PDBe-KB Ligand Pages (PDBeChem)

Examples: STI GLC NAG HEM CLC_000191 PRD_000468

RRX

(3R)-beta,beta-caroten-3-ol

Description

Synonyms

Kryptoxanthin, Cryptoxanthol, Cryptoxanthine, Neocryptoxanth...Show more

Formula

C40 H56 O

IUPAC InChI

InChI=1S/C40H56O/c1-30(18-13-20-32(3)23-25-37-34(5)22-15-27-39(37,7)8)16-11-12-17-31(2)19-14-21-33(4)24-26-38-35(6)28-36...Show more

IUPAC InChIKey

DMASLKHVQRHNES-FKKUPVFPSA-N

SMILES

CC1=C(C(CCC1)(C)C)/C=C/C(=C/C=C/C(=C/C=C/C=C(\C)/C=C/C=C(\C)...Show more

Source OpenEye

First observed in

3wu2

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 / 3

Atom labelled RRX

Physicochemical properties

Molecular properties

Molecular weight

Total mass of the molecule in Daltons

552.4 Da

Labute accessible surface area

Accessible surface area according to the Labute's definition

330.9 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

182.8

Wildman-Crippen Log P

Octanol/Water partition coefficient predicted using Wildman-Crippen method

11.6

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

20.2

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 32 distinct proteins and 96 PDB Structures. Group data by:

Proteins

Structures

1 to 10 of 33. Page 1 of 4

Protein name

Protein Overview

Total structures

Organism

EC number

Ligand function

Photosystem II reaction center protein H

P19052

Thermostichus vulcanus

Unannotated

Photosystem II reaction center protein X

D0VWR4

Thermostichus vulcanus

Unannotated

Photosystem II CP47 reaction center protein

D0VWR1

Thermostichus vulcanus

Unannotated

Unmapped

Unannotated

Photosystem II CP47 reaction center protein

Q8DIQ1

Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Unannotated

Photosystem II CP47 reaction center protein

P05429

Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)

Unannotated

Photosystem II reaction center protein H

A0A1C8XRP3

Dunaliella salina (Green alga)

Unannotated

Photosystem II reaction center protein H

Q8DJ43

Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Unannotated

Photosystem II reaction center protein H

P14835

Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)

Unannotated

Photosystem II reaction center protein X

P72575

Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)

Unannotated

Page Size:

1 to 10 of 33

Page 1 of 4

Protein name

Photosystem II reaction center protein H

PDB-KB Proteins

P19052

EC number

---

Ligand annotation

Unannotated

Total structures

Protein name

---

PDB-KB Proteins

EC number

---

Ligand annotation

Unannotated

Total structures

Protein name

Photosystem II CP47 reaction center protein

PDB-KB Proteins

Q8DIQ1

EC number

---

Ligand annotation

Unannotated

Total structures

Protein name

Photosystem II reaction center protein X

PDB-KB Proteins

D0VWR4

EC number

---

Ligand annotation

Unannotated

Total structures

Protein name

Photosystem II CP47 reaction center protein

PDB-KB Proteins

P05429

EC number

---

Ligand annotation

Unannotated

Total structures

Items per page:

1 – 5 of 33

Interaction statistics

Interaction statistics shows the summary of aggregated protein-ligand interaction data of RRX from 176 ligand instances in 33 PDB structures and 96 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 RRX 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