Chemical Components in the PDB

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DSL : Summary

Code

DSL

One-letter code

X

Molecule name

MONO-TRANS, OCTA-CIS DECAPRENYL-PHOSPHATE

Systematic names

ProgramVersionName
OpenEye OEToolkits 1.6.1 [(2Z,6Z,10Z,14Z,18Z,22Z,26Z,30Z,34E)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaenyl] dihydrogen phosphate

Formula

C50 H83 O4 P

Formal charge

0

Molecular weight

779.165 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.352 CC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCO[P](O)(O)=O
SMILES OpenEye OEToolkits 1.6.1 CC(=CCCC(=CCCC(=CCCC(=CCCC(=CCCC(=CCCC(=CCCC(=CCCC(=CCCC(=CCOP(=O)(O)O)C)C)C)C)C)C)C)C)C)C
Canonical SMILES CACTVS 3.352 CC(C)=CCC\C(C)=C\CC\C(C)=C/CC\C(C)=C/CC\C(C)=C/CC\C(C)=C/CC\C(C)=C/CC\C(C)=C/CC\C(C)=C/CC\C(C)=C/CO[P](O)(O)=O
Canonical SMILES OpenEye OEToolkits 1.6.1 CC(=CCC/C(=C/CC/C(=C\CC/C(=C\CC/C(=C\CC/C(=C\CC/C(=C\CC/C(=C\CC/C(=C\CC/C(=C\COP(=O)(O)O)/C)/C)/C)/C)/C)/C)/C)/C)/C)C

IUPAC InChI

InChI=1S/C50H83O4P/c1-41(2)21-12-22-42(3)23-13-24-43(4)25-14-26-44(5)27-15-28-45(6)29-16-30-46(7)31-17-32-47(8)33-18-34-48(9)35-19-36-49(10)37-20-38-50(11)39-40-54-55(51,52)53/h21,23,25,27,29,31,33,35,37,39H,12-20,22,24,26,28,30,32,34,36,38,40H2,1-11H3,(H2,51,52,53)/b42-23+,43-25-,44-27-,45-29-,46-31-,47-33-,48-35-,49-37-,50-39-

