Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

C2G : Summary

Code

C2G

One-letter code

X

Molecule name

[CYTIDINE-5'-PHOSPHATE] GLYCERYLPHOSPHORIC ACID ESTER

Synonyms

CYTIDINE 5'-DIPHOSPHOGLYCEROL

Systematic names

ProgramVersionName
ACDLabs 10.04 5'-O-[(S)-{[(R)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine
OpenEye OEToolkits 1.5.0 [(2R,3S,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [[(2S)-2,3-dihydroxypropoxy]-hydroxy-phosphoryl] hydrogen phosphate

Formula

C12 H21 N3 O13 P2

Formal charge

0

Molecular weight

477.255 Da

SMILES

TypeProgramVersionDescriptor
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 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

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
C2G

wwPDB Information

Atom count

51 (30 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2002-10-29

Last modified at

2021-03-01

Status

Released

Obsoleted

Not Assigned



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
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 C2 N C sing 1.34 N Y
2 N1 C6 N C sing 1.36 N Y
3 N1 C1' N C sing 1.46 N N
4 C2 N3 C N sing 1.33 N Y
5 C2 O2 C O doub 1.22 N N
6 N3 C4 N C doub 1.33 N Y
7 C4 C5 C C sing 1.41 N Y
8 C4 N4 C N sing 1.38 N N
9 C5 C6 C C doub 1.35 N Y
10 C5 HC5 C H sing 1.08 N N
11 C6 HC6 C H sing 1.08 N N
12 N4 HN41 N H sing 0.97 N N
13 N4 HN42 N H sing 0.97 N N
14 C1' C2' C C sing 1.54 N N
15 C1' O4' C O sing 1.44 N N
16 C1' HC1 C H sing 1.09 N N
17 C2' O2' C O sing 1.43 N N
18 C2' C3' C C sing 1.55 N N
19 C2' HC2 C H sing 1.09 N N
20 O2' HO2 O H sing 0.97 N N
21 C3' C4' C C sing 1.54 N N
22 C3' O3' C O sing 1.43 N N
23 C3' HC3 C H sing 1.09 N N
24 C4' O4' C O sing 1.44 N N
25 C4' C5' C C sing 1.53 N N
26 C4' HC4 C H sing 1.09 N N
27 O3' HO3 O H sing 0.97 N N
28 C5' O5' C O sing 1.43 N N
29 C5' HC51 C H sing 1.09 N N
30 C5' HC52 C H sing 1.09 N N
31 O5' PA O P sing 1.61 N N
32 PA O1A P O doub 1.48 N N
33 PA O2A P O sing 1.61 N N
34 PA O3A P O sing 1.61 N N
35 O2A H2A O H sing 0.97 N N
36 O3A PB O P sing 1.61 N N
37 PB O1B P O doub 1.48 N N
38 PB O2B P O sing 1.61 N N
39 PB O3B P O sing 1.61 N N
40 O2B H2B O H sing 0.97 N N
41 O3B C3G O C sing 1.43 N N
42 O1G C1G O C sing 1.43 N N
43 O1G H1G O H sing 0.97 N N
44 C1G C2G C C sing 1.53 N N
45 C1G H1G1 C H sing 1.09 N N
46 C1G H1G2 C H sing 1.09 N N
47 C2G O2G C O sing 1.43 N N
48 C2G C3G C C sing 1.53 N N
49 C2G H2G C H sing 1.09 N N
50 O2G HOG O H sing 0.97 N N
51 C3G H3G1 C H sing 1.09 N N
52 C3G H3G2 C H sing 1.09 N N



C2G : Used in PDB Entries

Total Number of PDB Entries: 4
Ligand Code PDB Entry ID Type Total Distinct
C2G 1n1d Open in New Window Bound ligand 4 1
C2G 3l7k Open in New Window Bound ligand 1 1
C2G 3l7l Open in New Window Bound ligand 1 1
C2G 4q7c Open in New Window Bound ligand 2 1