Receptor
PDB id Resolution Class Description Source Keywords
1B9J 1.8 Å NON-ENZYME: TRANSPORT OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KLK SALMONELLA TYPHIMURIUM COMPLEX (PEPTIDE TRANSPORT-PEPTIDE) PEPTIDE TRANSPORT PEPTBINDING PROTEIN
Ref.: CRYSTALLOGRAPHIC AND CALORIMETRIC ANALYSIS OF PEPTI BINDING TO OPPA PROTEIN. J.MOL.BIOL. V. 291 393 1999
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
IUM A:521;
A:522;
A:523;
A:524;
A:525;
A:526;
A:527;
A:528;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
 submit data
270.028 O2 U [O-][...
LYS LEU LYS B:1;
 Valid;
 none;
 Kd = 1100 nM
389.541 n/a O=C([...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1B7H 2 Å NON-ENZYME: TRANSPORT OLIGO-PEPTIDE BINDING PROTEIN COMPLEXED WITH LYSYL- NORLEUCYL-LYSINE SALMONELLA TYPHIMURIUM PERIPLASMIC PEPTIDE BINDING PROTEIN
Ref.: RELATING STRUCTURE TO THERMODYNAMICS: THE CRYSTAL STRUCTURES AND BINDING AFFINITY OF EIGHT OPPA-PEPTIDE COMPLEXES. PROTEIN SCI. V. 8 1432 1999
Members (31)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 232 families.
1 1B5H Kd = 0.97 uM LYS DPP LYS n/a n/a
2 1B3G Kd = 200 nM LYS ILE LYS n/a n/a
3 1B40 Kd = 53 nM LYS PHE LYS n/a n/a
4 1JET Kd = 56 nM LYS ALA LYS n/a n/a
5 1B5I Kd = 90 nM LYS ASN LYS n/a n/a
6 1B5J Kd = 37 nM LYS GLN LYS n/a n/a
7 2OLB Kd = 2900 nM LYS LYS LYS n/a n/a
8 1B6H Kd = 0.015 uM LYS NVA LYS n/a n/a
9 1B7H Kd = 0.0095 uM LYS NLE LYS n/a n/a
10 1B0H Kd = 0.2 uM LYS ALN LYS n/a n/a
11 1B46 Kd = 5200 nM LYS PRO LYS n/a n/a
12 1B4Z Kd = 5900 nM LYS ASP LYS n/a n/a
13 1B3L Kd = 1300 nM LYS GLY LYS n/a n/a
14 1QKA Kd = 1200 nM LYS ARG LYS n/a n/a
15 1B3F Kd = 130 nM LYS HIS LYS n/a n/a
16 1B52 Kd = 76 nM LYS THR LYS n/a n/a
17 1OLA - VAL LYS PRO GLY n/a n/a
18 1B2H Kd = 29 uM LYS ORN LYS n/a n/a
19 1B4H Kd = 3.44 uM LYS DAB LYS n/a n/a
20 1B9J Kd = 1100 nM LYS LEU LYS n/a n/a
21 1OLC Kd = 2.7 uM LYS LYS LYS ALA n/a n/a
22 1B3H Kd = 0.62 uM LYS ALC LYS n/a n/a
23 1JEU Kd = 150 nM LYS GLU LYS n/a n/a
24 2RKM Ki = 125 uM LYS LYS n/a n/a
25 1B51 Kd = 43 nM LYS SER LYS n/a n/a
26 1B58 Kd = 260 nM LYS TYR LYS n/a n/a
27 1JEV Kd = 130 nM LYS TRP LYS n/a n/a
28 1QKB Kd = 45 nM LYS VAL LYS n/a n/a
29 1B1H Kd = 0.093 uM LYS HPE LYS n/a n/a
30 1B32 Kd = 79 nM LYS MET LYS n/a n/a
31 1B05 Kd = 75 nM LYS CYS LYS n/a n/a
70% Homology Family (40)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 197 families.
