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NDN : Summary
Code ![](/pdbe/static/images/help.png)
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NDN
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One-letter code ![](/pdbe/static/images/help.png)
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U
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Molecule name ![](/pdbe/static/images/help.png)
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2'-DEOXY-5-NITROURIDINE 5'-(DIHYDROGEN PHOSPHATE)
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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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C9 H12 N3 O10 P
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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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353.179 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 |
10.04 |
[O-][N+](=O)C=1C(=O)NC(=O)N(C=1)C2OC(C(O)C2)COP(=O)(O)O |
SMILES
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CACTVS |
3.341 |
O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C(C(=O)NC2=O)[N+]([O-])=O |
SMILES
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OpenEye OEToolkits |
1.5.0 |
C1C(C(OC1N2C=C(C(=O)NC2=O)[N+](=O)[O-])COP(=O)(O)O)O |
Canonical SMILES
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CACTVS |
3.341 |
O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(C(=O)NC2=O)[N+]([O-])=O |
Canonical SMILES
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OpenEye OEToolkits |
1.5.0 |
C1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)[N+](=O)[O-])COP(=O)(O)O)O |
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IUPAC InChI ![](/pdbe/static/images/help.png) | InChI=1S/C9H12N3O10P/c13-5-1-7(22-6(5)3-21-23(18,19)20)11-2-4(12(16)17)8(14)10-9(11)15/h2,5-7,13H,1,3H2,(H,10,14,15)(H2,18,19,20)/t5-,6+,7+/m0/s1 |
IUPAC InChI key ![](/pdbe/static/images/help.png) | LVLPVLNNXRTCHP-RRKCRQDMSA-N |
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wwPDB Information |
Atom count ![](/pdbe/static/images/help.png)
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35 (23 without Hydrogen)
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Polymer type ![](/pdbe/static/images/help.png)
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Deoxy ribonucleotide
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Type description ![](/pdbe/static/images/help.png)
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DNA LINKING
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Type code ![](/pdbe/static/images/help.png)
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ATOMN
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Is modified ![](/pdbe/static/images/help.png)
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Yes
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Standard parent ![](/pdbe/static/images/help.png)
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DU
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Defined at ![](/pdbe/static/images/help.png)
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2007-11-07
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Last modified at ![](/pdbe/static/images/help.png)
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2020-06-17
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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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NDN : Atoms of Molecule
Total Number of Atoms: 35
Record |
Atom Name |
Symbol |
PDB Name |
Stereochemistry |
Is Aromatic |
Is Leaving Atom |
Charge |
X-Coordinate |
Y-Coordinate |
Z-Coordinate |
1 |
P |
P |
P |
N |
N |
N |
0 |
-4.772 |
-1.098 |
0.304 |
2 |
OP1 |
O |
OP1 |
N |
N |
N |
0 |
-5.899 |
-0.182 |
0.018 |
3 |
OP2 |
O |
OP2 |
N |
N |
N |
0 |
-5.133 |
-2.01 |
1.581 |
4 |
OP3 |
O |
OP3 |
N |
N |
Y |
0 |
-4.51 |
-2.043 |
-0.973 |
5 |
OR5 |
O |
OR5 |
N |
N |
N |
0 |
-3.447 |
-0.237 |
0.616 |
6 |
CR5 |
C |
CR5 |
N |
N |
N |
0 |
-2.93 |
0.747 |
-0.281 |
7 |
CR4 |
C |
CR4 |
R |
N |
N |
0 |
-1.669 |
1.372 |
0.32 |
8 |
CR3 |
C |
CR3 |
S |
N |
N |
0 |
-1.163 |
2.526 |
-0.574 |
9 |
CR2 |
C |
CR2 |
N |
N |
N |
0 |
0.377 |
2.411 |
-0.5 |
10 |
OR3 |
O |
OR3 |
N |
N |
N |
0 |
-1.596 |
3.786 |
-0.058 |
11 |
N3 |
N |
N3 |
N |
N |
N |
0 |
2.772 |
-0.919 |
-1.665 |
12 |
CR1 |
C |
CR1 |
R |
N |
N |
0 |
0.618 |
1.201 |
0.43 |
13 |
OR1 |
O |
OR1 |
N |
N |
N |
0 |
-0.589 |
0.413 |
0.332 |
14 |
N1 |
N |
N1 |
N |
N |
N |
0 |
1.773 |
0.426 |
-0.03 |
15 |
C2 |
C |
C2 |
N |
N |
N |
0 |
1.724 |
-0.202 |
-1.218 |
16 |
O2 |
O |
O2 |
N |
N |
N |
0 |
0.72 |
-0.12 |
-1.899 |
17 |
C4 |
C |
C4 |
N |
N |
N |
0 |
3.893 |
-1.02 |
-0.923 |
18 |
O4 |
O |
O4 |
N |
N |
N |
0 |
4.841 |
-1.669 |
-1.327 |
19 |
C5 |
C |
C5 |
N |
N |
N |
0 |
3.957 |
-0.364 |
0.33 |
20 |
C6 |
C |
C6 |
N |
N |
N |
0 |
2.895 |
0.354 |
0.752 |
21 |
HOP3 |
H |
HOP3 |
N |
N |
N |
0 |
-3.783 |
-2.67 |
-0.856 |
22 |
N5 |
N |
N5 |
N |
N |
N |
1 |
5.177 |
-0.459 |
1.164 |
23 |
O51 |
O |
O51 |
N |
N |
N |
0 |
5.224 |
0.108 |
2.241 |
24 |
O52 |
O |
O52 |
N |
N |
N |
-1 |
6.133 |
-1.105 |
0.774 |
25 |
HOP2 |
H |
HOP2 |
N |
N |
N |
0 |
-5.922 |
-2.556 |
1.464 |
26 |
HR5 |
H |
HR5 |
N |
N |
N |
0 |
-2.684 |
0.277 |
-1.234 |
27 |
HR5A |
H |
HR5A |
N |
N |
N |
0 |
-3.679 |
1.522 |
-0.441 |
28 |
HR4 |
H |
HR4 |
N |
N |
N |
0 |
-1.869 |
1.733 |
1.328 |
29 |
HR3 |
H |
HR3 |
N |
N |
N |
0 |
-1.506 |
2.394 |
-1.6 |
30 |
HOR3 |
H |
HOR3 |
N |
N |
Y |
0 |
-1.305 |
4.546 |
-0.581 |
31 |
HR2 |
H |
HR2 |
N |
N |
N |
0 |
0.794 |
2.221 |
-1.489 |
32 |
HR2A |
H |
HR2A |
N |
N |
N |
0 |
0.807 |
3.316 |
-0.071 |
33 |
HR1 |
H |
HR1 |
N |
N |
N |
0 |
0.77 |
1.535 |
1.456 |
34 |
H6 |
H |
H6 |
N |
N |
N |
0 |
2.926 |
0.861 |
1.704 |
35 |
HN3 |
H |
HN3 |
N |
N |
N |
0 |
2.72 |
-1.366 |
-2.525 |
NDN : Chemical Bonds
Total Number of Bonds: 36
NDN : Used in PDB Entries
Total Number of PDB Entries: 1
Ligand Code |
PDB Entry ID |
Type |
Total |
Distinct |
NDN |
3b5b ![Open in New Window](/pdbe-srv/pdbechem/images/newwin.png?_debugResources=y&n=1724095919528) |
Bound ligand
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1 |
1 |
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