Chemical Components in the PDB

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OFN : Summary

Code

OFN

One-letter code

X

Molecule name

~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 3-oxidanylideneicosanethioate

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 ~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 3-oxidanylideneicosanethioate

Formula

C41 H72 N7 O18 P3 S

Formal charge

0

Molecular weight

1076.033 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CCCCCCCCCCCCCCCCCC(=O)CC(=O)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
SMILES OpenEye OEToolkits 2.0.7 CCCCCCCCCCCCCCCCCC(=O)CC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
Canonical SMILES CACTVS 3.385 CCCCCCCCCCCCCCCCCC(=O)CC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
Canonical SMILES OpenEye OEToolkits 2.0.7 CCCCCCCCCCCCCCCCCC(=O)CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O

IUPAC InChI

InChI=1S/C41H72N7O18P3S/c1-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-29(49)24-32(51)70-23-22-43-31(50)20-21-44-39(54)36(53)41(2,3)26-63-69(60,61)66-68(58,59)62-25-30-35(65-67(55,56)57)34(52)40(64-30)48-28-47-33-37(42)45-27-46-38(33)48/h27-28,30,34-36,40,52-53H,4-26H2,1-3H3,(H,43,50)(H,44,54)(H,58,59)(H,60,61)(H2,42,45,46)(H2,55,56,57)/t30-,34-,35-,36+,40-/m1/s1