1 1B5H Kd = 0.97 uM LYS DPP LYS n/a n/a
2 1B3G Kd = 200 nM LYS ILE LYS n/a n/a
3 1B40 Kd = 53 nM LYS PHE LYS n/a n/a
4 1JET Kd = 56 nM LYS ALA LYS n/a n/a
5 1B5I Kd = 90 nM LYS ASN LYS n/a n/a
6 1B5J Kd = 37 nM LYS GLN LYS n/a n/a
7 2OLB Kd = 2900 nM LYS LYS LYS n/a n/a
8 1B6H Kd = 0.015 uM LYS NVA LYS n/a n/a
9 1B7H Kd = 0.0095 uM LYS NLE LYS n/a n/a
10 1B0H Kd = 0.2 uM LYS ALN LYS n/a n/a
11 1B46 Kd = 5200 nM LYS PRO LYS n/a n/a
12 1B4Z Kd = 5900 nM LYS ASP LYS n/a n/a
13 1B3L Kd = 1300 nM LYS GLY LYS n/a n/a
14 1QKA Kd = 1200 nM LYS ARG LYS n/a n/a
15 1B3F Kd = 130 nM LYS HIS LYS n/a n/a
16 1B52 Kd = 76 nM LYS THR LYS n/a n/a
17 1OLA - VAL LYS PRO GLY n/a n/a
18 1B2H Kd = 29 uM LYS ORN LYS n/a n/a
19 1B4H Kd = 3.44 uM LYS DAB LYS n/a n/a
20 1B9J Kd = 1100 nM LYS LEU LYS n/a n/a
21 1OLC Kd = 2.7 uM LYS LYS LYS ALA n/a n/a
22 1B3H Kd = 0.62 uM LYS ALC LYS n/a n/a
23 1JEU Kd = 150 nM LYS GLU LYS n/a n/a
24 2RKM Ki = 125 uM LYS LYS n/a n/a
25 1B51 Kd = 43 nM LYS SER LYS n/a n/a
26 1B58 Kd = 260 nM LYS TYR LYS n/a n/a
27 1JEV Kd = 130 nM LYS TRP LYS n/a n/a
28 1QKB Kd = 45 nM LYS VAL LYS n/a n/a
29 1B1H Kd = 0.093 uM LYS HPE LYS n/a n/a
30 1B32 Kd = 79 nM LYS MET LYS n/a n/a
31 1B05 Kd = 75 nM LYS CYS LYS n/a n/a
32 6DQT - LEU GLY GLY n/a n/a
33 6DTG - TYR LEU GLY ALA ASN GLY n/a n/a
34 6DQR - MET GLY GLY n/a n/a
35 6DTH - ARG PRO PRO GLY PHE n/a n/a
36 6DQQ - ALA ALA ALA ALA n/a n/a
37 6DQU - GLY ILE ILE ASN THR LEU n/a n/a
38 6DTF - LYS LYS LYS n/a n/a
39 3TCG Kd = 1.36 uM LYS GLY GLU n/a n/a
40 2Z23 - LYS LYS LYS n/a n/a
50% Homology Family (41)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 165 families.
1 3O9P Kd = 0.3 uM MHI C15 H26 N4 O8 C[C@@H](C(....
