Chemical Components in the PDB

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78K : Summary

Code

78K

One-letter code

X

Molecule name

(2~{R})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[[4-azanyl-1-(methoxymethyl)-2-oxidanylidene-pyrimidin-5-yl]methyl]amino]-2-azanyl-butanoic acid

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.5 (2~{R})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[[4-azanyl-1-(methoxymethyl)-2-oxidanylidene-pyrimidin-5-yl]methyl]amino]-2-azanyl-butanoic acid

Formula

C21 H30 N10 O7

Formal charge

0

Molecular weight

534.526 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 COCN1C=C(CN(CC[CH](N)C(O)=O)C[CH]2O[CH]([CH](O)[CH]2O)n3cnc4c(N)ncnc34)C(=NC1=O)N
SMILES OpenEye OEToolkits 2.0.5 COCN1C=C(C(=NC1=O)N)CN(CCC(C(=O)O)N)CC2C(C(C(O2)n3cnc4c3ncnc4N)O)O
Canonical SMILES CACTVS 3.385 COCN1C=C(CN(CC[C@@H](N)C(O)=O)C[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34)C(=NC1=O)N
Canonical SMILES OpenEye OEToolkits 2.0.5 COCN1C=C(C(=NC1=O)N)CN(CC[C@H](C(=O)O)N)C[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O

IUPAC InChI

InChI=1S/C21H30N10O7/c1-37-9-30-5-10(16(23)28-21(30)36)4-29(3-2-11(22)20(34)35)6-12-14(32)15(33)19(38-12)31-8-27-13-17(24)25-7-26-18(13)31/h5,7-8,11-12,14-15,19,32-33H,2-4,6,9,22H2,1H3,(H,34,35)(H2,23,28,36)(H2,24,25,26)/t11-,12-,14-,15-,19-/m1/s1

IUPAC InChI key

UCWJYOSDGSOMTM-FSVZYJJUSA-N
78K

wwPDB Information

Atom count

68 (38 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2016-09-12

Last modified at

2017-09-15

Status

Released

Obsoleted

Not Assigned



78K : Atoms of Molecule

Total Number of Atoms: 68
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C11 C C1 N N N 0 2.829 -1.316 1.184
2 C21 C C2 N N N 0 -0.129 -5.464 -0.193
3 C12 C C3 N N N 0 3.917 -0.595 0.431
4 C13 C C4 N N N 0 4.348 -1.065 -0.826
5 C14 C C5 N N N 0 5.859 0.678 -0.955
6 C15 C C6 N N N 0 4.491 0.516 0.948
7 C16 C C7 N N N 0 6.103 2.352 0.794
8 C17 C C8 N N N 0 4.324 3.942 0.565
9 C1 C C9 N Y N 0 -6.968 0.661 -0.082
10 C2 C C10 N Y N 0 -5.633 0.503 0.326
11 C3 C C11 N Y N 0 -4.629 1.131 -0.431
12 N1 N N1 N Y N 0 -4.976 1.846 -1.496
13 C4 C C12 N Y N 0 -6.24 1.967 -1.84
14 N2 N N2 N Y N 0 -7.218 1.396 -1.161
15 N3 N N3 N Y N 0 -3.442 0.816 0.18
16 C5 C C13 N Y N 0 -3.732 0.032 1.257
17 N4 N N4 N Y N 0 -5.018 -0.151 1.341
18 C6 C C14 R N N 0 -2.107 1.243 -0.246
19 O1 O O1 N N N 0 -1.104 0.329 0.248
20 C7 C C15 R N N 0 0.135 1.07 0.216
21 C8 C C16 S N N 0 -0.241 2.488 0.703
22 C9 C C17 R N N 0 -1.749 2.604 0.391
23 O2 O O2 N N N 0 -1.99 3.668 -0.532
24 O3 O O3 N N N 0 0.497 3.476 -0.019
25 C10 C C18 N N N 0 1.158 0.437 1.161
26 N5 N N5 N N N 0 1.518 -0.899 0.669
27 N6 N N6 N N N 0 -7.999 0.062 0.62
28 N7 N N7 N N N 0 5.304 -0.414 -1.477
29 N8 N N8 N N N 0 5.473 1.148 0.246
30 N9 N N9 N N N 0 3.782 -2.192 -1.375
31 O4 O O4 N N N 0 5.605 3.503 0.11
32 O5 O O5 N N N 0 6.733 1.262 -1.575
33 C18 C C19 N N N 0 0.481 -1.883 1.01
34 C19 C C20 N N N 0 0.715 -3.168 0.214
35 C20 C C21 R N N 0 -0.421 -4.154 0.493
36 N10 N N10 N N N 0 -1.683 -3.605 -0.019
37 O6 O O6 N N N 0 0.723 -6.339 0.366
38 O7 O O7 N N N 0 -0.661 -5.727 -1.245
39 H12 H H1 N N N 0 2.946 -2.391 1.053
40 H11 H H2 N N N 0 2.897 -1.07 2.244
41 H15 H H3 N N N 0 4.175 0.899 1.908
42 H19 H H4 N N N 0 5.871 2.432 1.856
43 H18 H H5 N N N 0 7.183 2.289 0.662
44 H21 H H6 N N N 0 3.595 3.144 0.424
45 H22 H H7 N N N 0 4.382 4.197 1.624
46 H20 H H8 N N N 0 4.017 4.819 -0.003
47 H1 H H9 N N N 0 -6.487 2.556 -2.712
48 H2 H H10 N N N 0 -3.002 -0.379 1.939
49 H3 H H11 N N N 0 -2.059 1.307 -1.333
50 H4 H H12 N N N 0 0.529 1.108 -0.799
51 H5 H H13 N N N 0 -0.061 2.585 1.773
52 H6 H H14 N N N 0 -2.318 2.758 1.308
53 H7 H H15 N N N 0 -1.782 4.546 -0.184
54 H8 H H16 N N N 0 0.301 4.385 0.246
55 H10 H H17 N N N 0 2.051 1.062 1.201
56 H9 H H18 N N N 0 0.729 0.353 2.159
57 H14 H H20 N N N 0 -7.804 -0.475 1.404
58 H13 H H21 N N N 0 -8.917 0.179 0.329
59 H16 H H22 N N N 0 3.084 -2.666 -0.897
60 H17 H H23 N N N 0 4.081 -2.513 -2.241
61 H24 H H24 N N N 0 0.526 -2.102 2.077
62 H23 H H25 N N N 0 -0.5 -1.476 0.765
63 H25 H H26 N N N 0 0.742 -2.936 -0.85
64 H26 H H27 N N N 0 1.664 -3.613 0.513
65 H27 H H28 N N N 0 -0.505 -4.318 1.567
66 H28 H H29 N N N 0 -1.934 -2.759 0.471
67 H29 H H30 N N N 0 -1.631 -3.444 -1.014
68 H30 H H32 N N N 0 0.878 -7.165 -0.112