IUPAC InChI key

FYBVHNZJDVUVLJ-IBYUJNRCSA-N
OFN

wwPDB Information

Atom count

142 (70 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-03-02

Last modified at

2020-05-08

Status

Released

Obsoleted

Not Assigned



OFN : Atoms of Molecule

Total Number of Atoms: 142
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C16 C C1 R N N 0 -12.829 -3.634 -0.095
2 C17 C C2 R N N 0 -11.541 -3.28 -0.871
3 C18 C C3 N Y N 0 -10.867 -5.383 -2.109
4 C19 C C4 N Y N 0 -11.557 -6.507 -3.991
5 C20 C C5 N Y N 0 -9.783 -7.413 -2.826
6 C21 C C6 N Y N 0 -9.873 -6.355 -1.906
7 C22 C C7 N Y N 0 -9.696 -4.905 -0.303
8 O10 O O1 N N N 0 -10.307 0.102 1.467
9 O14 O O2 N N N 0 -16.026 -3.05 2.065
10 O15 O O3 N N N 0 -13.93 -3.782 -0.994
11 C23 C C8 N N N 0 10.445 1.743 -2.325
12 C24 C C9 N N N 0 11.831 1.354 -2.772
13 C25 C C10 N N N 0 12.665 0.95 -1.554
14 O17 O O4 N N N 0 10.154 1.701 -1.153
15 C26 C C11 N N N 0 14.071 0.555 -2.008
16 C27 C C12 N N N 0 14.905 0.151 -0.79
17 C28 C C13 N N N 0 16.312 -0.244 -1.244
18 C29 C C14 N N N 0 17.146 -0.648 -0.026
19 C30 C C15 N N N 0 18.553 -1.043 -0.48
20 C31 C C16 N N N 0 19.387 -1.447 0.738
21 C32 C C17 N N N 0 20.794 -1.842 0.284
22 C33 C C18 N N N 0 21.627 -2.246 1.502
23 C34 C C19 N N N 0 23.034 -2.64 1.048
24 C35 C C20 N N N 0 23.868 -3.045 2.265
25 C36 C C21 N N N 0 25.275 -3.439 1.812
26 C37 C C22 N N N 0 26.109 -3.843 3.029
27 C38 C C23 N N N 0 27.516 -4.238 2.576
28 C39 C C24 N N N 0 28.349 -4.642 3.793
29 C40 C C25 N N N 0 29.756 -5.037 3.339
30 C C C26 N N N 0 9.422 2.184 -3.34
31 C1 C C27 N N N 0 8.129 2.514 -2.639
32 O O O5 N N N 0 8.047 2.402 -1.434
33 S S S1 N N N 0 6.777 3.047 -3.544
34 C2 C C28 N N N 0 5.576 3.276 -2.209
35 C3 C C29 N N N 0 4.25 3.764 -2.795
36 N N N1 N N N 0 3.278 3.949 -1.715
37 C4 C C30 N N N 0 2.031 4.377 -1.996
38 O1 O O6 N N N 0 1.714 4.609 -3.144
39 C5 C C31 N N N 0 1.031 4.567 -0.885
40 C6 C C32 N N N 0 -0.296 5.055 -1.47
41 N1 N N2 N N N 0 -1.268 5.24 -0.39
42 C7 C C33 N N N 0 -2.514 5.668 -0.672
43 O2 O O7 N N N 0 -2.804 5.989 -1.805
44 C8 C C34 R N N 0 -3.548 5.748 0.422
45 O3 O O8 N N N 0 -2.912 5.588 1.692
46 C9 C C35 N N N 0 -4.583 4.639 0.227
47 C10 C C36 N N N 0 -5.367 4.893 -1.062
48 C11 C C37 N N N 0 -3.872 3.288 0.132
49 C12 C C38 N N N 0 -5.547 4.625 1.416
50 O4 O O9 N N N 0 -6.514 3.589 1.233
51 P P P1 N N N 0 -7.686 3.287 2.295
52 O5 O O10 N N N 0 -7.093 3.054 3.631
53 O6 O O11 N N N 0 -8.686 4.547 2.363
54 O7 O O12 N N N 0 -8.503 1.978 1.835
55 P1 P P2 N N N 0 -9.545 0.995 2.569
56 O8 O O13 N N N 0 -8.751 0.032 3.585
57 O9 O O14 N N N 0 -10.534 1.799 3.322
58 C13 C C39 N N N 0 -11.371 -0.795 1.792
59 C14 C C40 R N N 0 -11.867 -1.481 0.518
60 O16 O O15 N N N 0 -10.842 -2.345 -0.02
61 C15 C C41 S N N 0 -13.049 -2.423 0.84
62 O11 O O16 N N N 0 -14.293 -1.784 0.547
63 P2 P P3 N N N 0 -15.464 -1.604 1.637
64 O13 O O17 N N N 0 -16.658 -0.73 1.003
65 O12 O O18 N N N 0 -14.926 -0.911 2.829
66 N2 N N3 N Y N 0 -10.729 -4.48 -1.085
67 N6 N N4 N Y N 0 -9.195 -6.004 -0.787
68 N5 N N5 N N N 0 -8.824 -8.4 -2.678
