Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ARG GLU A:801;
B:803;
Valid;
Valid;
none;
none;
submit data
303.319 n/a O=C([...
CL B:801;
B:802;
Invalid;
Invalid;
none;
none;
submit data
35.453 Cl [Cl-]
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 3 families.
1 5JWG - ARG ASP n/a n/a
2 5JWI - ARG GLU n/a n/a
70% Homology Family (2)
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
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 GLU; Similar ligands found: 36
No: Ligand ECFP6 Tc MDL keys Tc
1 ARG GLU 1 1
2 ARG ASP 0.692308 0.97561
3 ARG ARG ARG ARG ARG ARG ARG ARG ARG ARG 0.631579 0.906977
4 ARG GLU ALA ALA 0.625 0.930233
5 ARG SER ARG 0.610169 0.829787
6 ARG VAL 0.571429 0.883721
7 LYS ARG LYS 0.539683 0.906977
8 LEU GLU 0.537037 0.613636
9 ARG ARG ARG GLU THR GLN VAL 0.526316 0.816327
10 LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG 0.523077 0.886364
11 ARG ASP ALA ALA 0.523077 0.930233
12 ALA ARG 0.517857 0.926829
13 ARG ARG ALA ALA 0.515152 0.886364
14 ALA DGL 0.5 0.658537
15 ARG LEU GLY GLU SER 0.492308 0.804348
16 ALA ARG LYS LEU ASP 0.486486 0.833333
17 ARG ARG ARG ARG ARG ARG ARG ARG 0.484848 0.860465
18 LYS GLU LYS 0.483871 0.744186
19 MET ALA ARG 0.463768 0.8125
20 LYS ARG HIS ARG MLY VAL LEU ARG ASP ASN 0.461538 0.622642
21 LYS LYS 0.454545 0.690476
22 ARG ASP ARG ALA ALA LYS LEU 0.454545 0.829787
23 ARG ALA ARG 0.454545 0.837209
24 ARG ARG GLY ILE NH2 0.445946 0.808511
25 ARG ARG GLY CYS NH2 0.444444 0.863636
26 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.444444 0.769231
27 ARG GLY ASP 0.441176 0.930233
28 ARG GLY THR 0.441176 0.869565
29 ARG ILE ALA ALA ALA 0.434783 0.8
30 GLU ALY ARG 0.434211 0.869565
31 THR ALA ARG M3L SER THR 0.434211 0.633333
32 ARG ARG GLY LEU NH2 0.426667 0.808511
33 GLN LYS 0.416667 0.804878
34 ARG ARG GLY MET NH2 0.415584 0.76
35 LYS GLN LYS 0.409091 0.767442
36 LYS ARG LYS ARG LYS ARG LYS ARG 0.405405 0.840909
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5JWI; Ligand: ARG GLU; Similar sites found: 47
This union binding pocket(no: 1) in the query (biounit: 5jwi.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1ELE 0QN 0.00006567 0.44925 2.27596
2 1Q8A HCS 0.02467 0.40051 2.4735
3 1UTJ ABN 0.007913 0.40488 2.47934
4 5TZ9 7SD 0.001078 0.43711 3.04183
5 2OUA AES 0.00002676 0.41046 3.19149
6 4YLU R30 0.001237 0.4345 3.26797
7 4YOI 4F4 0.00183 0.42921 3.59477
8 1SQA UI1 0.0009965 0.46246 4.08163
9 5A8Y VBM 0.0004508 0.4559 4.12844
10 2CDO GAL AAL GAL AAL GAL AAL 0.01538 0.42099 4.375
11 3N7O N7O 0.0001663 0.42319 4.42478
12 1HPG BOC ALA ALA PRO GLU 0.000001 0.59284 4.81283
13 5WB6 9ZM 0.002582 0.43489 4.91803
14 4O97 NTX 0.003789 0.42578 4.97925
15 4NWK 2R8 0.004131 0.4192 5.02283
16 1T32 OHH 0.001064 0.43256 5.35714
17 2XCF BBQ 0.001403 0.43211 5.55556
18 2H9E DTY ILE ARG LEU LPD 0.008452 0.40529 6.00858
19 4ISS TAR 0.01679 0.40458 6.21118
20 1YF4 CYS TYR PHE GLN ASN CYS PRO ARG GLY NH2 0.001894 0.44402 6.27803
21 1IAU ACE ILE GLU PRO ASJ 0.001332 0.43744 6.60793
22 1SL3 170 0.008169 0.40595 6.62021
23 5FAH 5VT 0.0009307 0.44419 6.69643
24 1XUJ BOZ 0.0007969 0.48455 7.17489
25 5NB7 8NQ 0.001672 0.43676 7.3913
26 1PQ7 ARG 0.001306 0.42865 7.58929
27 3MMG GLU THR VAL ARG PHE GLN SER ASP 0.0001404 0.49247 8.29876
28 1N62 MCN 0.01969 0.40501 8.43373
29 4SGA ACE PRO ALA PRO PHE 0.00006007 0.47669 8.83978
30 2MBR EPU 0.02472 0.41426 9.41177
31 2MBR FAD 0.0255 0.41426 9.41177
32 2P8O BVA 0.001359 0.43272 10.3093
33 1T3Q MCN 0.02376 0.40011 10.7143
34 3KEE 30B 0.002657 0.42407 11.0526
35 1YGC 905 0.005536 0.40998 11.1111
36 3P8N L4T 0.004665 0.41852 11.828
37 5L2Z 70C 0.001279 0.45869 12.069
38 3SUD SUE 0.002206 0.42955 14.2857
39 4BTI 7R9 0.005615 0.4097 14.5833
40 2EC9 24X 0.0001669 0.48539 17.3333
41 4D8N 0HM 0.001626 0.43349 17.9372
42 3UTU 1TS 0.001556 0.45343 19.4444
43 3VXE DPN PRO ARG 0.0007766 0.44766 19.4444
44 1TMT DPN PRO ARG 0.0008893 0.44296 19.4444
45 2ANM CDO 0.002419 0.43301 19.4444
46 3BPX SAL 0.02468 0.40128 22.2973
47 1EB1 ZAL PRO MMO 0.001911 0.44526 25.9259
Pocket No.: 2; Query (leader) PDB : 5JWI; Ligand: ARG GLU; Similar sites found: 2
This union binding pocket(no: 2) in the query (biounit: 5jwi.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3W8X FAD 0.02206 0.41307 2.35043
2 2WOX NDP 0.02483 0.40124 3.88548
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