PDBe-KB Ligand Pages (PDBeChem)

Examples: STI GLC NAG HEM CLC_000191 PRD_000468

GDU

GALACTOSE-URIDINE-5'-DIPHOSPHATE

Description

Synonyms

UDPgal, UDP-galactose, UDP galactose, UDP-α-D-galactose, UDP...Show more

Formula

C15 H24 N2 O17 P2

Standard InChI

InChI=1S/C15H24N2O17P2/c18-3-5-8(20)10(22)12(24)14(32-5)33-36(28,29)34-35(26,27)30-4-6-9(21)11(23)13(31-6)17-2-1-7(19)16...Show more

Standard InChI Key

HSCJRCZFDFQWRP-ABVWGUQPSA-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

1gup

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 / 2

Physicochemical properties

Molecular properties

Molecular weight

Total mass of the molecule in Daltons

566.1 Da

Labute accessible surface area

Accessible surface area according to the Labute's definition

233.9 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

109.0

Wildman-Crippen Log P

Octanol/Water partition coefficient predicted using Wildman-Crippen method

-3.0

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

297.0

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 21 distinct proteins and 47 PDB Structures. Group data by:

Proteins

Structures

Protein name

Protein Overview

Total structures

Organism

EC number

Ligand function

Histo-blood group ABO system transferase

P16442

Homo sapiens (Human)

2.4.1.40, 2.4.1.37

Unannotated

Beta-1,4-galactosyltransferase 1

P08037

Bos taurus (Bovine)

2.4.1.-, 2.4.1.275, 2.4.1.90, 2.4.1.22, 2.4.1.38

Unannotated

UDP-galactopyranose mutase

Q4W1X2

Aspergillus fumigatus

5.4.99.9

Unannotated

UDP-glucose 4-epimerase

P9WN67

Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

5.1.3.2

Unannotated

N-acetyllactosaminide alpha-1,3-galactosyltransferase

P14769

Bos taurus (Bovine)

2.4.1.87

Unannotated

UDP-galactopyranose mutase

P9WIQ1

Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

5.4.99.9

Unannotated

UDP-galactopyranose mutase C-terminal domain-containing protein

Q6NER4

Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)

5.4.99.9

Unannotated

Beta-1,4-galactosyltransferase 7

Q9VBZ9

Drosophila melanogaster (Fruit fly)

2.4.1.133

Unannotated

UDP-galactopyranose mutase C-terminal domain-containing protein

Q9RYF1

Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

5.4.99.9

Unannotated

UDP-galactopyranose mutase

Q48485

Klebsiella pneumoniae

5.4.99.9

Unannotated

Page Size:

1 to 10 of 22

Page 1 of 3

Protein name

Beta-1,4-galactosyltransferase 1

PDB-KB Proteins

P08037

EC number

2.4.1.-, 2.4.1.275, 2.4.1.90, 2.4.1.22, 2.4.1.38

Ligand annotation

Unannotated

Total structures

Protein name

Glycosyl transferase family 1 domain-containing protein

PDB-KB Proteins

Q9HUF6

EC number

---

Ligand annotation

Unannotated

Total structures

Protein name

UDP-galactopyranose mutase

PDB-KB Proteins

P9WIQ1

EC number

5.4.99.9

Ligand annotation

Unannotated

Total structures

Protein name

UDP-glucose 4-epimerase

PDB-KB Proteins

Q14376

EC number

5.1.3.7, 5.1.3.2

Ligand annotation

Unannotated

Total structures

Protein name

UDP-galactopyranose mutase C-terminal domain-containing protein

PDB-KB Proteins

Q6NER4

EC number

5.4.99.9

Ligand annotation

Unannotated

Total structures

Items per page:

1 – 5 of 22

Interaction statistics

Interaction statistics shows the summary of aggregated protein-ligand interaction data of GDU from 82 ligand instances in 21 distinct proteins and 47 PDB Structures. 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 GDU 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