69 N4 N N6 N Y N 0 -10.639 -7.444 -3.842
70 N3 N N7 N Y N 0 -11.679 -5.498 -3.155
71 H1 H H1 N N N 0 -12.687 -4.544 0.486
72 H2 H H2 N N N 0 -11.788 -2.813 -1.824
73 H3 H H3 N N N 0 -12.233 -6.57 -4.832
74 H4 H H4 N N N 0 -9.343 -4.402 0.585
75 H5 H H5 N N N 0 -16.395 -3.562 1.332
76 H6 H H6 N N N 0 -13.816 -4.491 -1.641
77 H7 H H7 N N N 0 11.767 0.514 -3.463
78 H8 H H8 N N N 0 12.303 2.201 -3.27
79 H9 H H9 N N N 0 12.728 1.79 -0.862
80 H10 H H10 N N N 0 12.193 0.103 -1.055
81 H11 H H11 N N N 0 14.008 -0.285 -2.7
82 H12 H H12 N N N 0 14.543 1.402 -2.506
83 H13 H H13 N N N 0 14.969 0.991 -0.098
84 H14 H H14 N N N 0 14.434 -0.696 -0.292
85 H15 H H15 N N N 0 16.249 -1.084 -1.936
86 H16 H H16 N N N 0 16.784 0.603 -1.742
87 H17 H H17 N N N 0 17.21 0.192 0.666
88 H18 H H18 N N N 0 16.674 -1.494 0.472
89 H19 H H19 N N N 0 18.489 -1.882 -1.172
90 H20 H H20 N N N 0 19.025 -0.196 -0.979
91 H21 H H21 N N N 0 19.45 -0.607 1.429
92 H22 H H22 N N N 0 18.915 -2.293 1.236
93 H23 H H23 N N N 0 20.73 -2.681 -0.408
94 H24 H H24 N N N 0 21.265 -0.995 -0.215
95 H25 H H25 N N N 0 21.691 -1.406 2.193
96 H26 H H26 N N N 0 21.156 -3.092 2.0
97 H27 H H27 N N N 0 22.971 -3.48 0.356
98 H28 H H28 N N N 0 23.506 -1.794 0.549
99 H29 H H29 N N N 0 23.932 -2.205 2.957
100 H30 H H30 N N N 0 23.396 -3.891 2.764
101 H31 H H31 N N N 0 25.211 -4.279 1.12
102 H32 H H32 N N N 0 25.747 -2.593 1.313
103 H33 H H33 N N N 0 26.172 -3.004 3.721
104 H34 H H34 N N N 0 25.637 -4.69 3.528
105 H35 H H35 N N N 0 27.452 -5.078 1.884
106 H36 H H36 N N N 0 27.987 -3.392 2.077
107 H37 H H37 N N N 0 28.413 -3.803 4.485
108 H38 H H38 N N N 0 27.878 -5.489 4.292
109 H39 H H39 N N N 0 30.228 -4.19 2.841
110 H40 H H40 N N N 0 30.35 -5.325 4.207
111 H41 H H41 N N N 0 29.693 -5.877 2.648
112 H42 H H42 N N N 0 9.788 3.067 -3.864
113 H43 H H43 N N N 0 9.252 1.381 -4.057
114 H44 H H44 N N N 0 5.419 2.327 -1.695
115 H45 H H45 N N N 0 5.955 4.014 -1.502
116 H46 H H46 N N N 0 4.407 4.712 -3.309
117 H47 H H47 N N N 0 3.871 3.026 -3.502
118 H48 H H48 N N N 0 3.531 3.763 -0.797
119 H49 H H49 N N N 0 0.874 3.619 -0.371
120 H50 H H50 N N N 0 1.41 5.305 -0.178
121 H51 H H51 N N N 0 -0.139 6.004 -1.984
122 H52 H H52 N N N 0 -0.674 4.317 -2.178
123 H53 H H53 N N N 0 -1.014 5.055 0.527
124 H54 H H54 N N N 0 -4.044 6.718 0.383
125 H55 H H55 N N N 0 -2.45 4.745 1.797
126 H56 H H56 N N N 0 -6.156 4.148 -1.161
127 H57 H H57 N N N 0 -5.811 5.889 -1.027
128 H58 H H58 N N N 0 -4.694 4.826 -1.916
129 H59 H H59 N N N 0 -3.313 3.106 1.051
130 H60 H H60 N N N 0 -4.609 2.497 -0.007
131 H61 H H61 N N N 0 -3.185 3.297 -0.714
132 H62 H H62 N N N 0 -4.988 4.444 2.334
133 H63 H H63 N N N 0 -6.054 5.588 1.483
134 H64 H H64 N N N 0 -9.111 4.758 1.521
135 H65 H H65 N N N 0 -8.085 -0.526 3.159
136 H66 H H66 N N N 0 -11.009 -1.548 2.493
137 H67 H H67 N N N 0 -12.19 -0.239 2.248
138 H68 H H68 N N N 0 -12.163 -0.738 -0.222
139 H69 H H69 N N N 0 -13.015 -2.736 1.883
140 H70 H H70 N N N 0 -17.4 -0.582 1.605
141 H71 H H71 N N N 0 -8.771 -9.125 -3.32
142 H72 H H72 N N N 0 -8.205 -8.366 -1.932



