PDBe-KB Ligand Pages (PDBeChem)

Examples: STI GLC NAG HEM CLC_000191 PRD_000468

OXY

OXYGEN MOLECULE

Description

Synonyms

Oxygen, Dioxygen, Oxygen USP, Pure oxygen, Molecular oxygen

Formula

IUPAC InChI

InChI=1S/O2/c1-2

IUPAC InChIKey

MYMOFIZGZYHOMD-UHFFFAOYSA-N

SMILES

O=O

Source OpenEye

First observed in

1hmo

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

Atom labelled OXY

Physicochemical properties

Molecular properties

Molecular weight

Total mass of the molecule in Daltons

32.0 Da

Labute accessible surface area

Accessible surface area according to the Labute's definition

11.3 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

6.7

Wildman-Crippen Log P

Octanol/Water partition coefficient predicted using Wildman-Crippen method

0.1

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

34.1

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 208 distinct proteins and 634 PDB Structures. Group data by:

Proteins

Structures

1 to 10 of 209. Page 1 of 21

Protein name

Protein Overview

Total structures

Organism

EC number

Ligand function

Catalase-peroxidase

Q3JNW6

Burkholderia pseudomallei (strain 1710b)

1.11.1.21

Unannotated

Hemoglobin subunit alpha

P69905

Homo sapiens (Human)

Unannotated

Hemoglobin subunit beta

P68871

Homo sapiens (Human)

Unannotated

laccase

I1VE66

Steccherinum murashkinskyi

1.10.3.2

Unannotated

Two-domain laccase

A0A0M4FJ81

Streptomyces griseoflavus

1.10.3.2

Unannotated

Myoglobin

P02185

Physeter macrocephalus (Sperm whale)

1.11.1.-, 1.7.-.-

Unannotated

Uric acid degradation bifunctional protein

Q45697

Bacillus sp. (strain TB-90)

4.1.1.97, 1.7.3.3

Unannotated

Unmapped

Unannotated

Globin domain-containing protein

Q9NAV7

Amphitrite ornata

Unannotated

Methyl-accepting transducer domain-containing protein

Q8RBX6

Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4)

Unannotated

Page Size:

1 to 10 of 209

Page 1 of 21

Protein name

Gag-Pol polyprotein

PDB-KB Proteins

P12499

EC number

3.4.23.16, 3.1.26.13, 3.1.13.2, 2.7.7.49, 2.7.7.7, 3.1.-.-, 2.7.7.-

Ligand annotation

Unannotated

Total structures

Protein name

Hemoglobin subunit alpha-A

PDB-KB Proteins

P81023

EC number

---

Ligand annotation

Unannotated

Total structures

Protein name

Ferritin, mitochondrial

PDB-KB Proteins

Q8N4E7

EC number

1.16.3.1

Ligand annotation

Unannotated

Total structures

Protein name

Cytochrome c oxidase subunit 1-beta

PDB-KB Proteins

P98002

EC number

7.1.1.9

Ligand annotation

Unannotated

Total structures

Protein name

Extracellular globin

PDB-KB Proteins

S0BBU7

EC number

---

Ligand annotation

Unannotated

Total structures

Items per page:

1 – 5 of 209

Interaction statistics

Interaction statistics shows the summary of aggregated protein-ligand interaction data of OXY from 1665 ligand instances in 209 PDB structures and 634 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 OXY 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