PDBe-KB Ligand Pages (PDBeChem)

Examples: STI GLC NAG HEM CLC_000191 PRD_000468

A3P

ADENOSINE-3'-5'-DIPHOSPHATE

Description

Synonyms

3',5'-ADP, Phosphoadenosine phosphate, 3'-Phosphoadenosine 5...Show more

Formula

C10 H15 N5 O10 P2

IUPAC InChI

InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-6(16)7(25-27(20,21)22)4(24-10)1-23-26(17,18)19/h2-4,6-7,10,16H,1...Show more

IUPAC InChIKey

WHTCPDAXWFLDIH-KQYNXXCUSA-N

SMILES

c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O...Show more

Source OpenEye

Is part of

CLC_002188.

First observed in

1aqu

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 / 10

Atom labelled A3P

Physicochemical properties

Molecular properties

Molecular weight

Total mass of the molecule in Daltons

427.0 Da

Labute accessible surface area

Accessible surface area according to the Labute's definition

171.4 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

0.5

Wildman-Crippen molar refractivity

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

81.5

Wildman-Crippen Log P

Octanol/Water partition coefficient predicted using Wildman-Crippen method

-2.6

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

232.6

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 part of a polymer in 12 PDB structures. See detailed list here.

Found as a bound ligand in 55 distinct proteins and 133 PDB Structures. Group data by:

Proteins

Structures

1 to 10 of 56. Page 1 of 6

Protein name

Protein Overview

Total structures

Organism

EC number

Ligand function

Sulfotransferase oxamniquine resistance protein

G4VLE5

Schistosoma mansoni (Blood fluke)

2.8.2.-

Unannotated

Sulfotransferase 1A1

P50225

Homo sapiens (Human)

2.8.2.1

Unannotated

Unmapped

Unannotated

Nad dependent epimerase/dehydratase

A0A094ZWQ2

Schistosoma haematobium (Blood fluke)

2.8.2.-

Unannotated

Sulfotransferase domain-containing protein

Q26490

Spodoptera frugiperda (Fall armyworm)

Unannotated

Heparan sulfate glucosamine 3-O-sulfotransferase 3A1

Q9Y663

Homo sapiens (Human)

2.8.2.30

Unannotated

Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1

P52848

Homo sapiens (Human)

2.8.2.8, 3.5.1.-

Unannotated

Sulfotransferase 1 family member D1

Q3UZZ6

Mus musculus (Mouse)

2.8.2.-

Unannotated

Sulfotransferase 1E1

P49888

Homo sapiens (Human)

2.8.2.4

Unannotated

Sulfotransferase 1E1

P49891

Mus musculus (Mouse)

2.8.2.4

Unannotated

Page Size:

1 to 10 of 56

Page 1 of 6

Protein name

Decapping and exoribonuclease protein

PDB-KB Proteins

O70348

EC number

3.1.13.-, 3.6.1.-

Ligand annotation

Unannotated

Total structures

Protein name

Sulfotransferase 1B1

PDB-KB Proteins

O43704

EC number

2.8.2.1

Ligand annotation

Unannotated

Total structures

Protein name

Bifunctional NAD(P)H-hydrate repair enzyme Nnr

PDB-KB Proteins

Q9X024

EC number

5.1.99.6, 4.2.1.136

Ligand annotation

Unannotated

Total structures

Protein name

Nad dependent epimerase/dehydratase

PDB-KB Proteins

A0A094ZWQ2

EC number

2.8.2.-

Ligand annotation

Unannotated

Total structures

Protein name

3'-5' exonuclease

PDB-KB Proteins

X5MEI1

EC number

---

Ligand annotation

Unannotated

Total structures

Items per page:

1 – 5 of 56

Interaction statistics

Interaction statistics shows the summary of aggregated protein-ligand interaction data of A3P from 196 ligand instances in 56 PDB structures and 133 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 A3P 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