A database for detecting similar small-molecule binding sites on proteins
Data name | README |
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Description of data contents | HTML file to describe "PoSSuM" data. |
File | README_e.html (English) |
Data name | Known binding sites |
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Description of data contents | Known binding sites on protein |
File | possum_ksite.zip (7.9 MB) |
Data item | Description |
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PocketIndex | Internal ID for this binding site |
PDB_ID | PDB ID for the protein |
HET_Code | HET code for the ligand |
ChainID | ID for the chain where the binding site is |
HET_Res.No. | Residue sequence number of the ligand |
ResLength | Length of residue sequence of the site |
Atoms | Num of atoms of the ligand |
MolName | Molecular name of the site |
EC | EC ID for the site |
CATH | CATH ID for the site |
SCOPe | SCOPe ID for the site |
UniProt | UniProt ID for the site |
UniRef50 | UniRef50 cluster ID for the site (when it is analysed) |
GO1 | Gene ontology to indicate molecular function of the site |
GO2 | Gene ontology to indicate molecular function of the site |
GO3 | Gene ontology to indicate molecular function of the site |
Data name | Potential binding sites |
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Description of data contents | Not confirmed yet but putative binding sites on protein |
File | possum_psite.zip (27 MB) |
Data item | Description |
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PocketIndex | Internal ID for this binding site |
PDB_ID | PDB ID for the protein |
HET_Code | HET code for the ligand |
ChainID | ID for the chain where the binding site is |
ResLength | Length of residue sequence of the site |
Atoms | Num of atoms of the ligand |
MolName | Molecular name of the site |
EC | EC ID for the site |
CATH | CATH ID for the site |
SCOPe | SCOPe ID for the site |
UniProt | UniProt ID for the site |
UniRef50 | UniRef50 cluster ID for the site (when it is analysed) |
GO1 | Gene ontology to indicate molecular function of the site |
GO2 | Gene ontology to indicate molecular function of the site |
GO3 | Gene ontology to indicate molecular function of the site |
Data name | Known binding site similarities |
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Description of data contents | Similarity data between known binding sites |
File | possum_kpair.zip (3.9 GB) |
Data item | Description |
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Q:PocketIndex | Internal ID for query site |
T:PocketIndex | Internal ID for target site |
Q:PDB_ID | PDB ID for query site |
T:PDB_ID | PDB ID for target site |
Q:HET_Code | HED code for query site |
T:HET_Code | HED code for target site |
Q:ChainID | ID for the chain where the query site is |
T:ChainID | ID for the chain where the target site is |
Q:Res.No. | Residence number for the amino acid where the query site is |
T:Res.No. | Residence number for the amino acid where the target site is |
Cosine | Cosine similarity with physicochemical and geometric properties |
AlignedLength | Length of amino acid alignment |
RMSD | Root Mean Square Deviation |
TM-score | Template modeling score of protein structure |
Pval | P-Value of similarity |
AminoIdentity | Amino acid match rate |
MolName | Molecular name of the site |
EC | EC ID for the site |
CATH | CATH ID for the site |
SCOPe | SCOPe ID for the site |
UniProt | UniProt ID for the site |
UniRef50 | UniRef50 cluster ID for the site (when it is analysed) |
GO1 | Gene ontology to indicate molecular function of the site |
GO2 | Gene ontology to indicate molecular function of the site |
GO3 | Gene ontology to indicate molecular function of the site |
AlignedResidues | Amino acid alignment result |
Data name | Binding site similarities |
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Description of data contents | Similarity data between known/potential binding sites |
File | possum_ppair.zip (5.4 GB) |
Data item | Description |
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Q:PocketIndex | Internal ID for query site |
T:PocketIndex | Internal ID for target site |
Q:PDB_ID | PDB ID for query site |
T:PDB_ID | PDB ID for target site |
Q:HET_Code | HED code for query site |
T:HET_Code | HED code for target site |
Q:ChainID | ID for the chain where the query site is |
T:ChainID | ID for the chain where the target site is |
Q:Res.No. | Residence number for the amino acid where the query site is |
