PDBe-KB Ligand Pages (PDBeChem)

Examples: STI GLC NAG HEM CLC_000191 PRD_000468

PGW

(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate

Description

Synonyms

PHOSPHATIDYLGLYCEROL, 1-Palmitoyl-2-Oleoyl-sn-Glycero-3-[Pho...Show more

Formula

C40 H77 O10 P

Standard InChI

InChI=1S/C40H77O10P/c1-3-5-7-9-11-13-15-17-18-20-22-24-26-28-30-32-40(44)50-38(36-49-51(45,46)48-34-37(42)33-41)35-47-39...Show more

Standard InChI Key

PAZGBAOHGQRCBP-HGWHEPCSSA-N

SMILES

CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@H](CO)O)OC(=O...Show more

Source OpenEye

First observed in

2rl5

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

748.5 Da

Labute accessible surface area

Accessible surface area according to the Labute's definition

419.4 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

0.9

Wildman-Crippen molar refractivity

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

205.4

Wildman-Crippen Log P

Octanol/Water partition coefficient predicted using Wildman-Crippen method

10.4

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

148.8

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 34 distinct proteins and 76 PDB Structures. Group data by:

Proteins

Structures

1 to 10 of 35. Page 1 of 4

Protein name

Protein Overview

Total structures

Organism

EC number

Ligand function

Orexin/Hypocretin receptor type 1

O43613

Homo sapiens (Human)

Unannotated

Cyclic nucleotide-binding domain-containing protein

G0GA88

Spirochaeta thermophila (strain ATCC 700085 / DSM 6578 / Z-1203)

Unannotated

Plasma membrane channel protein

C7Z7K1

Fusarium vanettenii (strain ATCC MYA-4622 / CBS 123669 / FGSC 9596 / NRRL 45880 / 77-13-4)

Unannotated

Plasma membrane channel protein (Aqy1)

Q4WA18

Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293)

Unannotated

Unmapped

Unannotated

BK channel

Q5QJC5

Aplysia californica (California sea hare)

Unannotated

Calcium-gated potassium channel MthK

O27564

Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)

Unannotated

Potassium voltage-gated channel subfamily A member 2

P63142

Rattus norvegicus (Rat)

Unannotated

Reaction center protein L chain

A0A143BHR2

Gemmatimonas phototrophica

Unannotated

Photosynthetic reaction centre H subunit N-terminal domain-containing protein

A0A143BJ28

Gemmatimonas phototrophica

Unannotated

Page Size:

1 to 10 of 35

Page 1 of 4

Protein name

TraM protein

PDB-KB Proteins

Q46696

EC number

---

Ligand annotation

Unannotated

Total structures

Protein name

Neurotransmitter-gated ion-channel ligand-binding domain-containing protein

PDB-KB Proteins

E0SJQ4

EC number

---

Ligand annotation

Unannotated

Total structures

Protein name

Cyclic nucleotide-binding domain-containing protein

PDB-KB Proteins

G0GA88

EC number

---

Ligand annotation

Unannotated

Total structures

Protein name

Glutathione-regulated potassium-efflux system protein KefC

PDB-KB Proteins

P03819

EC number

---

Ligand annotation

Unannotated

Total structures

Protein name

Plasma membrane channel protein (Aqy1)

PDB-KB Proteins

Q4WA18

EC number

---

Ligand annotation

Unannotated

Total structures

Items per page:

1 – 5 of 35

Interaction statistics

Interaction statistics shows the summary of aggregated protein-ligand interaction data of PGW from 873 ligand instances in 34 distinct proteins and 76 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 PGW 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