Biological Structure Resource | NDB | Structure Finder | à la mode | mmCIF

À La Mode Component ID: cyt

Component name: (view abbreviated component mmCIF) (view full component mmCIF)

cytosine

Component description:

Model constructed for cytosine with an N1-glycosidic linkage.

Component formula and formula weight:

H4 C5 N3 O1 ( 122.1 grams/mole)

Modeled component diagram:


Modeled component formula and formula weight:

C5 N3 O1 ( 118.1 grams/mole)

Component canonical SMILES string [Created by the Daylight Toolkit]:

Cn1ccc(N)nc1=O

Component exchange SMILES string:

N1(C(N=C(C(=C1[H])[H])N([H])[H])=O)C([H])([H])[H]

Component constructed from 47 CSD V. 512 structures (CSD ID[Molecule No.])

acytid[1]bagxiq01[1]bivvil[1]bivvil[2]bofwoi[1]bomtay[1]
bosgof[1]botsim[1]botsim10[1]boxgie[1]budway10[1]cimjen[1]
cupyuh[1]cytcyp20[1]cytcyp20[2]cytidi01[1]cytidi02[1]decyuf[1]
dxcytd01[1]dxcytd01[2]dxcytd01[3]fikhow[1]fikhow[2]fovxet[1]
gahhom[1]gahhom01[1]gigmoy[1]gouger10[1]gouger10[2]jikhoa[1]
jikhoa[2]juhlaz[1]kosnov[1]marafc[1]metcyt01[1]nagliq[1]
segmas[1]sivzus[1]sivzus[2]waxluc[1]waxluc[2]wipwib[1]
wipwib[2]wisgek[1]xyfcyt10[1]yukliz[1]zozvuf[1]

Bond Distance Table:


Atom 1 Atom 2 Distance E.S.D. Type
N1 C2 1.3967 0.0096 sing
C2 N3 1.3546 0.0099 sing
N3 C4 1.3367 0.0100 doub
C4 C5 1.4243 0.0088 sing
C5 C6 1.3389 0.0087 doub
C6 N1 1.3653 0.0070 sing
C2 O2 1.2383 0.0089 doub
C4 N4 1.3328 0.0097 sing
N1 C1* 1.4713 0.0169 sing
N4 H4A n.a. n.a. sing
N4 H4B n.a. n.a. sing
C5 H5 n.a. n.a. sing
C6 H6 n.a. n.a. sing

View histograms of bond distance distributions.

Bond Angle Table:


Atom 1 Atom 2 Atom 3 Angle E.S.D.
C6 N1 C2 120.32 0.52
N1 C2 N3 119.12 0.65
C2 N3 C4 120.02 0.46
N3 C4 C5 121.68 0.70
C4 C5 C6 117.53 0.73
C5 C6 N1 121.12 0.51
N1 C2 O2 118.93 0.71
N3 C2 O2 121.95 0.67
N3 C4 N4 118.21 0.92
C5 C4 N4 120.11 0.73
C6 N1 C1* 120.96 1.24
C2 N1 C1* 118.59 1.30

View histograms of bond angle distributions.

Torsion Angle Table:


Atom 1 Atom 2 Atom 3 Atom 4 Angle E.S.D.
N1 C2 N3 C4 1.13 3.09
C2 N3 C4 C5 359.21 2.66
N3 C4 C5 C6 0.06 3.62
C4 C5 C6 N1 0.28 2.05
C5 C6 N1 C2 0.09 2.67
C6 N1 C2 N3 359.20 4.32
C6 N1 C2 O2 179.31 3.98
C4 N3 C2 O2 181.02 2.75
C2 N3 C4 N4 179.42 2.48
C6 C5 C4 N4 179.86 3.56
C5 C6 N1 C1* 180.14 4.19
O2 C2 N1 C1* 359.25 5.35
N3 C2 N1 C1* 179.14 5.67

View histograms of torsion angle distributions.
Biological Structure Resource | NDB | Structure Finder | à la mode | mmCIF

ndbadmin@ndbserver.rutgers.edu
The Nucleic Acid Database Project
Rutgers, The State University of New Jersey