Receptor
PDB id Resolution Class Description Source Keywords
1OLC 2.1 Å NON-ENZYME: TRANSPORT OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH LYS-LYS- LYS-ALA SALMONELLA TYPHIMURIUM PERIPLASMIC COMPLEX (BINDING PROTEIN/PEPTIDE) COMPLEX
Ref.: THE CRYSTAL STRUCTURES OF THE OLIGOPEPTIDE-BINDING PROTEIN OPPA COMPLEXED WITH TRIPEPTIDE AND TETRAPEPTIDE LIGANDS. STRUCTURE V. 3 1395 1995
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
IUM A:518;
A:519;
A:520;
A:521;
A:522;
A:523;
A:524;
A:525;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
 submit data
270.028 O2 U [O-][...
LYS LYS LYS ALA B:1;
 Valid;
 none;
 Kd = 2.7 uM
476.643 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 LYS LYS ALA; Similar ligands found: 61
No: Ligand ECFP6 Tc MDL keys Tc
1 LYS LYS LYS ALA 1 1
2 LYS LYS LYS 0.716981 0.972973
3 LYS NLE LYS 0.655172 0.925
4 LYS NVA LYS 0.637931 0.948718
5 LYS DAB LYS 0.631579 0.923077
6 LYS LEU LYS 0.616667 0.925
7 LYS ALA LYS 0.59322 1
8 LYS GLU LYS 0.590164 0.947368
9 LYS MET LYS 0.587302 0.880952
10 LYS GLN LYS 0.580645 0.947368
11 LYS ORN LYS 0.5625 0.923077
12 LYS DPP LYS 0.559322 0.9
13 LYS ARG LYS 0.552239 0.837209
14 LYS SER LYS 0.540984 0.857143
15 LYS CYS LYS 0.540984 0.923077
16 LYS THR LYS LEU LEU 0.534247 0.822222
17 LYS ASP LYS 0.532258 0.923077
18 LYS ASN LYS 0.52381 0.878049
19 LYS VAL LYS 0.52381 0.948718
20 LYS THR LYS 0.507692 0.880952
21 ALA LYS ALA ALA 0.507692 0.894737
22 LYS HPE LYS 0.5 0.9
23 ARG ARG ALA ALA 0.5 0.777778
24 LYS ILE LYS 0.5 0.925
25 LYS ASN LEU 0.492537 0.818182
26 LYS GLY LYS 0.484375 0.923077
27 SER LEU LEU LYS LYS LEU LEU ASP 0.473684 0.787234
28 SER LEU LEU LYS LYS LEU LEU LEU ALA 0.472222 0.8
29 LYS ALC LYS 0.472222 0.9
30 LEU LYS THR LYS LEU LEU 0.461538 0.822222
31 LYS ALA SER VAL GLY 0.447368 0.8
32 ALA LYS GLU LYS SER ASP 0.447368 0.840909
33 ALA LYS ALA ILE ALA 0.441558 0.85
34 ALA GLU LYS ASP GLU LEU 0.441558 0.880952
35 GLY THR LEU SER ASN ARG ALA SER LYS LEU 0.441558 0.8
36 ALA LYS 0.440678 0.918919
37 LYS TYR LYS 0.44 0.8
38 PRO LYS THR PRO LYS LYS ALA LYS LYS LEU 0.434783 0.875
39 ARG GLU ALA ALA 0.434211 0.777778
40 LYS HIS LYS 0.428571 0.765957
41 ALA ARG THR LYS GLN THR ALA ARG LYS SER 0.428571 0.795455
42 ALA LYS ALA SER GLN ALA ALA 0.426829 0.795455
43 ALA ARG LYS LEU ASP 0.426829 0.770833
44 DAS DLY 0.42623 0.785714
45 LYS LEU VAL GLN LEU LEU THR THR THR 0.420455 0.765957
46 VAL LYS 0.419355 0.871795
47 C0O DAL DAL 0.419355 0.842105
48 LYS CYS VAL VAL MET 0.417722 0.8
49 LYS LEU LEU PHE 0.417722 0.790698
50 SER PRO LYS ARG ILE ALA 0.414141 0.606557
51 LYS ALA THR LYS MLY 0.413333 0.711538
52 ALA ARG ALA ALA ALA ALA ALA ALA ALA 0.410959 0.795455
53 LYS LEU VAL VAL VAL ALA VAL GLY VAL 0.409091 0.878049
54 HIS GLU GLU LEU ALA LYS LEU 0.407407 0.878049
55 PHE LEU GLU LYS 0.406977 0.818182
56 ASN LEU LEU GLN LYS LYS 0.404762 0.795455
57 SER LEU LYS LEU MET THR THR VAL 0.404494 0.705882
58 LYS ALN LYS 0.402439 0.818182
59 GLY ALA ASP GLY VAL GLY LYS SER ALA 0.4 0.75
60 LEU LYS 0.4 0.85
61 LYS TRP LYS 0.4 0.75
Similar Ligands (3D)
Ligand no: 1; Ligand: LYS LYS LYS ALA; 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 : 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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