Overview:

P450s play vital roles in numerous biological processes, such as cellular metabolism, natural product biosynthesis, and drug metabolism. Despite the existence of more than 300,000 P450 genes in different databases, only 0.1% of them have been functionally characterized. The current version of P450Rdb documents over 1,600 manually curated in vivo reactions, involving more than 500 P450s across a range of over 120 species, spanning from animals and plants to fungi, bacteria, and archaea. In summary, P450Rdb provides a convenient and user-friendly interface for querying, browsing and visualizing detailed information about these in vivo reactions catalyzed by P450s, and will be of help in elucidating the functions and mechanisms of action of P450 proteins and promoting study on metabolism, synthetic biology, pharmacology, and enzyme engineering.

The homepage is displayed in the following Fig 1-1:

1. Main functions of the database are provided in menu bar form (boxed in red).

2. Introduction and overview for P450Rdb.

3. Quick search for users.

The search page is displayed in Fig 2-1 and 2-2:

Protein search:

1. Select Protein search.

2. Input a keyword in the blank (three types of keyword are provided: P450 Symbol/Uniprot ID/Gene ID).

3. The keyword examples.

Compound search:

1. Select Compound search.

2. Input a keyword in the blank (three types of keyword are provided: Compound name/ Compound CID/ Compound formula).

3. The keyword examples.

For the result page of Protein search and Compound search, all entries are listed with basic information including P450 Symbol, Uniprot ID, Gene ID, Substrate, Product.

Fig 3-1:

1. The result table (including P450 Symbol, Uniprot ID, Gene ID, Substrate, Product.).

2. Click to link to Detail page.

3. page up and page down.

In the Detail page, you can get the detail information of the reactions catalyzed by P450s including “P450 protein”, “Reaction”, “Substrate information”, “Product information” and “References”.

Fig 4-1:

1. P450 protein: including P450 Symbol, Protein name, Uniprot ID, Gene ID Species, Txid P450 protein structure Subcellular location and Protein Sequence.

2. Reaction: including Reaction type, Reaction site and the details of Reaction equation.

3. Substrate information: including Substrate Name, Substrate Chemical Formula, Substrate PubChem CID, Substrate PubChem SID, Substrate Smiles and Substrate Structure.

4. Product information: including Product Name, Product Chemical Formula, Product PubChem CID, Product PubChem SID, Product Smiles and Product Structure.

5. References: the PMID, Title, journal and published years of the references.

Blast search:

Fig 5-1:

1. Select blast method: BLASTP (Protein to Protein) or BLASTX (nucleotide to protein).

2. Select how many top entries show in the search result table (rank by the bit-score).

3. Enter a sequence to do blast search (protein or nucleotide sequence).

Result page of Blast search:

For the result page of Blast search, all entries are listed with basic information including P450 Symbol, Uniprot ID, Gene ID, Substrate, Product, Identity, E-value and Bit-score (rank by Bit-score).

Fig 5-2:

1. The result table (including P450 Symbol, Uniprot ID, Gene ID, Substrate, Product, Identity, E-value and Bit-score).

2. Click to link to Detail page.

The reactions catalyzed by P450s list was presented in the Browse page, Users can browse all the reactions by three filter ways: by species, by Reaction type and Chemical bond or functional group.

Fig 6-1:

1. Filter by species (3 classes: Animal, Plant and Microorganism).

2. Filter by Reaction type (6 types: Oxidation, Reduction, Decomposition, Combination, Oxidoreduction, Substitution).

3. Filter by Reaction site (48 types).

P450Rdb provide the download page for users. You can download all the reactions, P450s (including protein sequences) and compounds data in the download page.