T:Res.No. | Residence number for the amino acid where the target site is |
Cosine | Cosine similarity with physicochemical and geometric properties |
AlignedLength | Length of amino acid alignment |
RMSD | Root Mean Square Deviation |
TM-score | Template modeling score of protein structure |
Pval | P-Value of similarity |
AminoIdentity | Amino acid match rate |
MolName | Molecular name of the site |
EC | EC ID for the site |
CATH | CATH ID for the site |
SCOPe | SCOPe ID for the site |
UniProt | UniProt ID for the site |
UniRef50 | UniRef50 cluster ID for the site (when it is analysed) |
GO1 | Gene ontology to indicate molecular function of the site |
GO2 | Gene ontology to indicate molecular function of the site |
GO3 | Gene ontology to indicate molecular function of the site |
AlignedResidues | Amino acid alignment result |
Data name | (Drug Search)Ligand list |
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Description of data contents | Ligand list for Drug Search extracted from ChEMBL |
File | possum_ligand_list.zip (11 KB) |
Data item | Description |
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ID | Internal ID for this ligand |
HET_Code | HET Code |
Link | Link to tables in Drug Search (only in simple search) |
ChEMBL_ID | ChEMBL ID |
PrefName | Preferred name |
HeavyAtoms | Number of heavy atoms |
FullMWT | Full molocular weight |
Alogp | Value of ALogP |
HBA | Number of H-bond acceptors |
HBD | Number of H-bond donors |
RotatableBonds | Number of ratatable bonds |
PSA | Polar surface area |
ATC_Level1 | Classification in ATC level1 |
ATC_Level2 | Classification in ATC level2 |
ATC_Level3 | Classification in ATC level3 |
ATC_Level4 | Classification in ATC level4 |
Data name | (Drug Search)Query site list |
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Description of data contents | The list of binding sites (query) for ligands in (Drug Search) Ligand list |
File | possum_query_protein.zip (40 KB) |
Data item | Description |
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PocketIndex | Internal ID for this binding site |
PDB_ID | PDB ID for the protein |
HET_Code | HET code for the ligand |
ChainID | ID for the chain where the binding site is |
Res.No. | Residence number for the amino acid where the binding site is |
MolName | Molecular name of the protein |
UniProt | UniProt ID for the protein |
UniRef50 | UniRef50 claster ID for the protein (when it is analysed) |
EC | EC ID for the protein |
CATH | CATH ID for the protein |
SCOPe | SCOPe scope for the ligand |
Data name | (Drug Search)Target site list |
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Description of data contents | The list of binding sites (target) similar with query sites |
File | possum_target_protein.zip (844 KB) |
Data item | Description |
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PocketIndex | Internal ID for this binding site |
PDB_ID | PDB ID for the protein |
HET_Code | HET code for the ligand |
ChainID | ID for the chain where the binding site is |
Res.No. | Residence number for the amino acid where the binding site is |
MolName | Molecular name of the protein |
UniProt | UniProt ID for the protein |
UniRef50 | UniRef50 cluster ID for the protein (when it is analysed) |
EC | EC ID for the protein |
CATH | CATH ID for the protein |
SCOPe | SCOPe scope for the ligand |
Data name | (Drug Search)Target ligand list |
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Description of data contents | The list of target sites and binding ligands |
File | possum_target_ligand.zip (792 KB) |
Data item | Description |
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HET_Code | HET Code for the ligand |
SimilarPockets | Internal id of site binding the ligand |
JaccardIndex(MACCS) | Jaccard Index between ligand and target site (with MACCS) |
JaccardIndex(FP2) | Jaccard Index between ligand and target site (with FP2) |
InChi_Key | InChIKey of binding molocular |
CanonicalSmiles | Canonical SMILES of binding molocular |
Data name | (Drug Search)Known binding site similarity |
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Description of data contents | Similarity data between known binding sites in (Drug Search) query and target sites |
File | possum_binding_sites_known_similarity.zip (2.4 MB) |
Data item | Description |
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Q:PocketIndex | Internal ID for query site |
T:PocketIndex | Internal ID for target site |
Q:PDB_ID | PDB ID for query site |
T:PDB_ID | PDB ID for target site |
Q:HET_Code | HED code for query site |
