Chemical Components in the PDB

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NDN : Summary

Code

NDN

One-letter code

U

Molecule name

2'-DEOXY-5-NITROURIDINE 5'-(DIHYDROGEN PHOSPHATE)

Systematic names

ProgramVersionName
ACDLabs 10.04 2'-deoxy-5-nitrouridine 5'-(dihydrogen phosphate)
OpenEye OEToolkits 1.5.0 [(2R,3S,5R)-3-hydroxy-5-(5-nitro-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl dihydrogen phosphate

Formula

C9 H12 N3 O10 P

Formal charge

0

Molecular weight

353.179 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 [O-][N+](=O)C=1C(=O)NC(=O)N(C=1)C2OC(C(O)C2)COP(=O)(O)O
SMILES CACTVS 3.341 O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C(C(=O)NC2=O)[N+]([O-])=O
SMILES OpenEye OEToolkits 1.5.0 C1C(C(OC1N2C=C(C(=O)NC2=O)[N+](=O)[O-])COP(=O)(O)O)O
Canonical SMILES 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 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

IUPAC InChI

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

LVLPVLNNXRTCHP-RRKCRQDMSA-N
NDN

wwPDB Information

Atom count

35 (23 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

DNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

DU

Defined at

2007-11-07

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



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
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 P OP1 P O doub 1.48 N N
2 P OP2 P O sing 1.61 N N
3 OP3 HOP3 O H sing 0.97 N N
4 OP2 HOP2 O H sing 0.97 N N
5 OP3 P O P sing 1.61 N N
6 OR5 P O P sing 1.61 N N
7 CR5 OR5 C O sing 1.43 N N
8 CR5 CR4 C C sing 1.53 N N
9 CR5 HR5 C H sing 1.09 N N
10 CR5 HR5A C H sing 1.09 N N
11 CR4 CR3 C C sing 1.54 N N
12 CR4 HR4 C H sing 1.09 N N
13 CR3 CR2 C C sing 1.55 N N
14 CR3 OR3 C O sing 1.43 N N
15 CR3 HR3 C H sing 1.09 N N
16 OR3 HOR3 O H sing 0.97 N N
17 CR2 HR2 C H sing 1.09 N N
18 CR2 HR2A C H sing 1.09 N N
19 CR1 CR2 C C sing 1.55 N N
20 CR1 HR1 C H sing 1.09 N N
21 OR1 CR4 O C sing 1.44 N N
22 OR1 CR1 O C sing 1.44 N N
23 N1 CR1 N C sing 1.47 N N
24 N1 C2 N C sing 1.34 N N
25 C2 O2 C O doub 1.22 N N
26 N3 C2 N C sing 1.35 N N
27 N3 HN3 N H sing 0.97 N N
28 C4 N3 C N sing 1.35 N N
29 O4 C4 O C doub 1.22 N N
30 C5 C4 C C sing 1.42 N N
31 C5 C6 C C doub 1.35 N N
32 C6 N1 C N sing 1.37 N N
33 C6 H6 C H sing 1.08 N N
34 N5 C5 N C sing 1.48 N N
35 O51 N5 O N doub 1.22 N N
36 O52 N5 O N sing 1.22 N N



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 Bound ligand 1 1