PDBe-KB Ligand Pages (PDBeChem)

Examples: STI GLC NAG HEM CLC_000191 PRD_000468

PI

HYDROGENPHOSPHATE ION

Description

Synonyms

HYDROGENPHOSPHATE ION

Formula

H O4 P

Standard InChI

InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-2

Standard InChI Key

NBIIXXVUZAFLBC-UHFFFAOYSA-L

SMILES

OP(=O)([O-])[O-]

Source OpenEye

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

96.0 Da

Labute accessible surface area

Accessible surface area according to the Labute's definition

29.8 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

0.0

Wildman-Crippen molar refractivity

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

9.8

Wildman-Crippen Log P

Octanol/Water partition coefficient predicted using Wildman-Crippen method

-2.2

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

83.4

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 16 distinct proteins and 17 PDB Structures. Group data by:

Proteins

Structures

1 to 10 of 17. Page 1 of 2

Protein name

Protein Overview

Total structures

Organism

EC number

Ligand function

Unmapped

Unannotated

Fructose-1,6-bisphosphatase 1

P00636

Sus scrofa (Pig)

3.1.3.11

Unannotated

Phosphate-binding protein PstS

C3K8K1

Pseudomonas fluorescens (strain SBW25)

Unannotated

ATP synthase subunit beta

P07677

Bacillus sp. (strain PS3)

7.1.2.2

Unannotated

Adenylosuccinate synthetase

P0A7D4

Escherichia coli (strain K12)

6.3.4.4

Unannotated

Uncharacterized ABC transporter ATP-binding protein MJ0796

Q58206

Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)

Unannotated

D-3-phosphoglycerate dehydrogenase 2

P40510

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

1.1.1.95, 1.1.1.399

Unannotated

ATP synthase subunit alpha

A0A0M3VGF9

Bacillus sp. (strain PS3)

7.1.2.2

Unannotated

Phycoerythrin Beta subunit

A0A0E4G455

Phormidium rubidum A09DM

Unannotated

Listeriolysin regulatory protein

P22262

Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)

Unannotated

Page Size:

1 to 10 of 17

Page 1 of 2

Protein name

Adenylosuccinate synthetase

PDB-KB Proteins

P0A7D4

EC number

6.3.4.4

Ligand annotation

Unannotated

Total structures

Protein name

Uncharacterized ABC transporter ATP-binding protein MJ0796

PDB-KB Proteins

Q58206

EC number

---

Ligand annotation

Unannotated

Total structures

Protein name

D-3-phosphoglycerate dehydrogenase 2

PDB-KB Proteins

P40510

EC number

1.1.1.95, 1.1.1.399

Ligand annotation

Unannotated

Total structures

Protein name

ATP synthase subunit alpha

PDB-KB Proteins

A0A0M3VGF9

EC number

7.1.2.2

Ligand annotation

Unannotated

Total structures

Protein name

---

PDB-KB Proteins

EC number

---

Ligand annotation

Unannotated

Total structures

Items per page:

1 – 5 of 17

Interaction statistics

Interaction statistics shows the summary of aggregated protein-ligand interaction data of PI from 49 ligand instances in 16 distinct proteins and 17 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 PI 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