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C2G : Summary
Code
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C2G
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One-letter code
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X
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Molecule name
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[CYTIDINE-5'-PHOSPHATE] GLYCERYLPHOSPHORIC ACID ESTER
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Systematic names
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Formula
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C12 H21 N3 O13 P2
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Formal charge
|
0
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Molecular weight
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477.255 Da
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SMILES
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Type | Program | Version | Descriptor |
SMILES
|
ACDLabs |
10.04 |
O=P(O)(OCC(O)CO)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O |
SMILES
|
CACTVS |
3.341 |
NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH](O)CO)[CH](O)[CH]2O |
SMILES
|
OpenEye OEToolkits |
1.5.0 |
C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OCC(CO)O)O)O |
Canonical SMILES
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CACTVS |
3.341 |
NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@@H](O)CO)[C@@H](O)[C@H]2O |
Canonical SMILES
|
OpenEye OEToolkits |
1.5.0 |
C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@](=O)(O)O[P@](=O)(O)OC[C@H](CO)O)O)O |
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IUPAC InChI | InChI=1S/C12H21N3O13P2/c13-8-1-2-15(12(20)14-8)11-10(19)9(18)7(27-11)5-26-30(23,24)28-29(21,22)25-4-6(17)3-16/h1-2,6-7,9-11,16-19H,3-5H2,(H,21,22)(H,23,24)(H2,13,14,20)/t6-,7+,9+,10+,11+/m0/s1 |
IUPAC InChI key | HHPOUCCVONEPRK-CNYIRLTGSA-N |
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wwPDB Information |
Atom count
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51 (30 without Hydrogen)
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Polymer type
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Bound ligand
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Type description
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NON-POLYMER
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Type code
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HETAIN
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Is modified
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No
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Standard parent
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Not Assigned
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Defined at
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2002-10-29
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Last modified at
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2021-03-01
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Status
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Released
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Obsoleted
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Not Assigned
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C2G : Atoms of Molecule
Total Number of Atoms: 51
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 |
0.747 |
0.546 |
-5.04 |
2 |
C2 |
C |
C2 |
N |
Y |
N |
0 |
1.298 |
-0.673 |
-4.906 |
3 |
N3 |
N |
N3 |
N |
Y |
N |
0 |
