51 N N
30 P36 O35 P O sing 1.61 N N
31 P36 O39 P O sing 1.61 N N
32 C22 C24 C C doub 1.31 Z N
33 C22 C23 C C sing 1.51 N N
34 C30 O31 C O sing 1.43 N N
35 O35 P32 O P sing 1.61 N N
36 O39 C40 O C sing 1.43 N N
37 C40 C49 C C sing 1.53 N N
38 C40 O41 C O sing 1.43 N N
39 O48 C47 O C sing 1.43 N N
40 C49 C47 C C sing 1.53 N N
41 C49 N50 C N sing 1.47 N N
42 C45 C47 C C sing 1.53 N N
43 C45 O46 C O sing 1.43 N N
44 C45 C42 C C sing 1.53 N N
45 C43 O44 C O sing 1.43 N N
46 C43 C42 C C sing 1.53 N N
47 O31 P32 O P sing 1.61 N N
48 N50 C51 N C sing 1.35 N N
49 P32 O34 P O doub 1.48 N N
50 P32 O33 P O sing 1.61 N N
51 O41 C42 O C sing 1.43 N N
52 O53 C51 O C doub 1.21 N N
53 C51 C52 C C sing 1.51 N N
54 C01 H013 C H sing 1.09 N N
55 C01 H012 C H sing 1.09 N N
56 C01 H011 C H sing 1.09 N N
57 C03 H033 C H sing 1.09 N N
58 C03 H032 C H sing 1.09 N N
59 C03 H031 C H sing 1.09 N N
60 C04 H041 C H sing 1.08 N N
61 C05 H051 C H sing 1.09 N N
62 C05 H052 C H sing 1.09 N N
63 C06 H061 C H sing 1.09 N N
64 C06 H062 C H sing 1.09 N N
65 C08 H081 C H sing 1.09 N N
66 C08 H083 C H sing 1.09 N N
67 C08 H082 C H sing 1.09 N N
68 C09 H091 C H sing 1.08 N N
69 C10 H101 C H sing 1.09 N N
70 C10 H102 C H sing 1.09 N N
71 C11 H111 C H sing 1.09 N N
72 C11 H112 C H sing 1.09 N N
73 C13 H133 C H sing 1.09 N N
74 C13 H132 C H sing 1.09 N N
75 C13 H131 C H sing 1.09 N N
76 C14 H141 C H sing 1.08 N N
77 C15 H152 C H sing 1.09 N N
78 C15 H151 C H sing 1.09 N N
79 C16 H162 C H sing 1.09 N N
80 C16 H161 C H sing 1.09 N N
81 C18 H183 C H sing 1.09 N N
82 C18 H181 C H sing 1.09 N N
83 C18 H182 C H sing 1.09 N N
84 C19 H191 C H sing 1.08 N N
85 C20 H202 C H sing 1.09 N N
86 C20 H201 C H sing 1.09 N N
87 C21 H211 C H sing 1.09 N N
88 C21 H212 C H sing 1.09 N N
89 C23 H231 C H sing 1.09 N N
90 C23 H233 C H sing 1.09 N N
91 C23 H232 C H sing 1.09 N N
92 C24 H241 C H sing 1.08 N N
93 C25 H252 C H sing 1.09 N N
94 C25 H251 C H sing 1.09 N N
95 C26 H261 C H sing 1.09 N N
96 C26 H262 C H sing 1.09 N N
97 C28 H282 C H sing 1.09 N N
98 C28 H281 C H sing 1.09 N N
99 C28 H283 C H sing 1.09 N N
100 C29 H291 C H sing 1.08 N N
101 C30 H301 C H sing 1.09 N N
102 C30 H302 C H sing 1.09 N N
103 C40 H401 C H sing 1.09 N N
104 C42 H421 C H sing 1.09 N N
105 C43 H431 C H sing 1.09 N N
106 C43 H432 C H sing 1.09 N N
107 C45 H451 C H sing 1.09 N N
108 C47 H471 C H sing 1.09 N N
109 C49 H491 C H sing 1.09 N N
110 C52 H522 C H sing 1.09 N N
111 C52 H523 C H sing 1.09 N N
112 C52 H521 C H sing 1.09 N N
113 N50 H501 N H sing 0.97 N N
114 O33 H1 O H sing 0.97 N N
115 O38 H2 O H sing 0.97 N N
116 O44 H441 O H sing 0.97 N N
117 O46 H461 O H sing 0.97 N N
118 O48 H481 O H sing 0.97 N N



C30 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
C30 6mpt Open in New Window Bound ligand 1 1