T:HET_Code | HED code for target site |
Q:ChainID | ID for the chain where the query site is |
T:ChainID | ID for the chain where the target site is |
Q:Res.No. | Residence number for the amino acid where the query site is |
T:Res.No. | Residence number for the amino acid where the target site is |
AlignedLength | Length of amino acid alignment |
RMSD | Root Mean Square Deviation |
AminoIdentity | Amino acid match rate |
Q:MolName | Molecular name of the query site |
T:MolName | Molecular name of the target site |
Q:EC | EC ID for the query site |
T:EC | EC ID for the target site |
Q:CATH | CATH ID for the query site |
T:CATH | CATH ID for the target site |
Q:SCOPe | SCOPe ID for the query site |
T:SCOPe | SCOPe ID for the target site |
Q:UniProt | UniProt ID for the query site |
T:UniProt | UniProt ID for the target site |
Q:UniRef50 | UniRef50 cluster ID for the query site (when it is analysed) |
T:UniRef50 | UniRef50 cluster ID for the target site (when it is analysed) |
EC_Df | Different or not between query and target site in EC ID |
CATH_Df | Different or not between query and target site in CATH ID |
SCOPe_Df | Different or not between query and target site in SCOPe ID |
ChEMBL_Assay | Assay data in ChEMBL or none |
AlignedResidues | Amino acid alignment result |
Data name | (Drug Search)Known binding site similarity |
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Description of data contents | Similarity data between known/potential binding sites in (Drug Search) query and target sites |
File | possum_binding_sites_putative_similarity.zip (5 MB) |
Data item | Description |
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Q:PocketIndex | Internal ID for query site |
T:PocketIndex | Internal ID for target site |
Q:PDB_ID | PDB ID for query site |
T:PDB_ID | PDB ID for target site |
Q:HET_Code | HED code for query site |
T:HET_Code | HED code for target site |
Q:ChainID | ID for the chain where the query site is |
T:ChainID | ID for the chain where the target site is |
Q:Res.No. | Residence number for the amino acid where the query site is |
T:Res.No. | Residence number for the amino acid where the target site is |
AlignedLength | Length of amino acid alignment |
RMSD | Root Mean Square Deviation |
AminoIdentity | Amino acid match rate |
Q:MolName | Molecular name of the query site |
T:MolName | Molecular name of the target site |
Q:EC | EC ID for the query site |
T:EC | EC ID for the target site |
Q:CATH | CATH ID for the query site |
T:CATH | CATH ID for the target site |
Q:SCOPe | SCOPe ID for the query site |
T:SCOPe | SCOPe ID for the target site |
Q:UniProt | UniProt ID for the query site |
T:UniProt | UniProt ID for the target site |
Q:UniRef50 | UniRef50 cluster ID for the query site (when it is analysed) |
T:UniRef50 | UniRef50 cluster ID for the target site (when it is analysed) |
EC_Df | Different or not between query and target site in EC ID |
CATH_Df | Different or not between query and target site in CATH ID |
SCOPe_Df | Different or not between query and target site in SCOPe ID |
ChEMBL_Assay | Assay data in ChEMBL or none |
AlignedResidues | Amino acid alignment result |
You may use this database in compliance with the terms and conditions of the license described below. The license specifies the license terms regarding the use of this database and the requirements you must follow in using this database.
The license for this database is specified in the Creative Commons Attribution-Share Alike 4.0 International.
If you use data from this database, please be sure attribute this database as follows: "PoSSuM © Tokyo Waterfront, the National Institute of Advanced Industrial Science and Technology licensed under CC Attribution-Share Alike 4.0 International".
The summary of the Creative Commons Attribution-Share Alike 4.0 International is found here.
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2-4-7 Aomi, Koto-ku, Tokyo, 135-0064 Japan
National Institute of Advanced Industrial Science and Technology (AIST)
Kentaro TOMII, PhD
E-mail: k-tomii[at]aist[dot]go[dot]jp
You can freely provide links to all contents in this database. But, contents might be changed without notice.
Date | Update contents |
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2019/03/28 | PoSSuM English archive site is opened. |
2011/11/01 | PoSSuM (http://possum.cbrc.jp/PoSSuM/index.html) is opened. |
2-4-7 Aomi, Koto-ku, Tokyo, 135-0064 Japan
National Institute of Advanced Industrial Science and Technology (AIST)
Kentaro TOMII, PhD
E-mail: k-tomii[at]aist[dot]go[dot]jp