Receptor
PDB id Resolution Class Description Source Keywords
5JWG 2.2 Å EC: 3.4.14.- CRYSTAL STRUCTURE OF PORPHYROMONAS ENDODONTALIS DPP11 IN COM DIPEPTIDE ARG-ASP PORPHYROMONAS ENDODONTALIS PEPTIDASE BACTERIAL ENZYME DIPEPTIDE HYDROLASE
Ref.: BACTERIAL PROTEASE USES DISTINCT THERMODYNAMIC SIGN FOR SUBSTRATE RECOGNITION. SCI REP V. 7 2848 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ARG ASP B:801;
A:801;
 Valid;
Valid;
 none;
none;
 submit data
273.293 n/a O=C(N...
NA A:804;
 Part of Protein;
 none;
 submit data
22.99 Na [Na+]
EDO A:803;
 Invalid;
 none;
 submit data
62.068 C2 H6 O2 C(CO)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5JWI 2.1 Å EC: 3.4.14.- CRYSTAL STRUCTURE OF PORPHYROMONAS ENDODONTALIS DPP11 IN COM DIPEPTIDE ARG-GLU PORPHYROMONAS ENDODONTALIS PEPTIDASE BACTERIAL ENZYME DIPEPTIDE HYDROLASE
Ref.: BACTERIAL PROTEASE USES DISTINCT THERMODYNAMIC SIGN FOR SUBSTRATE RECOGNITION. SCI REP V. 7 2848 2017
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 5JWG - ARG ASP n/a n/a
2 5JWI - ARG GLU n/a n/a
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5JWG - ARG ASP n/a n/a
2 5JWI - ARG GLU n/a n/a
3 6JTB - CIT C6 H8 O7 C(C(=O)O)C....
4 6JTC Ki = 8.45 uM C8O C9 H11 N3 O4 c1cc(c(cc1....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5JWG - ARG ASP n/a n/a
2 6JTC Ki = 8.45 uM C8O C9 H11 N3 O4 c1cc(c(cc1....
3 3WON Ki = 0.41 mM VAL TYR n/a n/a
4 3WOP - VAL TYR ILE HIS PRO PHE n/a n/a
5 3WOL Ki = 0.41 mM VAL TYR n/a n/a
6 3WOQ - VAL TYR ILE HIS PRO PHE n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: ARG ASP; Similar ligands found: 21
No: Ligand ECFP6 Tc MDL keys Tc
1 ARG ASP 1 1
2 BEZ NLE LYS ARG OAR 0.606557 0.837209
3 ARG VAL 0.571429 0.866667
4 ARG ARG ARG ARG ARG ARG ARG ARG 0.553846 0.863636
5 ARG ARG ARG ARG ARG ARG ARG ARG ARG ARG 0.553846 0.863636
6 ARG GLU 0.55 0.97619
7 AAR 0.510204 0.785714
8 ARG GLY ASP 0.507463 0.976744
9 THR ALA ARG M3L SER THR 0.486486 0.639344
10 LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG 0.486486 0.844444
11 ARG 0.461538 0.744186
12 DAR 0.461538 0.744186
13 LYS ARG HIS ARG MLY VAL LEU ARG ASP ASN 0.454545 0.618182
14 ALA ARG VAL SER MET ARG ARG MET SEP ASN 0.449438 0.672131
15 LYS ARG LYS ARG LYS ARG LYS ARG 0.433962 0.666667
16 ARG ASP ALA ALA 0.416667 0.976744
17 GLY ALA ARG 0.411765 0.863636
18 ACE THR ARG GLU 0.411765 0.833333
19 MET ARG THR GLY ASN ALA XSN 0.405797 0.75
20 ALA ARG 0.403226 0.906977
21 ARG ALA ARG 0.4 0.840909
Similar Ligands (3D)
Ligand no: 1; Ligand: ARG ASP; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5JWI; Ligand: ARG GLU; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5jwi.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5JWI; Ligand: ARG GLU; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5jwi.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
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