Chemical Components in the PDB

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C5G : Summary

Code

C5G

One-letter code

X

Molecule name

[CYTIDINE-5'-PHOSPHATE]-BETA-GLUCOSYL-PHOSPHORIC ACID ESTER

Systematic names

ProgramVersionName
ACDLabs 10.04 [(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)
OpenEye OEToolkits 1.5.0 [(2R,3S,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-phosphoryl] hydrogen phosphate

Formula

C15 H25 N3 O16 P2

Formal charge

0

Molecular weight

565.317 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(OC1OC(C(O)C(O)C1O)CO)(O)OP(=O)(O)OCC3OC(N2C=CC(=NC2=O)N)C(O)C3O
SMILES CACTVS 3.341 NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[CH]3O[CH](CO)[CH](O)[CH](O)[CH]3O)[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)OC3C(C(C(C(O3)CO)O)O)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)O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)[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)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O)O)O

IUPAC InChI

InChI=1S/C15H25N3O16P2/c16-7-1-2-18(15(25)17-7)13-11(23)9(21)6(31-13)4-30-35(26,27)34-36(28,29)33-14-12(24)10(22)8(20)5(3-19)32-14/h1-2,5-6,8-14,19-24H,3-4H2,(H,26,27)(H,28,29)(H2,16,17,25)/t5-,6-,8-,9-,10+,11-,12-,13-,14-/m1/s1

IUPAC InChI key

CGPHZDRCVSLMCF-JZMIEXBBSA-N
C5G

wwPDB Information

Atom count

61 (36 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2004-07-26

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



C5G : Atoms of Molecule

Total Number of Atoms: 61
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 -5.978 0.775 0.705
2 C2 C C2 N Y N 0 -5.765 1.504 -0.405
3 N3 N N3 N Y N 0 -6.35 2.689 -0.573
4 C4 C C4 N Y N 0 -7.161 3.181 0.355
5 C5 C C5 N Y N 0 -7.4 2.444 1.533
6 C6 C C6 N Y N 0 -6.802 1.239 1.686
7 O2 O O2 N N N 0 -5.023 1.073 -1.273
8 N4 N N4 N N N 0 -7.759 4.406 0.171
9 C1D C C1* R N N 0 -5.32 -0.524 0.861
10 C2D C C2* R N N 0 -5.801 -1.505 -0.231
11 O2D O O2* N N N 0 -6.82 -2.369 0.276
12 C3D C C3* S N N 0 -4.533 -2.316 -0.591
13 C4D C C4* R N N 0 -3.439 -1.73 0.33
14 O4D O O4* N N N 0 -3.897 -0.397 0.645
15 O3D O O3* N N N 0 -4.73 -3.704 -0.314
16 C5D C C5* N N N 0 -2.098 -1.672 -0.403
17 O5D O O5* N N N 0 -1.093 -1.169 0.48
18 PA P PA R N N 0 0.284 -1.136 -0.353
19 O1A O O1A N N N 0 0.558 -2.481 -0.907
20 O2A O O2A N N N 0 0.158 -0.075 -1.556
21 O3A O O3A N N N 0 1.49 -0.702 0.622
22 PB P PB R N N 0 2.86 -1.069 -0.14
23 O1B O O1B N N N 0 2.772 -0.631 -1.551
24 O2B O O2B N N N 0 3.094 -2.66 -0.086
25 O1' O O1' N N N 0 4.091 -0.32 0.578
26 C1' C C1' R N N 0 5.253 -0.587 -0.209
27 C2' C C2' R N N 0 6.488 -0.599 0.694
28 O2' O O2' N N N 0 6.354 -1.632 1.673
29 C3' C C3' S N N 0 6.609 0.757 1.395
30 O3' O O3' N N N 0 7.836 0.816 2.125
31 C4' C C4' S N N 0 6.591 1.861 0.331
32 O4' O O4' N N N 0 6.554 3.14 0.966
33 C5' C C5' R N N 0 5.349 1.688 -0.546
34 C6' C C6' N N N 0 5.305 2.805 -1.59
35 O6' O O6' N N N 0 4.085 2.719 -2.33
36 O5' O O5' N N N 0 5.394 0.424 -1.205
37 H5 H H5 N N N 0 -8.058 2.831 2.297
38 H6 H H6 N N N 0 -6.974 0.654 2.577
39 H41 H 1H4 N N N 0 -7.589 4.912 -0.639
40 H42 H 2H4 N N N 0 -8.354 4.762 0.849
41 H1D H H1* N N N 0 -5.518 -0.933 1.852
42 H2D H H2* N N N 0 -6.164 -0.958 -1.101
43 HO'2 H 2HO* N N N 0 -7.034 -2.994 -0.43
44 H3D H H3* N N N 0 -4.269 -2.17 -1.638
45 H4D H H4* N N N 0 -3.349 -2.325 1.238
46 H3T H H3T N N N 0 -5.421 -4.013 -0.916
47 H5'1 H 1H5* N N N 0 -1.822 -2.673 -0.735
48 H5'2 H 2H5* N N N 0 -2.184 -1.014 -1.268
49 HO2A H HO2A N N N 0 -0.02 0.786 -1.153
50 HO2B H HO2B N N N 0 3.146 -2.904 0.848
51 H1' H H1' N N N 0 5.148 -1.559 -0.692
52 H2' H H2' N N N 0 7.379 -0.78 0.093
53 HOD H 2HO' N N N 0 6.281 -2.467 1.19
54 H3' H H3' N N N 0 5.77 0.894 2.077
55 HO'3 H 3HO' N N N 0 7.804 0.107 2.782
56 H4' H H4' N N N 0 7.486 1.786 -0.287
57 HO'4 H 4HO' N N N 0 7.353 3.207 1.507
58 H5' H H5' N N N 0 4.456 1.74 0.077
59 H6'1 H 1H6' N N N 0 5.36 3.772 -1.091
60 H6'2 H 2H6' N N N 0 6.151 2.699 -2.271
61 HO'6 H 6HO' N N N 0 4.098 3.439 -2.975



