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V3L : Summary
Code ![](/pdbe/static/images/help.png)
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V3L
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One-letter code ![](/pdbe/static/images/help.png)
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A
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Molecule name ![](/pdbe/static/images/help.png)
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2'-O-(5-O-phosphono-alpha-D-ribofuranosyl)adenosine 5'-(dihydrogen phosphate)
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Systematic names ![](/pdbe/static/images/help.png)
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Formula ![](/pdbe/static/images/help.png)
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C15 H23 N5 O14 P2
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Formal charge ![](/pdbe/static/images/help.png)
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0
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Molecular weight ![](/pdbe/static/images/help.png)
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559.316 Da
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SMILES ![](/pdbe/static/images/help.png)
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Type | Program | Version | Descriptor |
SMILES
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ACDLabs |
12.01 |
O=P(O)(O)OCC4OC(n1c2ncnc(N)c2nc1)C(OC3OC(C(O)C3O)COP(=O)(O)O)C4O |
SMILES
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CACTVS |
3.385 |
Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O[CH]4O[CH](CO[P](O)(O)=O)[CH](O)[CH]4O |
SMILES
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OpenEye OEToolkits |
1.7.6 |
c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)OC4C(C(C(O4)COP(=O)(O)O)O)O)N |
Canonical SMILES
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CACTVS |
3.385 |
Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O[C@H]4O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]4O |
Canonical SMILES
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OpenEye OEToolkits |
1.7.6 |
c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O[C@@H]4[C@@H]([C@@H]([C@H](O4)COP(=O)(O)O)O)O)N |
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IUPAC InChI ![](/pdbe/static/images/help.png) | InChI=1S/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-11(9(22)6(32-14)2-31-36(27,28)29)34-15-10(23)8(21)5(33-15)1-30-35(24,25)26/h3-6,8-11,14-15,21-23H,1-2H2,(H2,16,17,18)(H2,24,25,26)(H2,27,28,29)/t5-,6-,8-,9-,10-,11-,14-,15-/m1/s1 |
IUPAC InChI key ![](/pdbe/static/images/help.png) | BHIWBSNWEZIHHL-KEOHHSTQSA-N |
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wwPDB Information |
Atom count ![](/pdbe/static/images/help.png)
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59 (36 without Hydrogen)
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Polymer type ![](/pdbe/static/images/help.png)
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Ribonucleotide
