Chemical Components in the PDB

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C2P : Summary

Code

C2P

One-letter code

X

Molecule name

CYTIDINE-2'-MONOPHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 10.04 2'-cytidylic acid
OpenEye OEToolkits 1.5.0 [(2R,3R,4R,5R)-2-(4-amino-2-oxo-pyrimidin-1-yl)-4-hydroxy-5-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate

Formula

C9 H14 N3 O8 P

Formal charge

0

Molecular weight

323.197 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C1N=C(N)C=CN1C2OC(C(O)C2OP(=O)(O)O)CO
SMILES CACTVS 3.341 NC1=NC(=O)N(C=C1)[CH]2O[CH](CO)[CH](O)[CH]2O[P](O)(O)=O
SMILES OpenEye OEToolkits 1.5.0 C1=CN(C(=O)N=C1N)C2C(C(C(O2)CO)O)OP(=O)(O)O
Canonical SMILES CACTVS 3.341 NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O[P](O)(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)OP(=O)(O)O

IUPAC InChI

InChI=1S/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-7(20-21(16,17)18)6(14)4(3-13)19-8/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1

IUPAC InChI key

YQUAKORMLHPSLZ-XVFCMESISA-N
C2P

wwPDB Information

Atom count

35 (21 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



C2P : 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 N1 N N1 N N N 0 0.863 -0.557 1.099
2 C2 C C2 N N N 0 1.138 0.7 1.491
3 N3 N N3 N N N 0 1.256 1.008 2.781
4 C4 C C4 N N N 0 1.106 0.078 3.716
5 C5 C C5 N N N 0 0.823 -1.25 3.338
6 C6 C C6 N N N 0 0.7 -1.545 2.023
7 O2 O O2 N N N 0 1.28 1.573 0.651
8 N4 N N4 N N N 0 1.232 0.408 5.046
9 C1' C C1* R N N 0 0.738 -0.865 -0.327
10 C2' C C2* R N N 0 -0.373 -0.0050 -0.967
11 O2' O O2* N N N 0 -1.59 -0.747 -1.073
12 C3' C C3* R N N 0 0.177 0.333 -2.372
13 C4' C C4* R N N 0 1.555 -0.364 -2.413
14 O4' O O4* N N N 0 1.945 -0.493 -1.029
15 O3' O O3* N N N 0 -0.679 -0.191 -3.387
16 C5' C C5* N N N 0 2.567 0.494 -3.174
17 O5' O O5* N N N 0 3.849 -0.135 -3.137
18 P P P N N N 0 -2.721 0.101 -0.303
19 O1P O O1P N N N 0 -2.859 1.43 -0.94
20 O2P O O2P N N N 0 -4.126 -0.68 -0.383
21 O3P O O3P N N N 0 -2.296 0.286 1.238
22 H5 H H5 N N N 0 0.698 -2.018 4.087
23 H6 H H6 N N N 0 0.479 -2.555 1.708
24 HN41 H 1HN4 N N N 0 1.431 1.322 5.302
25 HN42 H 2HN4 N N N 0 1.118 -0.273 5.727
26 H1' H H1* N N N 0 0.528 -1.925 -0.469
27 H2' H H2* N N N 0 -0.531 0.904 -0.389
28 H3' H H3* N N N 0 0.292 1.411 -2.489
29 H4' H H4* N N N 0 1.469 -1.347 -2.877
30 HO3' H *HO3 N N N 0 -0.255 -0.0030 -4.236
31 H5'1 H 1H5* N N N 0 2.246 0.604 -4.209
32 H5'2 H 2H5* N N N 0 2.632 1.477 -2.707
33 HO5' H *HO5 N N N 0 4.456 0.436 -3.626
34 HOP2 H 2HOP N N N 0 -4.774 -0.139 0.088
35 HOP3 H 3HOP N N N 0 -2.217 -0.6 1.615



C2P : 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 N1 C2 N C sing 1.35 N N
2 N1 C6 N C sing 1.36 N N
3 N1 C1' N C sing 1.46 N N
4 C2 N3 C N sing 1.33 N N
5 C2 O2 C O doub 1.22 N N
6 N3 C4 N C doub 1.33 N N
7 C4 C5 C C sing 1.41 N N
8 C4 N4 C N sing 1.38 N N
9 C5 C6 C C doub 1.35 N N
10 C5 H5 C H sing 1.08 N N
11 C6 H6 C H sing 1.08 N N
12 N4 HN41 N H sing 0.97 N N
13 N4 HN42 N H sing 0.97 N N
14 C1' C2' C C sing 1.54 N N
15 C1' O4' C O sing 1.45 N N
16 C1' H1' C H sing 1.09 N N
17 C2' O2' C O sing 1.43 N N
18 C2' C3' C C sing 1.55 N N
19 C2' H2' C H sing 1.09 N N
20 O2' P O P sing 1.61 N N
21 C3' C4' C C sing 1.54 N N
22 C3' O3' C O sing 1.43 N N
23 C3' H3' C H sing 1.09 N N
24 C4' O4' C O sing 1.44 N N
25 C4' C5' C C sing 1.53 N N
26 C4' H4' C H sing 1.09 N N
27 O3' HO3' O H sing 0.97 N N
28 C5' O5' C O sing 1.43 N N
29 C5' H5'1 C H sing 1.09 N N
30 C5' H5'2 C H sing 1.09 N N
31 O5' HO5' O H sing 0.97 N N
32 P O1P P O doub 1.48 N N
33 P O2P P O sing 1.61 N N
34 P O3P P O sing 1.61 N N
35 O2P HOP2 O H sing 0.97 N N
36 O3P HOP3 O H sing 0.97 N N



C2P : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
C2P 1jvu Open in New Window Bound ligand 1 1
C2P 1rob Open in New Window Bound ligand 1 1