IUPAC InChI key

XBEJBEIXLWRYBT-DJNGBRKISA-N
DSL

wwPDB Information

Atom count

138 (55 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2010-11-11

Last modified at

2011-10-14

Status

Released

Obsoleted

Not Assigned



DSL : Atoms of Molecule

Total Number of Atoms: 138
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C06 C C06 N N N 0 15.604 3.865 1.731
2 C07 C C07 N N N 0 16.573 3.996 0.584
3 C08 C C08 N N N 0 17.276 5.306 0.336
4 C09 C C09 N N N 0 16.804 2.97 -0.198
5 C10 C C10 N N N 0 16.008 1.702 -0.033
6 C11 C C11 N N N 0 15.305 1.365 -1.349
7 C12 C C12 N N N 0 14.509 0.097 -1.184
8 C13 C C13 N N N 0 15.177 -1.242 -1.366
9 C14 C C14 N N N 0 13.235 0.158 -0.882
10 C15 C C15 N N N 0 12.469 -1.107 -0.589
11 C16 C C16 N N N 0 11.854 -1.018 0.809
12 C17 C C17 N N N 0 11.088 -2.282 1.102
13 C18 C C18 N N N 0 11.801 -3.48 1.673
14 C19 C C19 N N N 0 9.801 -2.339 0.861
15 C20 C C20 N N N 0 9.114 -1.195 0.161
16 C21 C C21 N N N 0 8.369 -1.722 -1.067
17 C22 C C22 N N N 0 7.682 -0.577 -1.767
18 C23 C C23 N N N 0 8.432 0.243 -2.785
19 C24 C C24 N N N 0 6.433 -0.296 -1.49
20 C25 C C25 N N N 0 5.717 -1.042 -0.393
21 C26 C C26 N N N 0 5.12 -0.041 0.598
22 C27 C C27 N N N 0 4.404 -0.787 1.695
23 C28 C C28 N N N 0 5.163 -1.25 2.911
24 C29 C C29 N N N 0 3.121 -1.033 1.59
25 C30 C C30 N N N 0 2.391 -0.7 0.315
26 C31 C C31 N N N 0 1.64 -1.938 -0.181
27 C32 C C32 N N N 0 0.91 -1.604 -1.456
28 C33 C C33 N N N 0 1.613 -1.734 -2.783
29 C34 C C34 N N N 0 -0.336 -1.202 -1.412
30 C35 C C35 N N N 0 -0.997 -0.94 -0.083
31 C36 C C36 N N N 0 -1.55 0.487 -0.062
32 C37 C C37 N N N 0 -2.211 0.749 1.267
33 C38 C C38 N N N 0 -1.393 1.25 2.43
34 C39 C C39 N N N 0 -3.496 0.541 1.412
35 C40 C C40 N N N 0 -4.287 -0.093 0.298
36 C41 C C41 N N N 0 -5.044 -1.309 0.838
37 C42 C C42 N N N 0 -5.835 -1.944 -0.277
38 C43 C C43 N N N 0 -5.19 -2.976 -1.166
39 C44 C C44 N N N 0 -7.083 -1.598 -0.473
40 C45 C C45 N N N 0 -7.686 -0.467 0.32
41 C46 C C46 N N N 0 -8.295 0.559 -0.638
42 C47 C C47 N N N 0 -8.897 1.69 0.154
43 C48 C C48 N N N 0 -8.042 2.861 0.565
44 C49 C C49 N N N 0 -10.164 1.656 0.486
45 C50 C C50 N N N 0 -10.984 0.424 0.202
46 C51 C C51 N N N 0 -11.663 -0.046 1.49
47 C52 C C52 N N N 0 -12.483 -1.278 1.206
48 C53 C C53 N N N 0 -11.838 -2.639 1.251
49 C54 C C54 N N N 0 -13.756 -1.165 0.919
50 C55 C C55 N N N 0 -14.374 0.2 0.758
51 H061 H H061 N N N 0 15.61 4.784 2.317
52 H062 H H062 N N N 0 14.602 3.689 1.341
53 H063 H H063 N N N 0 15.901 3.028 2.363
54 H081 H H081 N N N 0 16.959 6.035 1.082
55 H082 H H082 N N N 0 18.354 5.159 0.407
56 H083 H H083 N N N 0 17.023 5.671 -0.659
57 H09 H H09 N N N 0 17.566 3.034 -0.961
58 H101 H H101 N N N 0 16.677 0.886 0.241
59 H102 H H102 N N N 0 15.264 1.84 0.752
60 H111 H H111 N N N 0 14.636 2.181 -1.623
61 H112 H H112 N N N 0 16.049 1.227 -2.134
62 H131 H H131 N N N 0 16.204 -1.092 -1.7
63 H132 H H132 N N N 0 15.177 -1.779 -0.418
64 H133 H H133 N N N 0 14.633 -1.821 -2.112
65 H14 H H14 N N N 0 12.735 1.114 -0.842
66 H151 H H151 N N N 0 11.677 -1.231 -1.327
67 H152 H H152 N N N 0 13.146 -1.96 -0.634
