Chemical Components in the PDB

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YOY : Summary

Code

YOY

One-letter code

X

Molecule name

[[(2S,3aS,5S,6R,6aS)-2-dodecyl-6-oxidanyl-3a,5,6,6a-tetrahydrofuro[2,3-d][1,3]dioxol-5-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 [[(2~{S},3~{a}~{S},5~{S},6~{R},6~{a}~{S})-2-dodecyl-6-oxidanyl-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]dioxol-5-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate

Formula

C28 H47 N5 O14 P2

Formal charge

0

Molecular weight

739.645 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CCCCCCCCCCCC[CH]1O[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O1
SMILES OpenEye OEToolkits 2.0.7 CCCCCCCCCCCCC1OC2C(C(OC2O1)COP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O
Canonical SMILES CACTVS 3.385 CCCCCCCCCCCC[C@@H]1O[C@@H]2O[C@@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@@H]2O1
Canonical SMILES OpenEye OEToolkits 2.0.7 CCCCCCCCCCCC[C@H]1O[C@H]2[C@@H]([C@@H](O[C@H]2O1)COP(=O)(O)OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O

IUPAC InChI

InChI=1S/C28H47N5O14P2/c1-2-3-4-5-6-7-8-9-10-11-12-19-45-24-22(35)18(44-28(24)46-19)14-42-49(39,40)47-48(37,38)41-13-17-21(34)23(36)27(43-17)33-16-32-20-25(29)30-15-31-26(20)33/h15-19,21-24,27-28,34-36H,2-14H2,1H3,(H,37,38)(H,39,40)(H2,29,30,31)/t17-,18+,19+,21-,22-,23-,24+,27-,28+/m1/s1

