PDBe-KB Ligand Pages (PDBeChem)

Examples: STI GLC NAG HEM CLC_000191 PRD_000468

KDG

2-KETO-3-DEOXYGLUCONATE

Description

Synonyms

2-KETO-3-DEOXYGLUCONATE

Formula

C6 H10 O6

Standard InChI

InChI=1S/C6H10O6/c7-2-5(10)3(8)1-4(9)6(11)12/h3,5,7-8,10H,1-2H2,(H,11,12)/t3-,5+/m0/s1

Standard InChI Key

WPAMZTWLKIDIOP-WVZVXSGGSA-N

SMILES

C([C@@H]([C@@H](CO)O)O)C(=O)C(=O)O

Source OpenEye

First observed in

1v1a

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

178.0 Da

Labute accessible surface area

Accessible surface area according to the Labute's definition

82.5 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

0.7

Wildman-Crippen molar refractivity

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

36.4

Wildman-Crippen Log P

Octanol/Water partition coefficient predicted using Wildman-Crippen method

-2.3

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

115.1

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 6 distinct proteins and 8 PDB Structures. Group data by:

Proteins

Structures

Protein name

Protein Overview

Total structures

Organism

EC number

Ligand function

D-galactonate dehydratase family member ManD

Q1QT89

Chromohalobacter salexigens (strain ATCC BAA-138 / DSM 3043 / CIP 106854 / NCIMB 13768 / 1H11)

4.2.1.39, 4.2.1.-, 4.2.1.8

Unannotated

2-dehydro-3-deoxygluconokinase/2-dehydro-3-deoxygalactonokinase

Q97U29

Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

2.7.1.178

Unannotated

D-mannonate dehydratase

A4XF23

Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199)

4.2.1.8

Unannotated

Unmapped

Unannotated

2-dehydro-3-deoxygluconokinase

Q53W83

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

2.7.1.45

Unannotated

Putative 2-dehydro-3-deoxy-D-gluconate aldolase YagE

P75682

Escherichia coli (strain K12)

4.1.2.28, 4.1.2.51

Unannotated

Putative TRAP transporter solute receptor, DctP family

R4JTF7

Advenella mimigardefordensis (strain DSM 17166 / LMG 22922 / DPN7)

Unannotated

Page Size:

1 to 7 of 7

Page 1 of 1

Protein name

D-galactonate dehydratase family member ManD

PDB-KB Proteins

Q1QT89

EC number

4.2.1.39, 4.2.1.-, 4.2.1.8

Ligand annotation

Unannotated

Total structures

Protein name

2-dehydro-3-deoxygluconokinase/2-dehydro-3-deoxygalactonokinase

PDB-KB Proteins

Q97U29

EC number

2.7.1.178

Ligand annotation

Unannotated

Total structures

Protein name

D-mannonate dehydratase

PDB-KB Proteins

A4XF23

EC number

4.2.1.8

Ligand annotation

Unannotated

Total structures

Protein name

---

PDB-KB Proteins

EC number

---

Ligand annotation

Unannotated

Total structures

Protein name

2-dehydro-3-deoxygluconokinase

PDB-KB Proteins

Q53W83

EC number

2.7.1.45

Ligand annotation

Unannotated

Total structures

Items per page:

1 – 5 of 7

Interaction statistics

Interaction statistics shows the summary of aggregated protein-ligand interaction data of KDG from 30 ligand instances in 6 distinct proteins and 8 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 KDG 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