2 1B5H Kd = 0.97 uM LYS DPP LYS n/a n/a
3 1B3G Kd = 200 nM LYS ILE LYS n/a n/a
4 1B40 Kd = 53 nM LYS PHE LYS n/a n/a
5 1JET Kd = 56 nM LYS ALA LYS n/a n/a
6 1B5I Kd = 90 nM LYS ASN LYS n/a n/a
7 1B5J Kd = 37 nM LYS GLN LYS n/a n/a
8 2OLB Kd = 2900 nM LYS LYS LYS n/a n/a
9 1B6H Kd = 0.015 uM LYS NVA LYS n/a n/a
10 1B7H Kd = 0.0095 uM LYS NLE LYS n/a n/a
11 1B0H Kd = 0.2 uM LYS ALN LYS n/a n/a
12 1B46 Kd = 5200 nM LYS PRO LYS n/a n/a
13 1B4Z Kd = 5900 nM LYS ASP LYS n/a n/a
14 1B3L Kd = 1300 nM LYS GLY LYS n/a n/a
15 1QKA Kd = 1200 nM LYS ARG LYS n/a n/a
16 1B3F Kd = 130 nM LYS HIS LYS n/a n/a
17 1B52 Kd = 76 nM LYS THR LYS n/a n/a
18 1OLA - VAL LYS PRO GLY n/a n/a
19 1B2H Kd = 29 uM LYS ORN LYS n/a n/a
20 1B4H Kd = 3.44 uM LYS DAB LYS n/a n/a
21 1B9J Kd = 1100 nM LYS LEU LYS n/a n/a
22 1OLC Kd = 2.7 uM LYS LYS LYS ALA n/a n/a
23 1B3H Kd = 0.62 uM LYS ALC LYS n/a n/a
24 1JEU Kd = 150 nM LYS GLU LYS n/a n/a
25 2RKM Ki = 125 uM LYS LYS n/a n/a
26 1B51 Kd = 43 nM LYS SER LYS n/a n/a
27 1B58 Kd = 260 nM LYS TYR LYS n/a n/a
28 1JEV Kd = 130 nM LYS TRP LYS n/a n/a
29 1QKB Kd = 45 nM LYS VAL LYS n/a n/a
30 1B1H Kd = 0.093 uM LYS HPE LYS n/a n/a
31 1B32 Kd = 79 nM LYS MET LYS n/a n/a
32 1B05 Kd = 75 nM LYS CYS LYS n/a n/a
33 6DQT - LEU GLY GLY n/a n/a
34 6DTG - TYR LEU GLY ALA ASN GLY n/a n/a
35 6DQR - MET GLY GLY n/a n/a
36 6DTH - ARG PRO PRO GLY PHE n/a n/a
37 6DQQ - ALA ALA ALA ALA n/a n/a
38 6DQU - GLY ILE ILE ASN THR LEU n/a n/a
39 6DTF - LYS LYS LYS n/a n/a
40 3TCG Kd = 1.36 uM LYS GLY GLU n/a n/a
41 2Z23 - LYS LYS LYS n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: LYS LEU LYS; Similar ligands found: 73
No: Ligand ECFP6 Tc MDL keys Tc
1 LYS LEU LYS 1 1
2 LYS LYS LYS 0.735849 0.9
3 LYS DPP LYS 0.690909 0.837209
4 LYS NVA LYS 0.684211 0.926829
5 LYS DAB LYS 0.678571 0.857143
6 LYS NLE LYS 0.672414 0.904762
7 LYS SER LYS 0.666667 0.8
8 LYS ALA LYS 0.666667 0.925
9 LYS CYS LYS 0.666667 0.857143
10 LYS ASP LYS 0.655172 0.857143
11 LYS ASN LYS 0.644068 0.818182
12 LYS GLU LYS 0.633333 0.878049
13 LYS MET LYS 0.629032 0.863636
14 LYS GLN LYS 0.622951 0.878049
15 LYS VAL LYS 0.616667 0.975
16 LYS LYS LYS ALA 0.616667 0.925
17 LYS THR LYS LEU LEU 0.614286 0.888889
18 LYS ORN LYS 0.603175 0.857143
19 LYS ASN LEU 0.603175 0.886364
20 LYS THR LYS 0.596774 0.822222
21 LYS ILE LYS 0.587302 0.951219
22 LYS ARG LYS 0.567164 0.782609
23 PHE LEU GLU LYS 0.564103 0.886364
24 LEU LYS 0.559322 0.925
25 LYS ALC LYS 0.550725 0.837209
