Chemical Components in the PDB

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V7E : Summary

Code

V7E

One-letter code

X

Molecule name

3',3'-c-di-araAMP

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 (1~{S},6~{R},8~{R},9~{S},10~{S},15~{R},17~{R},18~{S})-8,17-bis(6-aminopurin-9-yl)-3,12-bis(oxidanyl)-3,12-bis(oxidanylidene)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.3.0.0^{6,10}]octadecane-9,18-diol

Formula

C20 H24 N10 O12 P2

Formal charge

0

Molecular weight

658.412 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 Nc1ncnc2n(cnc12)[CH]3O[CH]4CO[P](O)(=O)O[CH]5[CH](O)[CH](O[CH]5CO[P](O)(=O)O[CH]4[CH]3O)n6cnc7c(N)ncnc67
SMILES OpenEye OEToolkits 2.0.7 c1nc(c2c(n1)n(cn2)C3C(C4C(O3)COP(=O)(OC5C(COP(=O)(O4)O)OC(C5O)n6cnc7c6ncnc7N)O)O)N
Canonical SMILES CACTVS 3.385 Nc1ncnc2n(cnc12)[C@@H]3O[C@@H]4CO[P](O)(=O)O[C@H]5[C@H](O)[C@@H](O[C@@H]5CO[P](O)(=O)O[C@H]4[C@@H]3O)n6cnc7c(N)ncnc67
Canonical SMILES OpenEye OEToolkits 2.0.7 c1nc(c2c(n1)n(cn2)[C@H]3[C@H]([C@H]4[C@H](O3)COP(=O)(O[C@@H]5[C@@H](COP(=O)(O4)O)O[C@H]([C@H]5O)n6cnc7c6ncnc7N)O)O)N

IUPAC InChI

InChI=1S/C20H24N10O12P2/c21-15-9-17(25-3-23-15)29(5-27-9)19-11(31)13-7(39-19)1-37-43(33,34)42-14-8(2-38-44(35,36)41-13)40-20(12(14)32)30-6-28-10-16(22)24-4-26-18(10)30/h3-8,11-14,19-20,31-32H,1-2H2,(H,33,34)(H,35,36)(H2,21,23,25)(H2,22,24,26)/t7-,8-,11+,12+,13-,14-,19-,20-/m1/s1

