Chemical Components in the PDB

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0DC : Summary

Code

0DC

One-letter code

C

Molecule name

2'-DEOXY-L-RIBO-FURANOSYL CYTOSINE-5'-MONOPHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 11.02 4-amino-1-(2-deoxy-5-O-phosphono-beta-L-erythro-pentofuranosyl)pyrimidin-2(1H)-one
OpenEye OEToolkits 1.6.1 [(2S,3R,5S)-5-(4-azanyl-2-oxo-pyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methyl dihydrogen phosphate

Formula

C9 H14 N3 O7 P

Formal charge

0

Molecular weight

307.197 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 11.02 O=P(O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)CC2O
SMILES CACTVS 3.352 NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2
SMILES OpenEye OEToolkits 1.7.0 C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)O)O
Canonical SMILES CACTVS 3.352 NC1=NC(=O)N(C=C1)[C@@H]2C[C@@H](O)[C@H](CO[P](O)(O)=O)O2
Canonical SMILES OpenEye OEToolkits 1.7.0 C1[C@H]([C@@H](O[C@@H]1N2C=CC(=NC2=O)N)COP(=O)(O)O)O

IUPAC InChI

InChI=1S/C9H14N3O7P/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(19-8)4-18-20(15,16)17/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m1/s1

IUPAC InChI key

NCMVOABPESMRCP-CHKWXVPMSA-N
0DC

wwPDB Information

Atom count

34 (20 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

L-DNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

DC

Defined at

2009-07-16

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



0DC : Atoms of Molecule

Total Number of Atoms: 34
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 OP3 O O3P N N Y 0 4.723 1.691 -1.32
2 P P P N N N 0 4.19 0.861 -0.048
3 OP1 O O1P N N N 0 5.207 -0.136 0.352
4 OP2 O O2P N N N 0 3.918 1.871 1.176
5 O5' O O5' N N N 0 2.821 0.107 -0.435
6 C5' C C5' N N N 0 2.154 -0.796 0.448
7 C4' C C4' S N N 0 0.891 -1.333 -0.229
8 O4' O O4' N N N 0 -0.067 -0.27 -0.421
9 C3' C C3' R N N 0 0.177 -2.348 0.691
10 O3' O O3' N N N 0 0.51 -3.685 0.315
11 C2' C C2' N N N 0 -1.326 -2.077 0.453
12 C1' C C1' S N N 0 -1.341 -0.931 -0.583
13 N1 N N1 N N N 0 -2.438 -0.001 -0.298
14 C2 C C2 N N N 0 -3.712 -0.429 -0.363
15 O2 O O2 N N N 0 -3.94 -1.59 -0.66
16 N3 N N3 N N N 0 -4.727 0.394 -0.11
17 C4 C C4 N N N 0 -4.507 1.661 0.214
18 N4 N N4 N N N 0 -5.564 2.503 0.475
19 C5 C C5 N N N 0 -3.184 2.141 0.291
20 C6 C C6 N N N 0 -2.161 1.291 0.036
21 HOP3 H HOP3 N N N 0 5.547 2.172 -1.159
22 HOP2 H HOP2 N N N 0 3.26 2.554 0.984
23 H5' H H5'1 N N N 0 2.818 -1.627 0.689
24 H5'' H H5'2 N N N 0 1.88 -0.273 1.364
25 H4' H H4' N N N 0 1.141 -1.795 -1.184
26 H3' H H3' N N N 0 0.439 -2.168 1.733
27 HO3' H H3T N N Y 0 0.088 -4.364 0.86
28 H2' H H2'1 N N N 0 -1.814 -2.963 0.049
29 H2'' H H2'2 N N N 0 -1.808 -1.762 1.378
30 H1' H H1' N N N 0 -1.435 -1.332 -1.592
31 H41 H H41 N N N 0 -6.473 2.169 0.422
32 H42 H H42 N N N 0 -5.4 3.429 0.712
33 H5 H H5 N N N 0 -2.988 3.171 0.553
34 H6 H H6 N N N 0 -1.139 1.633 0.093



0DC : Chemical Bonds

Total Number of Bonds: 35
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OP3 P O P sing 1.61 N N
2 OP3 HOP3 O H sing 0.97 N N
3 P OP1 P O doub 1.48 N N
4 P OP2 P O sing 1.61 N N
5 P O5' P O sing 1.61 N N
6 OP2 HOP2 O H sing 0.97 N N
7 O5' C5' O C sing 1.43 N N
8 C5' C4' C C sing 1.53 N N
9 C5' H5' C H sing 1.09 N N
10 C5' H5'' C H sing 1.09 N N
11 C4' O4' C O sing 1.44 N N
12 C4' C3' C C sing 1.54 N N
13 C4' H4' C H sing 1.09 N N
14 O4' C1' O C sing 1.44 N N
15 C3' O3' C O sing 1.43 N N
16 C3' C2' C C sing 1.55 N N
17 C3' H3' C H sing 1.09 N N
18 O3' HO3' O H sing 0.97 N N
19 C2' C1' C C sing 1.54 N N
20 C2' H2' C H sing 1.09 N N
21 C2' H2'' C H sing 1.09 N N
22 C1' N1 C N sing 1.47 N N
23 C1' H1' C H sing 1.09 N N
24 N1 C2 N C sing 1.35 N N
25 N1 C6 N C sing 1.36 N N
26 C2 O2 C O doub 1.22 N N
27 C2 N3 C N sing 1.33 N N
28 N3 C4 N C doub 1.33 N N
29 C4 N4 C N sing 1.38 N N
30 C4 C5 C C sing 1.41 N N
31 N4 H41 N H sing 0.97 N N
32 N4 H42 N H sing 0.97 N N
33 C5 C6 C C doub 1.35 N N
34 C5 H5 C H sing 1.08 N N
35 C6 H6 C H sing 1.08 N N



0DC : Used in PDB Entries

Total Number of PDB Entries: 11
Ligand Code PDB Entry ID Type Total Distinct
0DC 1fv7 Open in New Window Polymer component 2 1
0DC 1r4d Open in New Window Polymer component 2 1
0DC 4wb2 Open in New Window Polymer component 2 1
0DC 4wb3 Open in New Window Polymer component 2 1
0DC 5vy7 Open in New Window Polymer component 12 12
0DC 6l97 Open in New Window Polymer component 11 11
0DC 7kw4 Open in New Window Polymer component 2 2
0DC 7moo Open in New Window Polymer component 4 2
0DC 8a71 Open in New Window Polymer component 6 3
0DC 8f27 Open in New Window Polymer component 4 2
0DC 8f5c Open in New Window Polymer component 2 2