OFN : Chemical Bonds

Total Number of Bonds: 144
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O12 P2 O P doub 1.48 N N
2 O14 P2 O P sing 1.61 N N
3 O13 P2 O P sing 1.61 N N
4 P2 O11 P O sing 1.61 N N
5 O15 C16 O C sing 1.43 N N
6 O11 C15 O C sing 1.43 N N
7 C15 C16 C C sing 1.55 N N
8 C15 C14 C C sing 1.55 N N
9 C16 C17 C C sing 1.54 N N
10 C14 C13 C C sing 1.53 N N
11 C14 O16 C O sing 1.44 N N
12 C17 O16 C O sing 1.44 N N
13 C17 N2 C N sing 1.46 N N
14 C13 O10 C O sing 1.43 N N
15 C22 N2 C N sing 1.36 N Y
16 C22 N6 C N doub 1.3 N Y
17 N2 C18 N C sing 1.37 N Y
18 O9 P1 O P doub 1.48 N N
19 O8 P1 O P sing 1.61 N N
20 O10 P1 O P sing 1.61 N N
21 N6 C21 N C sing 1.35 N Y
22 P1 O7 P O sing 1.61 N N
23 C18 N3 C N doub 1.33 N Y
24 C18 C21 C C sing 1.41 N Y
25 N3 C19 N C sing 1.32 N Y
26 C21 C20 C C doub 1.4 N Y
27 O7 P O P sing 1.61 N N
28 C19 N4 C N doub 1.32 N Y
29 C20 N4 C N sing 1.33 N Y
30 C20 N5 C N sing 1.38 N N
31 O5 P O P doub 1.48 N N
32 P O4 P O sing 1.61 N N
33 P O6 P O sing 1.61 N N
34 O4 C12 O C sing 1.43 N N
35 C10 C9 C C sing 1.53 N N
36 C12 C9 C C sing 1.53 N N
37 C9 C11 C C sing 1.53 N N
38 C9 C8 C C sing 1.53 N N
39 C8 O3 C O sing 1.43 N N
40 C8 C7 C C sing 1.51 N N
41 N1 C7 N C sing 1.35 N N
42 N1 C6 N C sing 1.46 N N
43 C7 O2 C O doub 1.21 N N
44 C5 C6 C C sing 1.53 N N
45 C5 C4 C C sing 1.51 N N
46 O1 C4 O C doub 1.21 N N
47 C4 N C N sing 1.35 N N
48 N C3 N C sing 1.46 N N
49 C3 C2 C C sing 1.53 N N
50 O C1 O C doub 1.21 N N
51 C2 S C S sing 1.81 N N
52 C1 S C S sing 1.71 N N
53 C1 C C C sing 1.51 N N
54 C C23 C C sing 1.51 N N
55 C23 C24 C C sing 1.51 N N
56 C23 O17 C O doub 1.21 N N
57 C24 C25 C C sing 1.53 N N
58 C25 C26 C C sing 1.53 N N
59 C26 C27 C C sing 1.53 N N
60 C27 C28 C C sing 1.53 N N
61 C28 C29 C C sing 1.53 N N
62 C29 C30 C C sing 1.53 N N
63 C30 C31 C C sing 1.53 N N
64 C32 C31 C C sing 1.53 N N
65 C32 C33 C C sing 1.53 N N
66 C34 C33 C C sing 1.53 N N
67 C34 C35 C C sing 1.53 N N
68 C35 C36 C C sing 1.53 N N
69 C36 C37 C C sing 1.53 N N
70 C37 C38 C C sing 1.53 N N
71 C38 C39 C C sing 1.53 N N
72 C39 C40 C C sing 1.53 N N
73 C16 H1 C H sing 1.09 N N
74 C17 H2 C H sing 1.09 N N
75 C19 H3 C H sing 1.08 N N
76 C22 H4 C H sing 1.08 N N
77 O14 H5 O H sing 0.97 N N
78 O15 H6 O H sing 0.97 N N
79 C24 H7 C H sing 1.09 N N
80 C24 H8 C H sing 1.09 N N
81 C25 H9 C H sing 1.09 N N
82 C25 H10 C H sing 1.09 N N
83 C26 H11 C H sing 1.09 N N
84 C26 H12 C H sing 1.09 N N
85 C27 H13 C H sing 1.09 N N
86 C27 H14 C H sing 1.09 N N
87 C28 H15 C H sing 1.09 N N
88 C28 H16 C H sing 1.09 N N
89 C29 H17 C H sing 1.09 N N
90 C29 H18 C H sing 1.09 N N
91 C30 H19 C H sing 1.09 N N
92 C30 H20 C H sing 1.09 N N
93 C31 H21 C H sing 1.09 N N
94 C31 H22 C H sing 1.09 N N
95 C32 H23 C H sing 1.09 N N
96 C32 H24 C H sing 1.09 N N
97 C33 H25 C H sing 1.09 N N
98 C33 H26 C H sing 1.09 N N
99 C34 H27 C H sing 1.09 N N
100 C34 H28 C H sing 1.09 N N
101 C35 H29 C H sing 1.09 N N
102 C35 H30 C H sing 1.09 N N
103 C36 H31 C H sing 1.09 N N
104 C36 H32 C H sing 1.09 N N
105 C37 H33 C H sing 1.09 N N
106 C37 H34 C H sing 1.09 N N
107 C38 H35 C H sing 1.09 N N
108 C38 H36 C H sing 1.09 N N
109 C39 H37 C H sing 1.09 N N
110 C39 H38 C H sing 1.09 N N
111 C40 H39 C H sing 1.09 N N
112 C40 H40 C H sing 1.09 N N
113 C40 H41 C H sing 1.09 N N
114 C H42 C H sing 1.09 N N
115 C H43 C H sing 1.09 N N
116 C2 H44 C H sing 1.09 N N
117 C2 H45 C H sing 1.09 N N
118 C3 H46 C H sing 1.09 N N
119 C3 H47 C H sing 1.09 N N
120 N H48 N H sing 0.97 N N
121 C5 H49 C H sing 1.09 N N
122 C5 H50 C H sing 1.09 N N
123 C6 H51 C H sing 1.09 N N
124 C6 H52 C H sing 1.09 N N
125 N1 H53 N H sing 0.97 N N
126 C8 H54 C H sing 1.09 N N
127 O3 H55 O H sing 0.97 N N
128 C10 H56 C H sing 1.09 N N
129 C10 H57 C H sing 1.09 N N
130 C10 H58 C H sing 1.09 N N
131 C11 H59 C H sing 1.09 N N
132 C11 H60 C H sing 1.09 N N
133 C11 H61 C H sing 1.09 N N
134 C12 H62 C H sing 1.09 N N
135 C12 H63 C H sing 1.09 N N
136 O6 H64 O H sing 0.97 N N
137 O8 H65 O H sing 0.97 N N
138 C13 H66 C H sing 1.09 N N
139 C13 H67 C H sing 1.09 N N
140 C14 H68 C H sing 1.09 N N
141 C15 H69 C H sing 1.09 N N
142 O13 H70 O H sing 0.97 N N
143 N5 H71 N H sing 0.97 N N
144 N5 H72 N H sing 0.97 N N



OFN : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
OFN 6y7f Open in New Window Bound ligand 2 1