IUPAC InChI key

PDXMFTWFFKBFIN-SVHUXIIHSA-N
V7E

wwPDB Information

Atom count

68 (44 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2021-04-22

Last modified at

2022-04-29

Status

Released

Obsoleted

Not Assigned



V7E : 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 P P P1 N N N 0 0.716 2.275 0.685
2 O1P O O1 N N N 0 0.921 2.508 -0.762
3 O2P O O2 N N N 0 0.45 3.682 1.423
4 O5' O O3 N N N 0 -0.554 1.309 0.899
5 C5' C C1 N N N 0 -1.901 1.735 0.684
6 C4' C C2 R N N 0 -2.86 0.736 1.334
7 O4' O O4 N N N 0 -4.205 1.214 1.235
8 C3' C C3 S N N 0 -2.793 -0.609 0.592
9 O3' O O5 N N N 0 -2.033 -1.556 1.346
10 C2' C C4 S N N 0 -4.26 -1.067 0.472
11 O2' O O6 N N N 0 -4.581 -1.351 -0.891
12 C1' C C5 R N N 0 -5.09 0.121 0.98
13 N9 N N1 N Y N 0 -6.073 0.507 -0.035
14 C8 C C6 N Y N 0 -5.924 1.489 -0.969
15 N7 N N2 N Y N 0 -6.991 1.562 -1.71
16 C5 C C7 N Y N 0 -7.89 0.635 -1.3
17 C6 C C8 N Y N 0 -9.18 0.26 -1.711
18 N6 N N3 N N N 0 -9.801 0.901 -2.769
19 N1 N N4 N Y N 0 -9.791 -0.725 -1.06
20 C2 C C9 N Y N 0 -9.206 -1.342 -0.05
21 N3 N N5 N Y N 0 -7.999 -1.025 0.369
22 C4 C C10 N Y N 0 -7.309 -0.056 -0.223
23 P1 P P2 N N N 0 -0.7 -2.259 0.779
24 O1P1 O O7 N N N 0 -0.529 -3.581 1.42
25 O2P1 O O8 N N N 0 -0.829 -2.448 -0.815
26 O5'1 O O9 N N N 0 0.575 -1.333 1.108
27 C5'1 C C11 N N N 0 1.92 -1.732 0.835
28 C4'1 C C12 R N N 0 2.883 -0.697 1.418
29 O4'1 O O10 N N N 0 4.23 -1.173 1.327
30 C3'1 C C13 S N N 0 2.8 0.607 0.607
31 O3'1 O O11 N N N 0 2.03 1.582 1.309
32 C2'1 C C14 S N N 0 4.263 1.074 0.463
33 C81 C C16 N Y N 0 5.918 -1.538 -0.887
34 O2'1 O O12 N N N 0 4.576 1.31 -0.912
35 C1'1 C C15 R N N 0 5.105 -0.088 1.011
36 N91 N N6 N Y N 0 6.075 -0.515 -0.001
37 N71 N N7 N Y N 0 6.974 -1.64 -1.64
38 C51 C C17 N Y N 0 7.874 -0.691 -1.286
39 C61 C C18 N Y N 0 9.156 -0.329 -1.732
40 N61 N N8 N N N 0 9.764 -1.014 -2.769
41 N11 N N9 N Y N 0 9.771 0.688 -1.136
42 C21 C C19 N Y N 0 9.198 1.347 -0.146
43 N31 N N10 N Y N 0 7.999 1.043 0.305
44 C41 C C20 N Y N 0 7.305 0.045 -0.233
45 H1 H H1 N N N 0 -0.327 4.156 1.097
46 H5'A H H2 N N N 0 -2.046 2.719 1.129
47 H5' H H3 N N N 0 -2.1 1.786 -0.386
48 H4' H H4 N N N 0 -2.597 0.595 2.382
49 H2' H H6 N N N 0 -4.435 -1.946 1.093
50 H3' H H5 N N N 0 -2.359 -0.474 -0.398
51 HO2' H H7 N N N 0 -5.493 -1.644 -1.027
52 H1' H H8 N N N 0 -5.604 -0.157 1.9
53 H8 H H9 N N N 0 -5.05 2.114 -1.078
54 H3 H H10 N N N 0 -9.345 1.619 -3.236
55 HN6 H H11 N N N 0 -10.692 0.633 -3.043
56 H2 H H12 N N N 0 -9.738 -2.138 0.451
57 H4 H H13 N N N 0 -0.06 -2.866 -1.225
58 HC5' H H14 N N N 0 2.111 -2.704 1.291
59 HC5A H H15 N N N 0 2.068 -1.8 -0.243
60 HC4' H H16 N N N 0 2.633 -0.5 2.46
61 HC3' H H17 N N N 0 2.37 0.414 -0.376
62 HC8 H H21 N N N 0 5.045 -2.171 -0.955
63 HC2' H H18 N N N 0 4.432 1.977 1.05
64 HO2A H H19 N N N 0 5.484 1.607 -1.063
65 HC1' H H20 N N N 0 5.632 0.232 1.91
66 H5 H H22 N N N 0 9.306 -1.754 -3.197
67 H1N6 H H23 N N N 0 10.65 -0.754 -3.069
68 HC2 H H24 N N N 0 9.733 2.167 0.311