IUPAC InChI key

KJBRVZZXXRAVKC-XBVYZWAMSA-N
YOY

wwPDB Information

Atom count

96 (49 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-11-08

Last modified at

2021-03-26

Status

Released

Obsoleted

Not Assigned



YOY : Atoms of Molecule

Total Number of Atoms: 96
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N N N1 N N N 0 6.772 4.927 4.687
2 C C C1 N Y N 0 6.355 5.08 3.376
3 O O O1 N N N 0 4.468 1.334 -0.753
4 C1 C C2 N Y N 0 5.789 6.445 1.603
5 C10 C C3 S N N 0 -3.624 -4.648 2.096
6 C11 C C4 S N N 0 -5.678 -4.036 1.21
7 C12 C C5 N N N 0 -5.868 -2.925 0.176
8 C13 C C6 N N N 0 -6.444 -1.684 0.861
9 C14 C C7 N N N 0 -6.634 -0.572 -0.173
10 C15 C C8 S N N 0 -4.342 -5.877 1.459
11 C16 C C9 R N N 0 -3.198 -6.518 0.638
12 C17 C C10 S N N 0 5.735 1.655 -2.766
13 C18 C C11 R N N 0 6.285 2.546 -1.626
14 C19 C C12 N N N 0 -7.21 0.669 0.512
15 C2 C C13 N Y N 0 5.675 4.178 1.246
16 C20 C C14 N N N 0 -7.399 1.78 -0.523
17 C21 C C15 N N N 0 -7.976 3.021 0.162
18 C22 C C16 N N N 0 -8.165 4.133 -0.872
19 C23 C C17 N N N 0 -8.741 5.373 -0.187
20 C24 C C18 N N N 0 -8.931 6.485 -1.221
21 C25 C C19 N N N 0 -9.507 7.726 -0.536
22 C26 C C20 N N N 0 -9.696 8.837 -1.571
23 C27 C C21 N N N 0 -10.273 10.078 -0.886
24 C3 C C22 N Y N 0 5.8 2.015 1.655
25 C4 C C23 N Y N 0 6.096 3.959 2.568
26 C5 C C24 R N N 0 5.065 2.646 -0.675
27 C6 C C25 R N N 0 4.537 0.923 -2.129
28 C7 C C26 N N N 0 4.749 -0.59 -2.21
29 C8 C C27 N N N 0 -0.856 -5.661 0.319
30 C9 C C28 S N N 0 -2.341 -5.302 0.232
31 N1 N N2 N Y N 0 6.186 6.29 2.853
32 N2 N N3 N Y N 0 5.539 5.426 0.809
33 N3 N N4 N Y N 0 5.5 2.934 0.694
34 N4 N N5 N Y N 0 6.152 2.618 2.753
35 O1 O O2 N N N 0 3.585 -1.261 -1.724
36 O13 O O3 N N N 0 -5.268 -5.245 0.55
37 O14 O O4 N N N 0 -2.441 -7.422 1.445
38 O15 O O5 N N N 0 5.303 2.459 -3.865
39 O16 O O6 N N N 0 6.654 3.835 -2.119
40 O2 O O7 N N N 0 3.479 -3.461 -3.159
41 O3 O O8 N N N 0 4.593 -3.421 -0.894
42 O4 O O9 N N N 0 2.075 -3.267 -0.945
43 O5 O O10 N N N 0 1.981 -5.789 -0.986
44 O6 O O11 N N N 0 2.122 -4.675 1.275
45 O7 O O12 N N N 0 -0.073 -4.57 -0.168
46 O8 O O13 N N N 0 -2.637 -4.24 1.142
47 O9 O O14 N N N 0 -4.665 -3.654 2.147
48 P P P1 N N N 0 3.458 -2.865 -1.664
49 P1 P P2 N N N 0 1.536 -4.601 -0.223
50 H1 H H1 N N N 0 6.944 5.708 5.235
51 H2 H H2 N N N 0 6.888 4.038 5.058
52 H3 H H3 N N N 0 5.663 7.447 1.219
53 H4 H H4 N N N 0 -3.195 -4.871 3.073
54 H5 H H5 N N N 0 -6.617 -4.207 1.737
55 H6 H H6 N N N 0 -4.906 -2.678 -0.273
56 H7 H H7 N N N 0 -6.555 -3.264 -0.6
57 H8 H H8 N N N 0 -7.406 -1.93 1.31
58 H9 H H9 N N N 0 -5.757 -1.345 1.637
59 H10 H H10 N N N 0 -5.672 -0.326 -0.622
60 H11 H H11 N N N 0 -7.32 -0.911 -0.949
61 H12 H H12 N N N 0 -4.801 -6.553 2.18
62 H13 H H13 N N N 0 -3.592 -7.023 -0.244
63 H14 H H14 N N N 0 6.492 0.941 -3.091
64 H15 H H15 N N N 0 7.128 2.066 -1.129
65 H16 H H16 N N N 0 -8.172 0.422 0.961
66 H17 H H17 N N N 0 -6.523 1.007 1.287
67 H18 H H18 N N N 0 -6.437 2.026 -0.972
68 H19 H H19 N N N 0 -8.086 1.441 -1.298
69 H20 H H20 N N N 0 -8.938 2.774 0.611
70 H21 H H21 N N N 0 -7.289 3.36 0.938
71 H22 H H22 N N N 0 -7.203 4.379 -1.321
72 H23 H H23 N N N 0 -8.852 3.794 -1.648
73 H24 H H24 N N N 0 -9.703 5.127 0.262
74 H25 H H25 N N N 0 -8.054 5.712 0.589
75 H26 H H26 N N N 0 -7.969 6.732 -1.67
76 H27 H H27 N N N 0 -9.618 6.146 -1.997
77 H28 H H28 N N N 0 -10.469 7.479 -0.087
78 H29 H H29 N N N 0 -8.82 8.065 0.239
79 H30 H H30 N N N 0 -8.734 9.084 -2.02
80 H31 H H31 N N N 0 -10.383 8.499 -2.346
81 H32 H H32 N N N 0 -11.235 9.832 -0.437
82 H33 H H33 N N N 0 -9.586 10.417 -0.11
83 H34 H H34 N N N 0 -10.408 10.87 -1.623
84 H35 H H35 N N N 0 5.756 0.944 1.523
85 H36 H H36 N N N 0 4.367 3.407 -1.025
86 H37 H H37 N N N 0 3.618 1.198 -2.645
87 H38 H H38 N N N 0 4.928 -0.877 -3.246
88 H39 H H39 N N N 0 5.61 -0.869 -1.602
89 H40 H H40 N N N 0 -0.592 -5.863 1.357
90 H41 H H41 N N N 0 -0.661 -6.547 -0.284
91 H42 H H42 N N N 0 -2.588 -4.998 -0.785
92 H43 H H43 N N N 0 -1.711 -7.851 0.978
93 H44 H H44 N N N 0 6.006 2.986 -4.267
94 H45 H H45 N N N 0 7.354 3.815 -2.786
95 H46 H H46 N N N 0 2.761 -3.139 -3.721
96 H47 H H47 N N N 0 1.87 -3.927 1.833