78K : Chemical Bonds

Total Number of Bonds: 71
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N6 C1 N C sing 1.38 N N
2 N2 C1 N C doub 1.33 N Y
3 N2 C4 N C sing 1.32 N Y
4 C1 C2 C C sing 1.4 N Y
5 C4 N1 C N doub 1.32 N Y
6 C2 N4 C N sing 1.36 N Y
7 C2 C3 C C doub 1.41 N Y
8 N4 C5 N C doub 1.3 N Y
9 N1 C3 N C sing 1.33 N Y
10 C3 N3 C N sing 1.37 N Y
11 C5 N3 C N sing 1.36 N Y
12 O2 C9 O C sing 1.43 N N
13 N3 C6 N C sing 1.46 N N
14 C9 C6 C C sing 1.54 N N
15 C9 C8 C C sing 1.54 N N
16 C6 O1 C O sing 1.44 N N
17 O1 C7 O C sing 1.44 N N
18 C8 O3 C O sing 1.43 N N
19 C8 C7 C C sing 1.55 N N
20 C7 C10 C C sing 1.53 N N
21 O5 C14 O C doub 1.22 N N
22 C17 O4 C O sing 1.43 N N
23 C10 N5 C N sing 1.47 N N
24 N7 C14 N C sing 1.33 N N
25 N7 C13 N C doub 1.33 N N
26 C14 N8 C N sing 1.35 N N
27 O4 C16 O C sing 1.43 N N
28 N9 C13 N C sing 1.38 N N
29 C13 C12 C C sing 1.41 N N
30 N8 C16 N C sing 1.47 N N
31 N8 C15 N C sing 1.36 N N
32 N5 C18 N C sing 1.47 N N
33 N5 C11 N C sing 1.47 N N
34 C12 C15 C C doub 1.35 N N
35 C12 C11 C C sing 1.51 N N
36 C18 C19 C C sing 1.53 N N
37 C19 C20 C C sing 1.53 N N
38 O7 C21 O C doub 1.21 N N
39 C20 N10 C N sing 1.47 N N
40 C20 C21 C C sing 1.51 N N
41 C21 O6 C O sing 1.34 N N
42 C11 H12 C H sing 1.09 N N
43 C11 H11 C H sing 1.09 N N
44 C15 H15 C H sing 1.08 N N
45 C16 H19 C H sing 1.09 N N
46 C16 H18 C H sing 1.09 N N
47 C17 H21 C H sing 1.09 N N
48 C17 H22 C H sing 1.09 N N
49 C17 H20 C H sing 1.09 N N
50 C4 H1 C H sing 1.08 N N
51 C5 H2 C H sing 1.08 N N
52 C6 H3 C H sing 1.09 N N
53 C7 H4 C H sing 1.09 N N
54 C8 H5 C H sing 1.09 N N
55 C9 H6 C H sing 1.09 N N
56 O2 H7 O H sing 0.97 N N
57 O3 H8 O H sing 0.97 N N
58 C10 H10 C H sing 1.09 N N
59 C10 H9 C H sing 1.09 N N
60 N6 H14 N H sing 0.97 N N
61 N6 H13 N H sing 0.97 N N
62 N9 H16 N H sing 0.97 N N
63 N9 H17 N H sing 0.97 N N
64 C18 H24 C H sing 1.09 N N
65 C18 H23 C H sing 1.09 N N
66 C19 H25 C H sing 1.09 N N
67 C19 H26 C H sing 1.09 N N
68 C20 H27 C H sing 1.09 N N
69 N10 H28 N H sing 1.01 N N
70 N10 H29 N H sing 1.01 N N
71 O6 H30 O H sing 0.97 N N



78K : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
78K 5lv4 Open in New Window Bound ligand 1 1
78K 5tbh Open in New Window Bound ligand 2 1