PDBe-KB Ligand Pages (PDBeChem)

Examples: STI GLC NAG HEM CLC_000191 PRD_000468

CTN

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

Description

Synonyms

CYTIDINE, MMV638723, Cytosine riboside, 1β-D-ribofuranosylcy...Show more

Formula

C9 H13 N3 O5

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 InChIKey

UHDGCWIWMRVCDJ-XVFCMESISA-N

SMILES

C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O

Source OpenEye

First observed in

1uej

Overall view, and highlighted
scaffolds and fragments
This image gallery displays several views of the ligand structure:
Basic Structural Representation: Shows the overall structure of the ligand.
Detailed Structural Representation: Highlights individual atoms within the ligand.
Murcko Scaffold: Presents the scaffold of the ligand highlighted in yellow.
Highlighted Fragments: Displays various ligand fragments, highlighted in yellow.

Displayed: 1 / 5

Atom labelled CTN

Physicochemical properties

Molecular properties

Molecular weight

Total mass of the molecule in Daltons

243.1 Da

Labute accessible surface area

Accessible surface area according to the Labute's definition

114.5 Å ²

Heavy atoms

Number of non-hydrogen atoms

Heteroatoms

Number of non-oxygen and non-carbon atoms

Carbon SP3 value

Fraction of C atoms that are SP3 hybridized

0.6

Wildman-Crippen molar refractivity

Wildman-Crippen molar refractivity is a common descriptor accounting for molecular size and polarizability

55.2

Wildman-Crippen Log P

Octanol/Water partition coefficient predicted using Wildman-Crippen method

-2.0

Conformational properties

Rotatable bonds

Number of single bonds, not part of a ring bound to a nonterminal heavy atom

Ring properties

Aromatic rings

Number of aromatic rings

Rings

Number of rings

Aliphatic rings

Number of aliphatic rings

Heterocycles

Number or rings with at least two different elements

Saturated rings

Number of saturated rings

Aromatic heterocycles

Number of aromatic heterocyles

Saturated heterocycles

Number of saturated heterocyles

Aliphatic heterocycles

Number of aliphatic heterocycles

Spiro atoms

Atoms shared between rings that share exactly one atom

Bridgehead atoms

Number of atoms shared between rings that share at least two bonds

Surface properties

Topological surface area

130.8

Functional group properties

Hydrogen bond donors

Number of hydrogen bond donors

Hydrogen bond acceptors

Number of hydrogen bond acceptors

Amide bonds

Number of amide bonds

Stereochemical properties

Stereocenters

Number of atoms with four attachments different from each other

Bound structures

Found as a bound ligand in 23 distinct proteins and 30 PDB Structures. Group data by:

Proteins

Structures

1 to 10 of 24. Page 1 of 3

Protein name

Protein Overview

Total structures

Organism

EC number

Ligand function

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

Q3JRA0

Burkholderia pseudomallei (strain 1710b)

4.6.1.12

Unannotated

Uridine phosphorylase

Q9K4U1

Vibrio cholerae

2.4.2.3

Unannotated

Dethiobiotin synthetase BioD

P9WPQ5

Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

6.3.3.3

Unannotated

Uridine kinase

Q5SKR5

Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

2.7.1.48

Unannotated

Cytidine deaminase

P56389

Mus musculus (Mouse)

3.5.4.5

Unannotated

CMP/dCMP-type deaminase domain-containing protein

Q82Y41

Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298)

3.5.-.-

Unannotated

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

Q8ZMF7

Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

4.6.1.12

Unannotated

ABC transporter substrate-binding protein PnrA-like domain-containing protein

A0A0H2UPF3

Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)

Unannotated

Single-stranded DNA cytosine deaminase

Q9GZX7

Homo sapiens (Human)

3.5.4.38

Unannotated

Purine nucleoside phosphorylase

A0A0U3AGT1

Schistosoma mansoni (Blood fluke)

2.4.2.1

Unannotated

Page Size:

1 to 10 of 24

Page 1 of 3

Protein name

Uridine phosphorylase

PDB-KB Proteins

Q9K4U1

EC number

2.4.2.3

Ligand annotation

Unannotated

Total structures

Protein name

Cytidine deaminase

PDB-KB Proteins

P56389

EC number

3.5.4.5

Ligand annotation

Unannotated

Total structures

Protein name

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

PDB-KB Proteins

Q3JRA0

EC number

4.6.1.12

Ligand annotation

Unannotated

Total structures

Protein name

CMP/dCMP-type deaminase domain-containing protein

PDB-KB Proteins

Q82Y41

EC number

3.5.-.-

Ligand annotation

Unannotated

Total structures

Protein name

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

PDB-KB Proteins

Q8ZMF7

EC number

4.6.1.12

Ligand annotation

Unannotated

Total structures

Items per page:

1 – 5 of 24

Interaction statistics

Interaction statistics shows the summary of aggregated protein-ligand interaction data of CTN from 68 ligand instances in 24 PDB structures and 30 PDB chains. The protein-ligand interactions are computed using PDBe Arpeggio

Documentation

Ligand atoms

Sort by:

Amino acid properties

Interactions

Ligand interactions

Percentage of interactions by ligand atom compared to the total interactions of the ligand

Amino acid interactions

Percentage of interactions between ligand atom-amino acid pair compared to the total interactions of the amino acid

Icons:

Positively charged

Negatively charged

Polar

Hydrophobic

Aromatic

Aromatic (Trp)

Glycine

Cysteine

Proline

Atom-wise interactions of CTN molecule
Percentage of interactions by ligand atom compared to the total interactions of the ligand

For full interaction statistics, including the heatmap showing ligand atom interaction frequency with different amino acids, please view on a larger screen