YOY : Chemical Bonds

Total Number of Bonds: 100
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C14 C19 C C sing 1.53 N N
2 C14 C13 C C sing 1.53 N N
3 C20 C19 C C sing 1.53 N N
4 C20 C21 C C sing 1.53 N N
5 C22 C23 C C sing 1.53 N N
6 C22 C21 C C sing 1.53 N N
7 C12 C13 C C sing 1.53 N N
8 C12 C11 C C sing 1.53 N N
9 C23 C24 C C sing 1.53 N N
10 C11 O9 C O sing 1.43 N N
11 C11 O13 C O sing 1.44 N N
12 C25 C24 C C sing 1.53 N N
13 C25 C26 C C sing 1.53 N N
14 O9 C10 O C sing 1.44 N N
15 C26 C27 C C sing 1.53 N N
16 O13 C15 O C sing 1.44 N N
17 C10 O8 C O sing 1.43 N N
18 C10 C15 C C sing 1.56 N N
19 O8 C9 O C sing 1.43 N N
20 C15 C16 C C sing 1.55 N N
21 C16 C9 C C sing 1.54 N N
22 C16 O14 C O sing 1.43 N N
23 C9 C8 C C sing 1.53 N N
24 C8 O7 C O sing 1.43 N N
25 O7 P1 O P sing 1.61 N N
26 O3 P O P doub 1.48 N N
27 O2 P O P sing 1.61 N N
28 P1 O5 P O doub 1.48 N N
29 P1 O4 P O sing 1.61 N N
30 P1 O6 P O sing 1.61 N N
31 P O4 P O sing 1.61 N N
32 P O1 P O sing 1.61 N N
33 O1 C7 O C sing 1.43 N N
34 C7 C6 C C sing 1.53 N N
35 C6 C17 C C sing 1.54 N N
36 C6 O C O sing 1.44 N N
37 C17 C18 C C sing 1.55 N N
38 C17 O15 C O sing 1.43 N N
39 C18 O16 C O sing 1.43 N N
40 C18 C5 C C sing 1.55 N N
41 C3 N4 C N doub 1.3 N Y
42 C3 N3 C N sing 1.36 N Y
43 O C5 O C sing 1.44 N N
44 N4 C4 N C sing 1.35 N Y
45 C5 N3 C N sing 1.47 N N
46 N3 C2 N C sing 1.37 N Y
47 C4 C2 C C doub 1.4 N Y
48 C4 C C C sing 1.41 N Y
49 C2 N2 C N sing 1.33 N Y
50 N C N C sing 1.38 N N
51 C N1 C N doub 1.33 N Y
52 N2 C1 N C doub 1.32 N Y
53 N1 C1 N C sing 1.32 N Y
54 N H1 N H sing 0.97 N N
55 N H2 N H sing 0.97 N N
56 C1 H3 C H sing 1.08 N N
57 C10 H4 C H sing 1.09 N N
58 C11 H5 C H sing 1.09 N N
59 C12 H6 C H sing 1.09 N N
60 C12 H7 C H sing 1.09 N N
61 C13 H8 C H sing 1.09 N N
62 C13 H9 C H sing 1.09 N N
63 C14 H10 C H sing 1.09 N N
64 C14 H11 C H sing 1.09 N N
65 C15 H12 C H sing 1.09 N N
66 C16 H13 C H sing 1.09 N N
67 C17 H14 C H sing 1.09 N N
68 C18 H15 C H sing 1.09 N N
69 C19 H16 C H sing 1.09 N N
70 C19 H17 C H sing 1.09 N N
71 C20 H18 C H sing 1.09 N N
72 C20 H19 C H sing 1.09 N N
73 C21 H20 C H sing 1.09 N N
74 C21 H21 C H sing 1.09 N N
75 C22 H22 C H sing 1.09 N N
76 C22 H23 C H sing 1.09 N N
77 C23 H24 C H sing 1.09 N N
78 C23 H25 C H sing 1.09 N N
79 C24 H26 C H sing 1.09 N N
80 C24 H27 C H sing 1.09 N N
81 C25 H28 C H sing 1.09 N N
82 C25 H29 C H sing 1.09 N N
83 C26 H30 C H sing 1.09 N N
84 C26 H31 C H sing 1.09 N N
85 C27 H32 C H sing 1.09 N N
86 C27 H33 C H sing 1.09 N N
87 C27 H34 C H sing 1.09 N N
88 C3 H35 C H sing 1.08 N N
89 C5 H36 C H sing 1.09 N N
90 C6 H37 C H sing 1.09 N N
91 C7 H38 C H sing 1.09 N N
92 C7 H39 C H sing 1.09 N N
93 C8 H40 C H sing 1.09 N N
94 C8 H41 C H sing 1.09 N N
95 C9 H42 C H sing 1.09 N N
96 O14 H43 O H sing 0.97 N N
97 O15 H44 O H sing 0.97 N N
98 O16 H45 O H sing 0.97 N N
99 O2 H46 O H sing 0.97 N N
100 O6 H47 O H sing 0.97 N N



YOY : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
YOY 6l71 Open in New Window Bound ligand 1 1