68 H161 H H161 N N N 0 12.646 -0.893 1.548
69 H162 H H162 N N N 0 11.177 -0.164 0.855
70 H181 H H181 N N N 0 11.78 -3.431 2.762
71 H182 H H182 N N N 0 11.304 -4.392 1.34
72 H183 H H183 N N N 0 12.836 -3.484 1.33
73 H19 H H19 N N N 0 9.233 -3.207 1.163
74 H201 H H201 N N N 0 8.405 -0.725 0.843
75 H202 H H202 N N N 0 9.857 -0.462 -0.152
76 H211 H H211 N N N 0 9.078 -2.191 -1.749
77 H212 H H212 N N N 0 7.626 -2.455 -0.754
78 H231 H H231 N N N 0 8.303 -0.199 -3.773
79 H232 H H232 N N N 0 8.042 1.261 -2.789
80 H233 H H233 N N N 0 9.491 0.259 -2.529
81 H24 H H24 N N N 0 5.916 0.471 -2.047
82 H251 H H251 N N N 0 4.919 -1.645 -0.826
83 H252 H H252 N N N 0 6.423 -1.69 0.126
84 H261 H H261 N N N 0 5.917 0.563 1.03
85 H262 H H262 N N N 0 4.413 0.607 0.079
86 H281 H H281 N N N 0 5.137 -0.471 3.674
87 H282 H H282 N N N 0 4.704 -2.158 3.303
88 H283 H H283 N N N 0 6.198 -1.456 2.637
89 H29 H H29 N N N 0 2.587 -1.475 2.419
90 H301 H H301 N N N 0 1.682 0.105 0.502
91 H302 H H302 N N N 0 3.109 -0.384 -0.442
92 H311 H H311 N N N 0 2.349 -2.743 -0.368
93 H312 H H312 N N N 0 0.922 -2.254 0.576
94 H331 H H331 N N N 0 1.465 -2.74 -3.175
95 H332 H H332 N N N 0 1.204 -1.007 -3.484
96 H333 H H333 N N N 0 2.679 -1.55 -2.648
97 H34 H H34 N N N 0 -0.89 -1.058 -2.328
98 H351 H H351 N N N 0 -1.812 -1.648 0.064
99 H352 H H352 N N N 0 -0.265 -1.057 0.716
100 H361 H H361 N N N 0 -0.735 1.195 -0.208
101 H362 H H362 N N N 0 -2.282 0.604 -0.861
102 H381 H H381 N N N 0 -1.384 2.34 2.425
103 H382 H H382 N N N 0 -1.83 0.894 3.362
104 H383 H H383 N N N 0 -0.372 0.878 2.342
105 H39 H H39 N N N 0 -3.989 0.825 2.33
106 H401 H H401 N N N 0 -4.999 0.63 -0.101
107 H402 H H402 N N N 0 -3.609 -0.41 -0.495
108 H411 H H411 N N N 0 -4.332 -2.032 1.236
109 H412 H H412 N N N 0 -5.722 -0.992 1.63
110 H431 H H431 N N N 0 -5.341 -3.967 -0.739
111 H432 H H432 N N N 0 -5.641 -2.934 -2.157
112 H433 H H433 N N N 0 -4.122 -2.772 -1.243
113 H44 H H44 N N N 0 -7.681 -2.125 -1.203
114 H451 H H451 N N N 0 -8.463 -0.857 0.977
115 H452 H H452 N N N 0 -6.91 0.011 0.918
116 H461 H H461 N N N 0 -7.518 0.949 -1.295
117 H462 H H462 N N N 0 -9.071 0.081 -1.237
118 H481 H H481 N N N 0 -8.078 3.627 -0.21
119 H482 H H482 N N N 0 -8.418 3.274 1.502
120 H483 H H483 N N N 0 -7.013 2.53 0.701
121 H49 H H49 N N N 0 -10.621 2.51 0.964
122 H501 H H501 N N N 0 -11.744 0.657 -0.544
123 H502 H H502 N N N 0 -10.335 -0.366 -0.176
124 H511 H H511 N N N 0 -10.903 -0.279 2.237
125 H512 H H512 N N N 0 -12.312 0.744 1.868
126 H531 H H531 N N N 0 -11.914 -3.044 2.261
127 H532 H H532 N N N 0 -12.346 -3.305 0.554
128 H533 H H533 N N N 0 -10.788 -2.553 0.973
129 H54 H H54 N N N 0 -14.363 -2.05 0.799
130 H551 H H551 N N N 0 -14.968 0.437 1.641
131 H552 H H552 N N N 0 -13.587 0.944 0.64
132 H59 H H59 N N N 0 -14.422 2.415 -2.039
133 H60 H H60 N N N 0 -17.5 1.858 -2.465
134 O56 O O56 N N N 0 -15.215 0.208 -0.397
135 O58 O O58 N N N 0 -16.881 1.994 0.242
136 O59 O O59 N N N 0 -15.007 2.665 -1.311
137 O60 O O60 N N N 0 -16.974 1.121 -2.125
138 P57 P P57 N N N 0 -16.038 1.508 -0.873