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Type description ![](/pdbe/static/images/help.png)
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RNA linking
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Type code ![](/pdbe/static/images/help.png)
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ATOMN
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Is modified ![](/pdbe/static/images/help.png)
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Yes
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Standard parent ![](/pdbe/static/images/help.png)
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A
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Defined at ![](/pdbe/static/images/help.png)
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2011-12-21
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Last modified at ![](/pdbe/static/images/help.png)
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2014-05-29
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Status ![](/pdbe/static/images/help.png)
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Released
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Obsoleted ![](/pdbe/static/images/help.png)
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Not Assigned
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V3L : Atoms of Molecule
Total Number of Atoms: 59
Record |
Atom Name |
Symbol |
PDB Name |
Stereochemistry |
Is Aromatic |
Is Leaving Atom |
Charge |
X-Coordinate |
Y-Coordinate |
Z-Coordinate |
1 |
N1 |
N |
N1 |
N |
Y |
N |
0 |
-4.929 |
4.245 |
-0.019 |
2 |
C2 |
C |
C2 |
N |
Y |
N |
0 |
-3.902 |
4.069 |
-0.831 |
3 |
N3 |
N |
N3 |
N |
Y |
N |
0 |
-3.257 |
2.926 |
-0.917 |
4 |
C4 |
C |
C4 |
N |
Y |
N |
0 |
-3.622 |
1.885 |
-0.175 |
5 |
C5 |
C |
C5 |
N |
Y |
N |
0 |
-4.708 |
2.02 |
0.705 |
6 |
C6 |
C |
C6 |
N |
Y |
N |
0 |
-5.366 |
3.261 |
0.761 |
7 |
N6 |
N |
N6 |
N |
N |
N |
0 |
-6.443 |
3.454 |
1.608 |
8 |
N7 |
N |
N7 |
N |
Y |
N |
0 |
-4.867 |
0.829 |
1.33 |
9 |
C8 |
C |
C8 |
N |
Y |
N |
0 |
-3.968 |
-0.009 |
0.9 |
10 |
N9 |
N |
N9 |
N |
Y |
N |
0 |
-3.176 |
0.595 |
-0.03 |
11 |
P |
P |
P |
N |
N |
N |
0 |
-1.478 |
-5.77 |
0.006 |
12 |
PB |
P |
PB |
N |
N |
N |
0 |
5.999 |
-0.09 |
0.481 |
13 |
C10 |
C |
C1'' |
R |
N |
N |
0 |
0.597 |
2.217 |
0.528 |
14 |
C1' |
C |
C1' |
R |
N |
N |
0 |
-2.054 |
-0.02 |
-0.743 |
15 |
OP3 |
O |
OP3 |
N |
N |
Y |
0 |
-2.64 |
-6.627 |
-0.706 |
16 |
O1B |
O |
O1B |
N |
N |
N |
0 |
6.189 |
-0.047 |
2.079 |
17 |
C12 |
C |
C2'' |
R |
N |
N |
0 |
0.915 |
3.648 |
0.055 |
18 |
O12 |
O |
O2'' |
N |
N |
N |
0 |
0.321 |
3.897 |
-1.221 |
19 |
C2' |
C |
C2' |
R |
N |
N |
0 |
-0.715 |
0.289 |
-0.026 |
20 |
O2' |
O |
O2' |
N |
N |
N |
0 |
-0.179 |
1.539 |
-0.463 |
21 |
OP1 |
O |
OP1 |
N |
N |
N |
0 |
-1.743 |
-5.692 |
1.46 |
22 |
O2B |
O |
O2B |
N |
N |
N |
0 |
7.074 |
0.695 |
-0.165 |
23 |
C13 |
C |
C3'' |
S |
N |
N |
0 |
2.46 |
3.678 |
-0.052 |
24 |
O13 |
O |
O3'' |
N |
N |
N |
0 |
2.877 |
4.386 |
-1.221 |
25 |
C3' |
C |
C3' |
R |
N |
N |
0 |
0.179 |
-0.888 |
