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829 : Summary
Code ![](/pdbe/static/images/help.png)
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829
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One-letter code ![](/pdbe/static/images/help.png)
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X
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Molecule name ![](/pdbe/static/images/help.png)
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5'-deoxy-5'-[(pyridin-4-ylcarbonyl)amino]cytidine
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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 H17 N5 O5
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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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347.326 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 |
11.02 |
O=C1N=C(N)C=CN1C2OC(C(O)C2O)CNC(=O)c3ccncc3 |
SMILES
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CACTVS |
3.352 |
NC1=NC(=O)N(C=C1)[CH]2O[CH](CNC(=O)c3ccncc3)[CH](O)[CH]2O |
SMILES
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OpenEye OEToolkits |
1.7.0 |
c1cnccc1C(=O)NCC2C(C(C(O2)N3C=CC(=NC3=O)N)O)O |
Canonical SMILES
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CACTVS |
3.352 |
NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CNC(=O)c3ccncc3)[C@@H](O)[C@H]2O |
Canonical SMILES
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OpenEye OEToolkits |
1.7.0 |
c1cnccc1C(=O)NC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=NC3=O)N)O)O |
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IUPAC InChI ![](/pdbe/static/images/help.png) | InChI=1S/C15H17N5O5/c16-10-3-6-20(15(24)19-10)14-12(22)11(21)9(25-14)7-18-13(23)8-1-4-17-5-2-8/h1-6,9,11-12,14,21-22H,7H2,(H,18,23)(H2,16,19,24)/t9-,11-,12-,14-/m1/s1 |
IUPAC InChI key ![](/pdbe/static/images/help.png) | XQXWUTWGJVGDNS-XIDUGBJDSA-N |
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wwPDB Information |
Atom count ![](/pdbe/static/images/help.png)
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42 (25 without Hydrogen)
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Polymer type ![](/pdbe/static/images/help.png)
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Bound ligand
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Type description ![](/pdbe/static/images/help.png)
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NON-POLYMER
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Type code ![](/pdbe/static/images/help.png)
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HETAIN
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Is modified ![](/pdbe/static/images/help.png)
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No
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Standard parent ![](/pdbe/static/images/help.png)
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Not Assigned
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Defined at ![](/pdbe/static/images/help.png)
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2009-10-28
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Last modified at ![](/pdbe/static/images/help.png)
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2011-06-04