DSL : Chemical Bonds

Total Number of Bonds: 137
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C06 C07 C C sing 1.51 N N
2 C07 C08 C C sing 1.51 N N
3 C07 C09 C C doub 1.31 N N
4 C09 C10 C C sing 1.51 N N
5 C10 C11 C C sing 1.53 N N
6 C11 C12 C C sing 1.51 N N
7 C12 C13 C C sing 1.51 N N
8 C12 C14 C C doub 1.31 N N
9 C14 C15 C C sing 1.51 N N
10 C15 C16 C C sing 1.53 N N
11 C16 C17 C C sing 1.51 N N
12 C17 C18 C C sing 1.51 N N
13 C17 C19 C C doub 1.31 N N
14 C19 C20 C C sing 1.51 N N
15 C20 C21 C C sing 1.53 N N
16 C21 C22 C C sing 1.51 N N
17 C22 C23 C C sing 1.51 N N
18 C22 C24 C C doub 1.31 N N
19 C24 C25 C C sing 1.51 E N
20 C25 C26 C C sing 1.53 N N
21 C26 C27 C C sing 1.51 N N
22 C27 C28 C C sing 1.51 N N
23 C27 C29 C C doub 1.31 N N
24 C29 C30 C C sing 1.51 N N
25 C30 C31 C C sing 1.53 N N
26 C31 C32 C C sing 1.51 N N
27 C32 C33 C C sing 1.51 N N
28 C32 C34 C C doub 1.31 N N
29 C34 C35 C C sing 1.51 N N
30 C35 C36 C C sing 1.53 N N
31 C36 C37 C C sing 1.51 N N
32 C37 C38 C C sing 1.51 Z N
33 C37 C39 C C doub 1.31 N N
34 C39 C40 C C sing 1.51 N N
35 C40 C41 C C sing 1.53 N N
36 C41 C42 C C sing 1.51 N N
37 C42 C43 C C sing 1.51 N N
38 C42 C44 C C doub 1.31 N N
39 C44 C45 C C sing 1.51 N N
40 C45 C46 C C sing 1.53 N N
41 C46 C47 C C sing 1.51 N N
42 C47 C48 C C sing 1.51 N N
43 C47 C49 C C doub 1.31 N N
44 C49 C50 C C sing 1.51 N N
45 C50 C51 C C sing 1.53 Z N
46 C51 C52 C C sing 1.51 N N
47 C52 C53 C C sing 1.51 N N
48 C52 C54 C C doub 1.31 N N
49 C54 C55 C C sing 1.51 N N
50 C55 O56 C O sing 1.43 N N
51 O56 P57 O P sing 1.61 N N
52 P57 O58 P O doub 1.48 N N
53 P57 O59 P O sing 1.61 N N
54 P57 O60 P O sing 1.61 N N
55 C06 H061 C H sing 1.09 N N
56 C06 H062 C H sing 1.09 N N
57 C06 H063 C H sing 1.09 N N
58 C08 H081 C H sing 1.09 Z N
59 C08 H082 C H sing 1.09 N N
60 C08 H083 C H sing 1.09 N N
61 C09 H09 C H sing 1.08 N N
62 C10 H101 C H sing 1.09 N N
63 C10 H102 C H sing 1.09 N N
64 C11 H111 C H sing 1.09 N N
65 C11 H112 C H sing 1.09 N N
66 C13 H131 C H sing 1.09 N N
67 C13 H132 C H sing 1.09 N N
68 C13 H133 C H sing 1.09 N N
69 C14 H14 C H sing 1.08 N N
70 C15 H151 C H sing 1.09 N N
71 C15 H152 C H sing 1.09 Z N
72 C16 H161 C H sing 1.09 N N
