Receptor
PDB id Resolution Class Description Source Keywords
5JXF 2.1 Å EC: 3.4.14.- CRYSTAL STRUCTURE OF FLAVOBACTERIUM PSYCHROPHILUM DPP11 IN C WITH DIPEPTIDE ARG-ASP FLAVOBACTERIUM PSYCHROPHILUM 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;
Atoms found LESS than expected: % Diff = 0.05;
Atoms found LESS than expected: % Diff = 0.05;
submit data
289.292 n/a O=C([...
CL D:802;
C:801;
D:801;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
35.453 Cl [Cl-]
NA D:803;
Part of Protein;
none;
submit data
22.99 Na [Na+]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5JXF 2.1 Å EC: 3.4.14.- CRYSTAL STRUCTURE OF FLAVOBACTERIUM PSYCHROPHILUM DPP11 IN C WITH DIPEPTIDE ARG-ASP FLAVOBACTERIUM PSYCHROPHILUM PEPTIDASE BACTERIAL ENZYME DIPEPTIDE HYDROLASE
Ref.: BACTERIAL PROTEASE USES DISTINCT THERMODYNAMIC SIGN FOR SUBSTRATE RECOGNITION. SCI REP V. 7 2848 2017
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5JXF - ARG ASP n/a n/a
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5JXF - ARG ASP n/a n/a
50% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5JWG - ARG ASP n/a n/a
2 5JWI - ARG GLU n/a n/a
3 5JXF - ARG ASP n/a n/a
4 3WON Ki = 0.41 mM VAL TYR n/a n/a
5 3WOP - VAL TYR ILE HIS PRO PHE n/a n/a
6 3WOL Ki = 0.41 mM VAL TYR n/a n/a
7 3WOQ - VAL TYR ILE HIS PRO PHE n/a n/a
8 3WOM Ki = 0.41 mM VAL TYR n/a n/a
9 4Y06 - LEU GLU n/a n/a
10 3WOO - VAL TYR ILE HIS PRO PHE n/a n/a
11 3WOR - ASP ARG VAL TYR ILE HIS PRO PHE n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ARG ASP; Similar ligands found: 31
No: Ligand ECFP6 Tc MDL keys Tc
1 ARG ASP 1 1
2 ARG GLU 0.692308 0.97561
3 ALA ARG LYS LEU ASP 0.636364 0.854167
4 ARG ARG ARG ARG ARG ARG ARG ARG ARG ARG 0.625 0.886364
5 ARG ASP ALA ALA 0.616667 0.953488
6 ARG SER ARG 0.603448 0.851064
7 ARG VAL 0.592593 0.863636
8 LYS ARG LYS 0.532258 0.886364
9 ARG ARG ALA ALA 0.53125 0.866667
10 ARG GLU ALA ALA 0.522388 0.909091
11 LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG 0.515625 0.866667
12 ALA ARG 0.509091 0.904762
13 ARG LEU GLY GLU SER 0.507937 0.787234
14 ARG ARG ARG ARG ARG ARG ARG ARG 0.5 0.840909
15 ARG GLY ASP 0.5 0.953488
16 LYS ARG HIS ARG MLY VAL LEU ARG ASP ASN 0.47619 0.611111
17 ARG ALA ARG 0.46875 0.818182
18 ARG ASP ARG ALA ALA LYS LEU 0.466667 0.8125
19 ARG ARG GLY CYS NH2 0.457143 0.844444
20 MET ALA ARG 0.455882 0.795918
21 ARG GLY THR 0.454545 0.851064
22 ARG ILE ALA ALA ALA 0.447761 0.782609
23 ARG ARG ARG GLU THR GLN VAL 0.443038 0.836735
24 LYS ASP LYS 0.442623 0.75
25 ARG ARG GLY LEU NH2 0.438356 0.791667
26 ARG ARG GLY ILE NH2 0.438356 0.791667
27 ARG ARG GLY MET NH2 0.426667 0.745098
28 THR ALA ARG M3L SER THR 0.426667 0.622951
29 LYS LYS 0.418182 0.674419
30 LYS ARG LYS ARG LYS ARG LYS ARG 0.416667 0.822222
31 ALA LYS GLU LYS SER ASP 0.405405 0.693878
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5JXF; Ligand: ARG ASP; Similar sites found: 26
This union binding pocket(no: 1) in the query (biounit: 5jxf.bio4) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1IA7 BGC BGC 0.01808 0.40648 2.26757
2 5NB7 8NQ 0.01504 0.40082 2.6087
3 4D8N 0HM 0.005889 0.41638 2.69058
4 1IAU ACE ILE GLU PRO ASJ 0.006145 0.40126 3.0837
5 1SL3 170 0.008087 0.41346 3.83275
6 1SQA UI1 0.005661 0.43487 4.08163
7 4SGA ACE PRO ALA PRO PHE 0.0002756 0.46816 4.41989
8 5A8Y VBM 0.001108 0.44784 4.58716
9 2BDG PBZ 0.002246 0.40371 4.93274
10 2CDO GAL AAL GAL AAL GAL AAL 0.0101 0.43275 5.625
11 5WB6 9ZM 0.01204 0.41132 5.7377
12 1HPG BOC ALA ALA PRO GLU 0.0000294 0.51857 5.88235
13 1ELE 0QN 0.000407 0.40878 7.5
14 5TP0 BRN 0.01202 0.41292 8.03571
15 2H9E DTY ILE ARG LEU LPD 0.003389 0.43114 8.33333
16 2EC9 24X 0.0007063 0.46661 10.8333
17 1YGC 905 0.004763 0.42065 11.1111
18 3MMG GLU THR VAL ARG PHE GLN SER ASP 0.002971 0.44032 11.2033
19 4BTI 7R9 0.003604 0.42625 11.4583
20 5TZ9 7SD 0.0007242 0.45409 11.7871
21 5L2Z 70C 0.0057 0.4359 12.069
22 3UTU 1TS 0.003251 0.44661 16.6667
23 3VXE DPN PRO ARG 0.004049 0.42391 16.6667
24 1TMT DPN PRO ARG 0.005334 0.41648 16.6667
25 2ANM CDO 0.009613 0.41309 16.6667
26 2P8O BVA 0.005073 0.41548 38.4615
Feedback