PDBe-KB Ligand Pages (PDBeChem)

Examples: STI GLC NAG HEM CLC_000191 PRD_000468

UGA

URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID

Description

Synonyms

UDPglucuronate, UDP-glucuronate, UDP-D-glucuronate, UDP-GLUC...Show more

Formula

C15 H22 N2 O18 P2

IUPAC InChI

InChI=1S/C15H22N2O18P2/c18-5-1-2-17(15(26)16-5)12-9(22)6(19)4(32-12)3-31-36(27,28)35-37(29,30)34-14-10(23)7(20)8(21)11(3...Show more

IUPAC InChIKey

HDYANYHVCAPMJV-LXQIFKJMSA-N

SMILES

C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)...Show more

Source OpenEye

First observed in

1dlj

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 / 8

Atom labelled UGA

Physicochemical properties

Molecular properties

Molecular weight

Total mass of the molecule in Daltons

580.0 Da

Labute accessible surface area

Accessible surface area according to the Labute's definition

235.3 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

0.7

Wildman-Crippen molar refractivity

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

109.6

Wildman-Crippen Log P

Octanol/Water partition coefficient predicted using Wildman-Crippen method

-2.9

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

314.1

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 14 distinct proteins and 19 PDB Structures. Group data by:

Proteins

Structures

1 to 10 of 15. Page 1 of 2

Protein name

Protein Overview

Total structures

Organism

EC number

Ligand function

UDP-glucose 6-dehydrogenase

C9E261

Burkholderia cepacia

1.1.1.22

Unannotated

Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3

O60568

Homo sapiens (Human)

2.4.1.50, 1.14.11.4, 2.4.1.66

Unannotated

Unmapped

Unannotated

UDP-glucuronic acid decarboxylase 1

Q8NBZ7

Homo sapiens (Human)

4.1.1.35

Unannotated

UDP-glucose 6-dehydrogenase

A0A0J9WZA6

Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044

1.1.1.22

Unannotated

UDP-glucose 6-dehydrogenase

P0C0F4

Streptococcus pyogenes

1.1.1.22

Unannotated

UDP-glucose 6-dehydrogenase

Q7MVC7

Porphyromonas gingivalis (strain ATCC BAA-308 / W83)

1.1.1.22

Unannotated

Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 3

O94766

Homo sapiens (Human)

2.4.1.135

Unannotated

Bifunctional polymyxin resistance protein ArnA

P77398

Escherichia coli (strain K12)

2.1.2.13, 1.1.1.305

Unannotated

Bifunctional polymyxin resistance protein ArnA

O52325

Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

2.1.2.13, 1.1.1.305

Unannotated

Page Size:

1 to 10 of 15

Page 1 of 2

Protein name

UDP-glucuronic acid decarboxylase 1

PDB-KB Proteins

Q8NBZ7

EC number

4.1.1.35

Ligand annotation

Unannotated

Total structures

Protein name

UDP-glucose 6-dehydrogenase

PDB-KB Proteins

A0A0J9WZA6

EC number

1.1.1.22

Ligand annotation

Unannotated

Total structures

Protein name

UDP-glucose 6-dehydrogenase

PDB-KB Proteins

P0C0F4

EC number

1.1.1.22

Ligand annotation

Unannotated

Total structures

Protein name

UDP-glucose 6-dehydrogenase

PDB-KB Proteins

Q7MVC7

EC number

1.1.1.22

Ligand annotation

Unannotated

Total structures

Protein name

Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3

PDB-KB Proteins

O60568

EC number

2.4.1.50, 1.14.11.4, 2.4.1.66

Ligand annotation

Unannotated

Total structures

Items per page:

1 – 5 of 15

Interaction statistics

Interaction statistics shows the summary of aggregated protein-ligand interaction data of UGA from 58 ligand instances in 15 PDB structures and 19 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 UGA 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