73 C16 H162 C H sing 1.09 N N
74 C18 H181 C H sing 1.09 N N
75 C18 H182 C H sing 1.09 N N
76 C18 H183 C H sing 1.09 N N
77 C19 H19 C H sing 1.08 N N
78 C20 H201 C H sing 1.09 N N
79 C20 H202 C H sing 1.09 N N
80 C21 H211 C H sing 1.09 N N
81 C21 H212 C H sing 1.09 N N
82 C23 H231 C H sing 1.09 N N
83 C23 H232 C H sing 1.09 N N
84 C23 H233 C H sing 1.09 Z N
85 C24 H24 C H sing 1.08 N N
86 C25 H251 C H sing 1.09 N N
87 C25 H252 C H sing 1.09 N N
88 C26 H261 C H sing 1.09 N N
89 C26 H262 C H sing 1.09 N N
90 C28 H281 C H sing 1.09 N N
91 C28 H282 C H sing 1.09 N N
92 C28 H283 C H sing 1.09 N N
93 C29 H29 C H sing 1.08 N N
94 C30 H301 C H sing 1.09 N N
95 C30 H302 C H sing 1.09 N N
96 C31 H311 C H sing 1.09 N N
97 C31 H312 C H sing 1.09 Z N
98 C33 H331 C H sing 1.09 N N
99 C33 H332 C H sing 1.09 N N
100 C33 H333 C H sing 1.09 N N
101 C34 H34 C H sing 1.08 N N
102 C35 H351 C H sing 1.09 N N
103 C35 H352 C H sing 1.09 N N
104 C36 H361 C H sing 1.09 N N
105 C36 H362 C H sing 1.09 N N
106 C38 H381 C H sing 1.09 N N
107 C38 H382 C H sing 1.09 N N
108 C38 H383 C H sing 1.09 N N
109 C39 H39 C H sing 1.08 N N
110 C40 H401 C H sing 1.09 Z N
111 C40 H402 C H sing 1.09 N N
112 C41 H411 C H sing 1.09 N N
113 C41 H412 C H sing 1.09 N N
114 C43 H431 C H sing 1.09 N N
115 C43 H432 C H sing 1.09 N N
116 C43 H433 C H sing 1.09 N N
117 C44 H44 C H sing 1.08 N N
118 C45 H451 C H sing 1.09 N N
119 C45 H452 C H sing 1.09 N N
120 C46 H461 C H sing 1.09 N N
121 C46 H462 C H sing 1.09 N N
122 C48 H481 C H sing 1.09 N N
123 C48 H482 C H sing 1.09 Z N
124 C48 H483 C H sing 1.09 N N
125 C49 H49 C H sing 1.08 N N
126 C50 H501 C H sing 1.09 N N
127 C50 H502 C H sing 1.09 N N
128 C51 H511 C H sing 1.09 N N
129 C51 H512 C H sing 1.09 N N
130 C53 H531 C H sing 1.09 N N
131 C53 H532 C H sing 1.09 N N
132 C53 H533 C H sing 1.09 N N
133 C54 H54 C H sing 1.08 N N
134 C55 H551 C H sing 1.09 N N
135 C55 H552 C H sing 1.09 N N
136 O60 H60 O H sing 0.97 N N
137 O59 H59 O H sing 0.97 N N



DSL : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
DSL 2xxp Open in New Window Bound ligand 1 1
DSL 5ezm Open in New Window Bound ligand 1 1
DSL 7bvf Open in New Window Bound ligand 1 1