Examples: STIGLCNAGHEMCLC_000191PRD_000468

DR9

1-CIS-9-OCTADECANOYL-2-CIS-9-HEXADECANOYL PHOSPHATIDYL GLYCEROL

Description

Synonyms
(2R)-3-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]...Show more
Formula
C40 H75 O10 P
Standard InChI
InChI=1S/C40H75O10P/c1-3-5-7-9-11-13-15-17-18-20-21-23-25-27-29-31-39(43)47-35-38(36-49-51(45,46)48-34-37(42)33-41)50-40...Show more
Standard InChI Key
QGIXWNRQEFVVRM-CTDKCSBDSA-N
SMILES
CCCCCCCC\C=C/CCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@@H](CO)O...Show more
Source OpenEye
First observed in

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
746.5 Da
Labute accessible surface area
Accessible surface area according to the Labute's definition
415.9 Å 2
Heavy atoms
Number of non-hydrogen atoms
51
Heteroatoms
Number of non-oxygen and non-carbon atoms
11
Carbon SP3 value
Fraction of C atoms that are SP3 hybridized
0.8
Wildman-Crippen molar refractivity
Wildman-Crippen molar refractivity is a common descriptor accounting for molecular size and polarizability
205.3
Wildman-Crippen Log P
Octanol/Water partition coefficient predicted using Wildman-Crippen method
10.2
Conformational properties
Rotatable bonds
Number of single bonds, not part of a ring bound to a nonterminal heavy atom
43
Ring properties
Aromatic rings
Number of aromatic rings
0
Rings
Number of rings
0
Aliphatic rings
Number of aliphatic rings
0
Heterocycles
Number or rings with at least two different elements
0
Saturated rings
Number of saturated rings
0
Aromatic heterocycles
Number of aromatic heterocyles
0
Saturated heterocycles
Number of saturated heterocyles
0
Aliphatic heterocycles
Number of aliphatic heterocycles
0
Spiro atoms
Atoms shared between rings that share exactly one atom
0
Bridgehead atoms
Number of atoms shared between rings that share at least two bonds
0
Surface properties
Topological surface area
Topological surface area
148.8
Functional group properties
Hydrogen bond donors
Number of hydrogen bond donors
3
Hydrogen bond acceptors
Number of hydrogen bond acceptors
10
Amide bonds
Number of amide bonds
0
Stereochemical properties
Stereocenters
Number of atoms with four attachments different from each other
3

Bound structures

Found as a bound ligand in 7 distinct proteins and 6 PDB Structures. Group data by:

1 to 7 of 7. Page 1 of 1

Protein name

FAD-binding domain-containing protein

PDB-KB Proteins

A0A372LQN7

EC number

---

Ligand annotation

Unannotated

Total structures

9

Protein name

Protein wntless homolog

PDB-KB Proteins

Q5T9L3

EC number

---

Ligand annotation

Unannotated

Total structures

1

Protein name

Steroidogenic factor 1

PDB-KB Proteins

P33242

EC number

---

Ligand annotation

Unannotated

Total structures

1

Protein name

Formate hydrogenlyase subunit 4

PDB-KB Proteins

P16430

EC number

---

Ligand annotation

Unannotated

Total structures

1

Protein name

Formate hydrogenlyase subunit 5

PDB-KB Proteins

P16431

EC number

---

Ligand annotation

Unannotated

Total structures

1

Items per page:
1 – 5 of 7

Interaction statistics

Interaction statistics shows the summary of aggregated protein-ligand interaction data of DR9 from 18 ligand instances in 7 distinct proteins and 6 PDB Structures. The protein-ligand interactions are computed using PDBe Arpeggio
Documentation

Ligand atoms

Sort by:
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 DR9 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

Ligand-specific databases

PubChem

5288113

DrugBank

DB04683

Probes And Drugs

PD005905

ZINC

ZINC000053683609