-0.488 |
26 |
O3' |
O |
O3' |
N |
N |
N |
0 |
1.002 |
-0.489 |
-1.586 |
27 |
OP2 |
O |
OP2 |
N |
N |
N |
0 |
-0.056 |
-6.482 |
-0.243 |
28 |
O3B |
O |
O3B |
N |
N |
N |
0 |
6.07 |
-1.617 |
-0.027 |
29 |
C14 |
C |
C4'' |
R |
N |
N |
0 |
2.806 |
2.171 |
-0.164 |
30 |
O14 |
O |
O4'' |
N |
N |
N |
0 |
1.85 |
1.539 |
0.714 |
31 |
C4' |
C |
C4' |
R |
N |
N |
0 |
-0.822 |
-1.972 |
-0.93 |
32 |
O4' |
O |
O4' |
N |
N |
N |
0 |
-2.143 |
-1.46 |
-0.686 |
33 |
C15 |
C |
C5'' |
N |
N |
N |
0 |
4.235 |
1.91 |
0.316 |
34 |
O15 |
O |
O5'' |
N |
N |
N |
0 |
4.569 |
0.538 |
0.094 |
35 |
C5' |
C |
C5' |
N |
N |
N |
0 |
-0.598 |
-3.25 |
-0.119 |
36 |
O5' |
O |
O5' |
N |
N |
N |
0 |
-1.45 |
-4.284 |
-0.615 |
37 |
H2 |
H |
H2 |
N |
N |
N |
0 |
-3.58 |
4.896 |
-1.447 |
38 |
HN6 |
H |
HN6 |
N |
N |
N |
0 |
-6.888 |
4.316 |
1.638 |
39 |
HN6A |
H |
HN6A |
N |
N |
N |
0 |
-6.752 |
2.729 |
2.172 |
40 |
H8 |
H |
H8 |
N |
N |
N |
0 |
-3.866 |
-1.031 |
1.232 |
41 |
H1'' |
H |
H1'' |
N |
N |
N |
0 |
0.05 |
2.251 |
1.47 |
42 |
H1' |
H |
H1' |
N |
N |
N |
0 |
-2.024 |
0.324 |
-1.777 |
43 |
HOP3 |
H |
HOP3 |
N |
N |
N |
0 |
-2.715 |
-7.535 |
-0.381 |
44 |
HO1B |
H |
HO1B |
N |
N |
N |
0 |
5.518 |
-0.542 |
2.569 |
45 |
H2'' |
H |
H2'' |
N |
N |
N |
0 |
0.57 |
4.378 |
0.787 |
46 |
HO2' |
H |
HO2' |
N |
N |
N |
0 |
-0.643 |
3.834 |
-1.225 |
47 |
H2' |
H |
H2' |
N |
N |
N |
0 |
-0.843 |
0.279 |
1.056 |
48 |
H3'' |
H |
H3'' |
N |
N |
N |
0 |
2.903 |
4.113 |
0.844 |
49 |
HO13 |
H |
HO3A |
N |
N |
N |
0 |
2.603 |
5.313 |
-1.237 |
50 |
H3' |
H |
H3' |
N |
N |
N |
0 |
0.793 |
-1.247 |
0.338 |
51 |
HO3' |
H |
HO3' |
N |
N |
Y |
0 |
1.583 |
-1.188 |
-1.915 |
52 |
HOP2 |
H |
HOP2 |
N |
N |
N |
0 |
0.183 |
-6.568 |
-1.176 |
53 |
HO3B |
H |
HO3B |
N |
N |
N |
0 |
6.907 |
-2.059 |
0.173 |
54 |
H5AA |
H |
H5AA |
N |
N |
N |
0 |
4.307 |
2.133 |
1.38 |
55 |
H4'' |
H |
H4'' |
N |
N |
N |
0 |
2.677 |
1.823 |
-1.189 |
56 |
H4' |
H |
H4' |
N |
N |
N |
0 |
-0.697 |
-2.181 |
-1.993 |
57 |
H5'' |
H |
H5'' |
N |
N |
N |
0 |
4.926 |
2.546 |
-0.237 |
58 |
H5' |
H |
H5' |
N |
N |
N |
0 |
0.443 |
-3.561 |
-0.212 |
59 |
H5'A |
H |
H5'A |
N |
N |
N |
0 |
-0.829 |
-3.06 |
0.929 |
V3L : Chemical Bonds
Total Number of Bonds: 62
V3L : Used in PDB Entries
Total Number of PDB Entries: 4
Ligand Code |
PDB Entry ID |
Type |
Total |
Distinct |
V3L |
3v3l ![Open in New Window](/pdbe-srv/pdbechem/images/newwin.png?_debugResources=y&n=1724230715548) |
Bound ligand
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2 |
1 |
V3L |
4n9y ![Open in New Window](/pdbe-srv/pdbechem/images/newwin.png?_debugResources=y&n=1724230715548) |
Bound ligand
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1 |
1 |
V3L |
4n9z ![Open in New Window](/pdbe-srv/pdbechem/images/newwin.png?_debugResources=y&n=1724230715548) |
Bound ligand
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2 |
1 |
V3L |
4qpl ![Open in New Window](/pdbe-srv/pdbechem/images/newwin.png?_debugResources=y&n=1724230715548) |
Bound ligand
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2 |
1 |
|