Chemical Components in the PDB

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V3L : Summary

Code

V3L

One-letter code

A

Molecule name

2'-O-(5-O-phosphono-alpha-D-ribofuranosyl)adenosine 5'-(dihydrogen phosphate)

Systematic names

ProgramVersionName
ACDLabs 12.01 2'-O-(5-O-phosphono-alpha-D-ribofuranosyl)adenosine 5'-(dihydrogen phosphate)
OpenEye OEToolkits 1.7.6 [(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[(2R,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]oxy-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate

Formula

C15 H23 N5 O14 P2

Formal charge

0

Molecular weight

559.316 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O)(O)OCC4OC(n1c2ncnc(N)c2nc1)C(OC3OC(C(O)C3O)COP(=O)(O)O)C4O
SMILES 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 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 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 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

IUPAC InChI

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

BHIWBSNWEZIHHL-KEOHHSTQSA-N
V3L

wwPDB Information

Atom count

59 (36 without Hydrogen)

Polymer type

Ribonucleotide

Type description

RNA linking

Type code

ATOMN

Is modified

Yes

Standard parent

A

Defined at

2011-12-21

Last modified at

2014-05-29

Status

Released

Obsoleted

Not Assigned



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
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 C6 N C doub 1.33 N Y
2 N1 C2 N C sing 1.32 N Y
3 C2 N3 C N doub 1.32 N Y
4 C2 H2 C H sing 1.08 N N
5 C4 N3 C N sing 1.33 N Y
6 C5 C4 C C doub 1.4 N Y
7 C4 N9 C N sing 1.37 N Y
8 C6 C5 C C sing 1.41 N Y
9 C5 N7 C N sing 1.35 N Y
10 N6 C6 N C sing 1.38 N N
11 N6 HN6 N H sing 0.97 N N
12 N6 HN6A N H sing 0.97 N N
13 N7 C8 N C doub 1.3 N Y
14 C8 N9 C N sing 1.36 N Y
15 C8 H8 C H sing 1.08 N N
16 N9 C1' N C sing 1.46 N N
17 OP1 P O P doub 1.48 N N
18 P O5' P O sing 1.61 N N
19 P OP3 P O sing 1.61 N N
20 P OP2 P O sing 1.61 N N
21 O15 PB O P sing 1.61 N N
22 O2B PB O P doub 1.48 N N
23 PB O3B P O sing 1.61 N N
24 PB O1B P O sing 1.61 N N
25 O2' C10 O C sing 1.43 N N
26 C10 C12 C C sing 1.54 N N
27 C10 O14 C O sing 1.44 N N
28 C10 H1'' C H sing 1.09 N N
29 O4' C1' O C sing 1.44 N N
30 C1' C2' C C sing 1.55 N N
31 C1' H1' C H sing 1.09 N N
32 OP3 HOP3 O H sing 0.97 N N
33 O1B HO1B O H sing 0.97 N N
34 O12 C12 O C sing 1.43 N N
35 C12 C13 C C sing 1.55 N N
36 C12 H2'' C H sing 1.09 N N
37 O12 HO2' O H sing 0.97 N N
38 C3' C2' C C sing 1.55 N N
39 C2' O2' C O sing 1.43 N N
40 C2' H2' C H sing 1.09 N N
41 O13 C13 O C sing 1.43 N N
42 C13 C14 C C sing 1.55 N N
43 C13 H3'' C H sing 1.09 N N
44 O13 HO13 O H sing 0.97 N N
45 C4' C3' C C sing 1.54 N N
46 C3' O3' C O sing 1.43 N N
47 C3' H3' C H sing 1.09 N N
48 O3' HO3' O H sing 0.97 N N
49 OP2 HOP2 O H sing 0.97 N N
50 O3B HO3B O H sing 0.97 N N
51 O14 C14 O C sing 1.44 N N
52 C14 C15 C C sing 1.53 N N
53 C14 H4'' C H sing 1.09 N N
54 O4' C4' O C sing 1.44 N N
55 C5' C4' C C sing 1.53 N N
56 C4' H4' C H sing 1.09 N N
57 C15 O15 C O sing 1.43 N N
58 C15 H5'' C H sing 1.09 N N
59 C15 H5AA C H sing 1.09 N N
60 C5' O5' C O sing 1.43 N N
61 C5' H5' C H sing 1.09 N N
62 C5' H5'A C H sing 1.09 N N



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 Bound ligand 2 1
V3L 4n9y Open in New Window Bound ligand 1 1
V3L 4n9z Open in New Window Bound ligand 2 1
V3L 4qpl Open in New Window Bound ligand 2 1