C5G : Chemical Bonds

Total Number of Bonds: 63
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 C1D 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 H5 C H sing 1.08 N N
11 C6 H6 C H sing 1.08 N N
12 N4 H41 N H sing 0.97 N N
13 N4 H42 N H sing 0.97 N N
14 C1D C2D C C sing 1.54 N N
15 C1D O4D C O sing 1.44 N N
16 C1D H1D C H sing 1.09 N N
17 C2D O2D C O sing 1.43 N N
18 C2D C3D C C sing 1.55 N N
19 C2D H2D C H sing 1.09 N N
20 O2D HO'2 O H sing 0.97 N N
21 C3D C4D C C sing 1.55 N N
22 C3D O3D C O sing 1.43 N N
23 C3D H3D C H sing 1.09 N N
24 C4D O4D C O sing 1.44 N N
25 C4D C5D C C sing 1.53 N N
26 C4D H4D C H sing 1.09 N N
27 O3D H3T O H sing 0.97 N N
28 C5D O5D C O sing 1.43 N N
29 C5D H5'1 C H sing 1.09 N N
30 C5D H5'2 C H sing 1.09 N N
31 O5D 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 HO2A 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 O1' P O sing 1.61 N N
40 O2B HO2B O H sing 0.97 N N
41 O1' C1' O C sing 1.43 N N
42 C1' C2' C C sing 1.53 N N
43 C1' O5' C O sing 1.43 N N
44 C1' H1' C H sing 1.09 N N
45 C2' O2' C O sing 1.43 N N
46 C2' C3' C C sing 1.53 N N
47 C2' H2' C H sing 1.09 N N
48 O2' HOD O H sing 0.97 N N
49 C3' O3' C O sing 1.43 N N
50 C3' C4' C C sing 1.53 N N
51 C3' H3' C H sing 1.09 N N
52 O3' HO'3 O H sing 0.97 N N
53 C4' O4' C O sing 1.43 N N
54 C4' C5' C C sing 1.53 N N
55 C4' H4' C H sing 1.09 N N
56 O4' HO'4 O H sing 0.97 N N
57 C5' C6' C C sing 1.53 N N
58 C5' O5' C O sing 1.43 N N
59 C5' H5' C H sing 1.09 N N
60 C6' O6' C O sing 1.43 N N
61 C6' H6'1 C H sing 1.09 N N
62 C6' H6'2 C H sing 1.09 N N
63 O6' HO'6 O H sing 0.97 N N



C5G : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
C5G 1tzf Open in New Window Bound ligand 1 1