Chemical Components in the PDB

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CTN : Summary

Code

CTN

One-letter code

X

Molecule name

4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE

Synonyms

CYTIDINE

Systematic names

ProgramVersionName
ACDLabs 10.04 cytidine
OpenEye OEToolkits 1.5.0 4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one

Formula

C9 H13 N3 O5

Formal charge

0

Molecular weight

243.217 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C1N=C(N)C=CN1C2OC(C(O)C2O)CO
SMILES CACTVS 3.341 NC1=NC(=O)N(C=C1)[CH]2O[CH](CO)[CH](O)[CH]2O
SMILES OpenEye OEToolkits 1.5.0 C1=CN(C(=O)N=C1N)C2C(C(C(O2)CO)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
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)O

IUPAC InChI

InChI=1S/C9H13N3O5/c10-5-1-2-12(9(16)11-5)8-7(15)6(14)4(3-13)17-8/h1-2,4,6-8,13-15H,3H2,(H2,10,11,16)/t4-,6-,7-,8-/m1/s1

IUPAC InChI key

UHDGCWIWMRVCDJ-XVFCMESISA-N
CTN

wwPDB Information

Atom count

30 (17 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2003-05-20

Last modified at

2021-03-01

Status

Released

Obsoleted

Not Assigned



CTN : Atoms of Molecule

Total Number of Atoms: 30
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O5' O O5* N N N 0 -3.369 2.603 -0.738
2 C5' C C5* N N N 0 -3.251 1.561 0.232
3 C4' C C4* R N N 0 -2.46 0.395 -0.365
4 O4' O O4* N N N 0 -1.093 0.789 -0.612
5 C1' C C1* R N N 0 -0.348 -0.446 -0.687
6 N1 N N1 N Y N 0 1.075 -0.199 -0.446
7 C6 C C6 N Y N 0 2.003 -0.659 -1.333
8 C5 C C5 N Y N 0 3.315 -0.419 -1.102
9 C4 C C4 N Y N 0 3.686 0.292 0.058
10 N3 N N3 N Y N 0 2.748 0.72 0.893
11 C2 C C2 N Y N 0 1.461 0.481 0.649
12 O2 O O2 N N N 0 0.617 0.886 1.432
13 N4 N N4 N N N 0 5.013 0.545 0.32
14 C2' C C2* R N N 0 -0.937 -1.334 0.432
15 O2' O O2* N N N 0 -1.002 -2.699 0.014
16 C3' C C3* S N N 0 -2.359 -0.765 0.65
17 O3' O O3* N N N 0 -3.345 -1.761 0.372
18 H5' H H5* N N N 0 -3.873 3.316 -0.323
19 H5'1 H 1H5* N N N 0 -4.245 1.216 0.519
20 H5'2 H 2H5* N N N 0 -2.73 1.94 1.112
21 H4' H H4* N N N 0 -2.929 0.052 -1.287
22 H1' H H1* N N N 0 -0.492 -0.917 -1.66
23 H6 H H6 N N N 0 1.694 -1.205 -2.212
24 H5 H H5 N N N 0 4.067 -0.774 -1.791
25 HN41 H 1HN4 N N N 0 5.265 1.038 1.116
26 HN42 H 2HN4 N N N 0 5.697 0.227 -0.291
27 H2' H H2* N N N 0 -0.344 -1.241 1.342
28 H1 H H1 N N N 0 -1.432 -3.189 0.728
29 H3' H H3* N N N 0 -2.47 -0.393 1.669
30 H2 H H2 N N N 0 -4.208 -1.334 0.465



CTN : Chemical Bonds

Total Number of Bonds: 31
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O5' C5' O C sing 1.43 N N
2 O5' H5' O H sing 0.97 N N
3 C5' C4' C C sing 1.53 N N
4 C5' H5'1 C H sing 1.09 N N
5 C5' H5'2 C H sing 1.09 N N
6 C4' O4' C O sing 1.44 N N
7 C4' C3' C C sing 1.54 N N
8 C4' H4' C H sing 1.09 N N
9 O4' C1' O C sing 1.44 N N
10 C1' N1 C N sing 1.46 N N
11 C1' C2' C C sing 1.55 N N
12 C1' H1' C H sing 1.09 N N
13 N1 C6 N C sing 1.36 N Y
14 N1 C2 N C sing 1.35 N Y
15 C6 C5 C C doub 1.35 N Y
16 C6 H6 C H sing 1.08 N N
17 C5 C4 C C sing 1.41 N Y
18 C5 H5 C H sing 1.08 N N
19 C4 N3 C N doub 1.33 N Y
20 C4 N4 C N sing 1.38 N N
21 N3 C2 N C sing 1.33 N Y
22 C2 O2 C O doub 1.22 N N
23 N4 HN41 N H sing 0.97 N N
24 N4 HN42 N H sing 0.97 N N
25 C2' O2' C O sing 1.43 N N
26 C2' C3' C C sing 1.55 N N
27 C2' H2' C H sing 1.09 N N
28 O2' H1 O H sing 0.97 N N
29 C3' O3' C O sing 1.43 N N
30 C3' H3' C H sing 1.09 N N
31 O3' H2 O H sing 0.97 N N



CTN : Used in PDB Entries

Total Number of PDB Entries: 26
Ligand Code PDB Entry ID Type Total Distinct
CTN 1uej Open in New Window Bound ligand 2 1
CTN 2fr6 Open in New Window Bound ligand 3 1
CTN 2v34 Open in New Window Bound ligand 2 1
CTN 3ive Open in New Window Bound ligand 1 1
CTN 3p0z Open in New Window Bound ligand 3 1
CTN 3p10 Open in New Window Bound ligand 3 1
CTN 3qhd Open in New Window Bound ligand 3 1
CTN 3t80 Open in New Window Bound ligand 6 1
CTN 3tka Open in New Window Bound ligand 1 1
CTN 3w34 Open in New Window Bound ligand 2 1
CTN 3w8r Open in New Window Bound ligand 2 1
CTN 4js1 Open in New Window Bound ligand 1 1
CTN 4jwk Open in New Window Bound ligand 1 1
CTN 4lbx Open in New Window Bound ligand 2 1
CTN 4ld2 Open in New Window Bound ligand 1 1
CTN 4nwi Open in New Window Bound ligand 2 1
CTN 4pda Open in New Window Bound ligand 1 1
CTN 5cso Open in New Window Bound ligand 1 1
CTN 5efo Open in New Window Bound ligand 2 1
CTN 5ey3 Open in New Window Bound ligand 1 1
CTN 5lok Open in New Window Bound ligand 6 1
CTN 5tbt Open in New Window Bound ligand 1 1
CTN 5w1c Open in New Window Bound ligand 2 1
CTN 6cvu Open in New Window Bound ligand 4 1
CTN 6nn0 Open in New Window Bound ligand 2 1
CTN 6ya4 Open in New Window Bound ligand 4 1