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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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829 : Atoms of Molecule
Total Number of Atoms: 42
Record |
Atom Name |
Symbol |
PDB Name |
Stereochemistry |
Is Aromatic |
Is Leaving Atom |
Charge |
X-Coordinate |
Y-Coordinate |
Z-Coordinate |
1 |
N1 |
N |
N1 |
N |
N |
N |
0 |
-2.936 |
0.418 |
0.465 |
2 |
C2 |
C |
C2 |
N |
N |
N |
0 |
-3.044 |
0.806 |
-0.819 |
3 |
O2 |
O |
O2 |
N |
N |
N |
0 |
-2.361 |
0.261 |
-1.67 |
4 |
N3 |
N |
N3 |
N |
N |
N |
0 |
-3.884 |
1.776 |
-1.176 |
5 |
C4 |
C |
C4 |
N |
N |
N |
0 |
-4.638 |
2.386 |
-0.271 |
6 |
N4 |
N |
N4 |
N |
N |
N |
0 |
-5.503 |
3.386 |
-0.652 |
7 |
C5 |
C |
C5 |
N |
N |
N |
0 |
-4.549 |
2.003 |
1.083 |
8 |
C6 |
C |
C6 |
N |
N |
N |
0 |
-3.695 |
1.011 |
1.429 |
9 |
C07 |
C |
C07 |
N |
N |
N |
0 |
3.391 |
-0.474 |
-0.739 |
10 |
C08 |
C |
C08 |
N |
Y |
N |
0 |
4.244 |
1.014 |
1.088 |
11 |
C09 |
C |
C09 |
N |
Y |
N |
0 |
5.245 |
1.817 |
1.599 |
12 |
C1' |
C |
C1* |
R |
N |
N |
0 |
-2.004 |
-0.652 |
0.827 |
13 |
N10 |
N |
N10 |
N |
Y |
N |
0 |
6.366 |
2.007 |
0.933 |
14 |
C11 |
C |
C11 |
N |
Y |
N |
0 |
6.587 |
1.448 |
-0.24 |
15 |
C12 |
C |
C12 |
N |
Y |
N |
0 |
5.639 |
0.631 |
-0.825 |
16 |
C13 |
C |
C13 |
N |
Y |
N |
0 |
4.437 |
0.396 |
-0.152 |
17 |
O15 |
O |
O15 |
N |
N |
N |
0 |
3.573 |
-0.995 |
-1.822 |
18 |
C2' |
C |
C2* |
R |
N |
N |
0 |
-2.395 |
-1.969 |
0.121 |
19 |
O2' |
O |
O2* |
N |
N |
N |
0 |
-3.138 |
-2.811 |
1.005 |
20 |
C3' |
C |
C3* |
S |
N |
N |
0 |
-1.041 |
-2.621 |
-0.237 |
21 |
O3' |
O |
O3* |
N |
N |
N |
0 |
-0.905 |
-3.884 |
0.416 |
22 |
C4' |
C |
C4* |
R |
N |
N |
0 |
0.009 |
-1.621 |
0.296 |
23 |
O4' |
O |
O4* |
N |
N |
N |
0 |
-0.678 |
-0.351 |
0.338 |
24 |
C5' |
C |
C5* |
N |
N |
N |
0 |
1.206 |
-1.547 |
-0.655 |
25 |
N5' |
N |
N5* |
N |
N |
N |
0 |
2.239 |
-0.687 |
-0.073 |
26 |
HN4 |
H |
HN4 |
N |
N |
N |
0 |
-5.562 |
3.647 |
-1.584 |
27 |
HN4A |
H |
HN4A |
N |
N |
N |
0 |
-6.053 |
3.83 |
0.012 |
28 |
H5 |
H |
H5 |
N |
N |
N |
0 |
-5.156 |
2.49 |
1.832 |
29 |
H6 |
H |
H6 |
N |
N |
N |
0 |
-3.609 |
0.699 |
2.46 |
30 |
H08 |
H |
H08 |
N |
N |
N |
0 |
3.328 |
0.862 |
1.639 |
31 |
H09 |
H |
H09 |
N |
N |
N |
0 |
5.107 |
2.295 |
2.557 |
32 |
H1' |
H |
H1* |
N |
N |
N |
0 |
-1.987 |
-0.79 |
1.908 |
33 |
H11 |
H |
H11 |
N |
N |
N |
0 |
7.52 |
1.632 |
-0.751 |
34 |
H12 |
H |
H12 |
N |
N |
N |
0 |
5.826 |
0.176 |
-1.787 |
35 |
H2' |
H |
H2* |
N |
N |
N |
0 |
-2.971 |
-1.762 |
-0.781 |
36 |
HO2' |
H |
HO2* |
N |
N |
N |
0 |
-3.409 |
-3.651 |
0.613 |
37 |
H3' |
H |
H3* |
N |
N |
N |
0 |
-0.945 |
-2.736 |
-1.316 |
38 |
HO3' |
H |
HO3* |
N |
N |
N |
0 |
-1.577 |
-4.532 |
0.163 |
39 |
H4' |
H |
H4* |
N |
N |
N |
0 |
0.335 |
-1.909 |
1.296 |
40 |
H5' |
H |
H5* |
N |
N |
N |
0 |
1.61 |
-2.547 |
-0.808 |
41 |
H5'A |
H |
H5*A |
N |
N |
N |
0 |
0.885 |
-1.134 |
-1.611 |
42 |
HN5' |
H |
HN5* |
N |
N |
N |
0 |
2.094 |
-0.27 |
0.79 |
829 : Chemical Bonds
Total Number of Bonds: 44
829 : Used in PDB Entries
Total Number of PDB Entries: 1
Ligand Code |
PDB Entry ID |
Type |
Total |
Distinct |
829 |
3ke1 ![Open in New Window](/pdbe-srv/pdbechem/images/newwin.png?_debugResources=y&n=1724404470138) |
Bound ligand
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3 |
1 |
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