2.427 |
-0.99 |
-5.538 |
4 |
C4 |
C |
C4 |
N |
Y |
N |
0 |
3.038 |
-0.108 |
-6.318 |
5 |
C5 |
C |
C5 |
N |
Y |
N |
0 |
2.49 |
1.18 |
-6.474 |
6 |
C6 |
C |
C6 |
N |
Y |
N |
0 |
1.338 |
1.486 |
-5.83 |
7 |
O2 |
O |
O2 |
N |
N |
N |
0 |
0.756 |
-1.502 |
-4.195 |
8 |
N4 |
N |
N4 |
N |
N |
N |
0 |
4.204 |
-0.447 |
-6.965 |
9 |
C1' |
C |
C1* |
R |
N |
N |
0 |
-0.494 |
0.866 |
-4.332 |
10 |
C2' |
C |
C2* |
R |
N |
N |
0 |
-1.615 |
-0.114 |
-4.743 |
11 |
O2' |
O |
O2* |
N |
N |
N |
0 |
-2.459 |
0.468 |
-5.738 |
12 |
C3' |
C |
C3* |
S |
N |
N |
0 |
-2.404 |
-0.349 |
-3.433 |
13 |
C4' |
C |
C4* |
R |
N |
N |
0 |
-1.667 |
0.519 |
-2.39 |
14 |
O4' |
O |
O4* |
N |
N |
N |
0 |
-0.329 |
0.668 |
-2.911 |
15 |
O3' |
O |
O3* |
N |
N |
N |
0 |
-3.758 |
0.082 |
-3.579 |
16 |
C5' |
C |
C5* |
N |
N |
N |
0 |
-1.635 |
-0.186 |
-1.033 |
17 |
O5' |
O |
O5* |
N |
N |
N |
0 |
-0.888 |
0.601 |
-0.104 |
18 |
PA |
P |
PA |
S |
N |
N |
0 |
-0.895 |
-0.196 |
1.294 |
19 |
O1A |
O |
O1A |
N |
N |
N |
0 |
-0.267 |
-1.523 |
1.107 |
20 |
O2A |
O |
O2A |
N |
N |
N |
0 |
-2.413 |
-0.386 |
1.796 |
21 |
O3A |
O |
O3A |
N |
N |
N |
0 |
-0.066 |
0.639 |
2.393 |
22 |
PB |
P |
PB |
R |
N |
N |
0 |
-0.114 |
-0.212 |
3.758 |
23 |
O1B |
O |
O1B |
N |
N |
N |
0 |
0.5 |
-1.539 |
3.534 |
24 |
O2B |
O |
O2B |
N |
N |
N |
0 |
-1.645 |
-0.402 |
4.219 |
25 |
O3B |
O |
O3B |
N |
N |
N |
0 |
0.698 |
0.568 |
4.907 |
26 |
O1G |
O |
O1G |
N |
N |
N |
0 |
2.0 |
0.241 |
9.549 |
27 |
C1G |
C |
C1G |
N |
N |
N |
0 |
1.292 |
-0.402 |
8.487 |
28 |
C2G |
C |
C2G |
S |
N |
N |
0 |
1.377 |
0.456 |
7.224 |
29 |
O2G |
O |
O2G |
N |
N |
N |
0 |
0.793 |
1.735 |
7.477 |
30 |
C3G |
C |
C3G |
N |
N |
N |
0 |
0.619 |
-0.233 |
6.087 |
31 |
HC5 |
H |
HC5 |
N |
N |
N |
0 |
2.975 |
1.91 |
-7.106 |
32 |
HC6 |
H |
HC6 |
N |
N |
N |
0 |
0.896 |
2.466 |
-5.938 |
33 |
HN41 |
H |
1HN4 |
N |
N |
N |
0 |
4.581 |
-1.333 |
-6.852 |
34 |
HN42 |
H |
2HN4 |
N |
N |
N |
0 |
4.646 |
0.198 |
-7.537 |
35 |
HC1 |
H |
HC1 |
N |
N |
N |
0 |
-0.794 |
1.894 |
-4.539 |
36 |
HC2 |
H |
HC2 |
N |
N |
N |
0 |
-1.188 |
-1.049 |
-5.105 |
37 |
HO2 |
H |
HO2 |
N |
N |
N |
0 |
-3.17 |
-0.165 |
-5.907 |
38 |
HC3 |
H |
HC3 |
N |
N |
N |
0 |
-2.368 |
-1.401 |
-3.148 |
39 |
HC4 |
H |
HC4 |
N |
N |
N |
0 |
-2.149 |
1.493 |
-2.299 |
40 |
HO3 |
H |
HO3 |
N |
N |
N |
0 |
-4.165 |
-0.493 |
-4.24 |
41 |
HC51 |
H |
1HC5 |
N |
N |
N |
0 |
-2.653 |
-0.313 |
-0.665 |
42 |
HC52 |
H |
2HC5 |
N |
N |
N |
0 |
-1.163 |
-1.162 |
-1.142 |
43 |
H2A |
H |
H2A |
N |
N |
N |
0 |
-2.784 |
0.5 |
1.905 |
44 |
H2B |
H |
H2B |
N |
N |
N |
0 |
-2.008 |
0.484 |
4.354 |
45 |
H1G |
H |
H1G |
N |
N |
N |
0 |
1.922 |
-0.33 |
10.324 |
46 |
H1G1 |
H |
1H1G |
N |
N |
N |
0 |
0.247 |
-0.529 |
8.771 |
47 |
H1G2 |
H |
2H1G |
N |
N |
N |
0 |
1.737 |
-1.378 |
8.294 |
48 |
H2G |
H |
H2G |
N |
N |
N |
0 |
2.421 |
0.583 |
6.94 |
49 |
HOG |
H |
HOG |
N |
N |
N |
0 |
-0.127 |
1.578 |
7.725 |
50 |
H3G1 |
H |
1H3G |
N |
N |
N |
0 |
-0.424 |
-0.36 |
6.371 |
51 |
H3G2 |
H |
2H3G |
N |
N |
N |
0 |
1.064 |
-1.209 |
5.894 |
C2G : Chemical Bonds
Total Number of Bonds: 52
C2G : Used in PDB Entries
Total Number of PDB Entries: 4
Ligand Code |
PDB Entry ID |
Type |
Total |
Distinct |
C2G |
1n1d |
Bound ligand
|
4 |
1 |
C2G |
3l7k |
Bound ligand
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1 |
1 |
C2G |
3l7l |
Bound ligand
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1 |
1 |
C2G |
4q7c |
Bound ligand
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2 |
1 |
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