26 LYS GLY LYS 0.548387 0.857143
27 LYS HIS LYS 0.541667 0.72
28 ALA LYS 0.535714 0.85
29 LYS HPE LYS 0.535211 0.837209
30 LYS TYR LYS 0.535211 0.75
31 LYS LEU LEU PHE 0.527027 0.860465
32 LEU LEU LEU 0.517241 0.8
33 LEU LYS THR LYS LEU LEU 0.513158 0.888889
34 VAL LYS 0.508475 0.9
35 SER LEU LEU LYS LYS LEU LEU LEU ALA 0.507042 0.866667
36 SER LEU LEU LYS LYS LEU LEU ASP 0.506667 0.851064
37 PRO LEU SER LYS 0.506494 0.784314
38 LYS LEU VAL VAL VAL ALA VAL GLY VAL 0.506024 0.951219
39 LYS LEU VAL GLN LEU LEU THR THR THR 0.5 0.829787
40 PHE LEU ALA TYR LYS 0.488889 0.78
41 PHE LEU SER TYR LYS 0.488889 0.722222
42 LYS LEU VAL VAL GLY ALA VAL GLY VAL 0.488095 0.928571
43 LYS LEU VAL VAL VAL GLY ALA VAL GLY VAL 0.488095 0.928571
44 LYS ALN LYS 0.487179 0.765957
45 ALA ARG LYS LEU ASP 0.475 0.833333
46 LYS ILE LEU GLY PRV VAL PHE PRQ VAL 0.472222 0.860465
47 LYS LYS 0.466667 0.875
48 DAS DLY 0.466667 0.733333
49 LYS TRP LYS 0.463415 0.705882
50 GLN LYS 0.460317 0.853659
51 HIS GLU GLU LEU ALA LYS LEU 0.455696 0.951219
52 ALA GLU LYS ASP GLU LEU 0.454545 0.952381
53 LYS CYS VAL VAL MET 0.448718 0.866667
54 SER LEU LYS LEU MET THR THR VAL 0.448276 0.764706
55 LYS ALA THR LYS MLY 0.445946 0.769231
56 ALA LEU ALA LEU 0.4375 0.8
57 GLY THR LEU SER ASN ARG ALA SER LYS LEU 0.435897 0.866667
58 ASN LEU LEU GLN LYS LYS 0.433735 0.863636
59 API DAL C0O 0.424242 0.8
60 LYS LEU VAL ALA LEU GLY ILE ASN ALA VAL 0.42 0.847826
61 CYS ASP PTR ALA ASN PHE LYS 0.419753 0.765957
62 LYS SER LEU LEU GLN GLN LEU LEU THR GLU 0.416667 0.833333
63 LYS VAL LEU PHE LEU ASP GLY 0.416667 0.847826
64 GLU LEU ASP LYS TYR ALA SER 0.415842 0.735849
65 ALA LYS ALA ALA 0.414286 0.875
66 GLN LEU ALA 0.411765 0.780488
67 ARG ASP ARG ALA ALA LYS LEU 0.411765 0.869565
68 GLU ASP LEU 0.411765 0.809524
69 GLU LEU ARG ARG LYS MET MET TYR MET 0.411215 0.666667
70 LEU THR THR LYS LEU THR ASN THR ASN ILE 0.406593 0.78
71 LYS LEU THR PRO LEU CYS VAL THR LEU 0.40566 0.677966
72 LYS ALA SER VAL GLY 0.405063 0.826087
73 SER LEU LEU LYS LYS LEU LEU LEU ALA PRO 0.404494 0.672414
Similar Ligands (3D)
Ligand no: 1; Ligand: LYS LEU LYS; Similar ligands found: 2
No: Ligand Similarity coefficient
1 LYS PRO LYS 0.9170
2 LYS PHE LYS 0.8790
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1B7H; Ligand: LYS NLE LYS; 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: 1b7h.bio1) has 34 residues
No: Leader PDB Ligand Sequence Similarity
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