V7E : Chemical Bonds

Total Number of Bonds: 74
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 P O1P P O doub 1.48 N N
2 P O2P P O sing 1.61 N N
3 P O5' P O sing 1.61 N N
4 P O3'1 P O sing 1.61 N N
5 O5' C5' O C sing 1.43 N N
6 C5' C4' C C sing 1.53 N N
7 C4' O4' C O sing 1.43 N N
8 C4' C3' C C sing 1.54 N N
9 O4' C1' O C sing 1.43 N N
10 C3' O3' C O sing 1.43 N N
11 C3' C2' C C sing 1.54 N N
12 O3' P1 O P sing 1.61 N N
13 C2' O2' C O sing 1.43 N N
14 C2' C1' C C sing 1.54 N N
15 C1' N9 C N sing 1.46 N N
16 N9 C8 N C sing 1.36 N Y
17 N9 C4 N C sing 1.37 N Y
18 C8 N7 C N doub 1.3 N Y
19 N7 C5 N C sing 1.35 N Y
20 C5 C6 C C doub 1.4 N Y
21 C5 C4 C C sing 1.41 N Y
22 C6 N6 C N sing 1.38 N N
23 C6 N1 C N sing 1.33 N Y
24 N1 C2 N C doub 1.32 N Y
25 C2 N3 C N sing 1.32 N Y
26 N3 C4 N C doub 1.33 N Y
27 P1 O1P1 P O doub 1.48 N N
28 P1 O2P1 P O sing 1.61 N N
29 P1 O5'1 P O sing 1.61 N N
30 O5'1 C5'1 O C sing 1.43 N N
31 C5'1 C4'1 C C sing 1.53 N N
32 C4'1 O4'1 C O sing 1.43 N N
33 C4'1 C3'1 C C sing 1.54 N N
34 O4'1 C1'1 O C sing 1.43 N N
35 C3'1 O3'1 C O sing 1.43 N N
36 C3'1 C2'1 C C sing 1.54 N N
37 C2'1 O2'1 C O sing 1.43 N N
38 C2'1 C1'1 C C sing 1.54 N N
39 C1'1 N91 C N sing 1.47 N N
40 N91 C81 N C sing 1.36 N Y
41 N91 C41 N C sing 1.37 N Y
42 C81 N71 C N doub 1.3 N Y
43 N71 C51 N C sing 1.35 N Y
44 C51 C61 C C doub 1.4 N Y
45 C51 C41 C C sing 1.41 N Y
46 C61 N61 C N sing 1.38 N N
47 C61 N11 C N sing 1.33 N Y
48 N11 C21 N C doub 1.32 N Y
49 C21 N31 C N sing 1.32 N Y
50 N31 C41 N C doub 1.33 N Y
51 O2P H1 O H sing 0.97 N N
52 C5' H5'A C H sing 1.09 N N
53 C5' H5' C H sing 1.09 N N
54 C4' H4' C H sing 1.09 N N
55 C3' H3' C H sing 1.09 N N
56 C2' H2' C H sing 1.09 N N
57 O2' HO2' O H sing 0.97 N N
58 C1' H1' C H sing 1.09 N N
59 C8 H8 C H sing 1.08 N N
60 N6 H3 N H sing 0.97 N N
61 N6 HN6 N H sing 0.97 N N
62 C2 H2 C H sing 1.08 N N
63 O2P1 H4 O H sing 0.97 N N
64 C5'1 HC5' C H sing 1.09 N N
65 C5'1 HC5A C H sing 1.09 N N
66 C4'1 HC4' C H sing 1.09 N N
67 C3'1 HC3' C H sing 1.09 N N
68 C2'1 HC2' C H sing 1.09 N N
69 O2'1 HO2A O H sing 0.97 N N
70 C1'1 HC1' C H sing 1.09 N N
71 C81 HC8 C H sing 1.08 N N
72 N61 H5 N H sing 0.97 N N
73 N61 H1N6 N H sing 0.97 N N
74 C21 HC2 C H sing 1.08 N N



V7E : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
V7E 7ob3 Open in New Window Bound ligand 1 1