Receptor
PDB id Resolution Class Description Source Keywords
1B58 1.8 Å NON-ENZYME: TRANSPORT OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KYK SALMONELLA TYPHIMURIUM COMPLEX (PEPTIDE TRANSPORT/PEPTIDE) PEPTIDE TRANSPORT PEPTIDE BINDING PROTEIN
Ref.: CRYSTALLOGRAPHIC AND CALORIMETRIC ANALYSIS OF PEPTIDE 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: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 TYR LYS B:1;
Valid;
none;
Kd = 260 nM
439.557 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 TYR LYS; Similar ligands found: 86
No: Ligand ECFP6 Tc MDL keys Tc
1 LYS TYR LYS 1 1
2 ALA MET TYR LYS 0.670886 0.843137
3 PHE LEU ALA TYR LYS 0.593407 0.86
4 PHE LEU SER TYR LYS 0.593407 0.796296
5 LYS LYS LYS 0.584615 0.818182
6 LYS SER LYS 0.58209 0.770833
7 LYS DPP LYS 0.575758 0.765957
8 LYS DAB LYS 0.567164 0.782609
9 LYS HIS LYS 0.564103 0.764706
10 LYS CYS LYS 0.558824 0.782609
11 LYS GLU LYS 0.557143 0.8
12 LYS ASP LYS 0.550725 0.782609
13 LYS NVA LYS 0.550725 0.765957
14 LYS GLN LYS 0.549296 0.8
15 LYS ALN LYS 0.548781 0.851064
16 LYS ASN LYS 0.542857 0.75
17 LYS NLE LYS 0.542857 0.75
18 LYS TRP LYS 0.541176 0.784314
19 LYS HPE LYS 0.538462 0.886364
20 LYS LEU LYS 0.535211 0.75
21 GLY GLY LYS LYS LYS TYR LYS LEU 0.527473 0.88
22 CYS ASP PTR ALA ASN PHE LYS 0.518072 0.77551
23 LYS MET LYS 0.513514 0.72
24 LYS ORN LYS 0.513514 0.782609
25 LYS THR LYS 0.506849 0.791667
26 LYS PHE LYS 0.506329 0.818182
27 GLU LEU ARG ARG LYS MET MET TYR MET 0.5 0.733333
28 GLU LEU ASP LYS TYR ALA SER 0.495146 0.811321
29 LYS ALA LYS 0.492958 0.8
30 LYS ARG LYS 0.487179 0.72
31 LYS GLY LYS 0.486111 0.782609
32 GLU GLN TYR LYS PHE TYR SER VAL 0.485714 0.814815
33 GLY GLY LYS LYS LYS TYR GLN LEU 0.484848 0.88
34 LYS VAL LYS 0.479452 0.765957
35 THR ASN GLU TYR LYS VAL 0.479167 0.843137
36 LYS ALC LYS 0.475 0.844444
37 GLU ASN GLN LYS GLU TYR PHE PHE 0.474747 0.88
38 ALA THR ILE GLY THR ALA MET TYR LYS 0.474138 0.754386
39 TYR GLN SER LYS LEU 0.463158 0.811321
40 ASP TYR ASN PRO TYR LEU LEU PHE LEU LYS 0.462185 0.666667
41 GLY GLY ARG LYS LYS TYR LYS LEU 0.461538 0.785714
42 GLY GLY LYS LYS ARG TYR LYS LEU 0.461538 0.785714
43 GLY GLY LYS LYS LYS TYR ARG LEU 0.461538 0.785714
44 LYS ILE LYS 0.460526 0.75
45 ASP ASP ASP ASP TYR 0.455696 0.765957
46 GLU ASN LEU TYR PHE GLN 0.455446 0.722222
47 VAL LYS VAL VAL ALA LYS LYS TYR ARG ASN 0.451923 0.77193
48 SER SER ARG LYS GLU TYR TYR ALA 0.45098 0.8
49 GLU LEU LYS ARG LYS MET ILE TYR MET 0.45 0.733333
50 LYS LYS LYS ALA 0.44 0.8
51 ALA ALA SER LEU TYR GLU LYS LYS ALA ALA 0.435185 0.830189
52 TYR GLY GLY PHE MET 0.434343 0.777778
53 TYR GLN PHE 0.430233 0.808511
54 PHE LEU GLU LYS 0.430108 0.77551
55 ASN GLY TYR GLU ASN PRO THR TYR LYS 0.426357 0.6875
56 CYS THR PHE LYS THR LYS THR ASN 0.425743 0.773585
57 SER LEU ASN TYR ILE ILE LYS VAL LYS GLU 0.425 0.785714
58 GLY TYR 0.422535 0.804348
59 TI2 0.421687 0.708333
60 GLU LEU ASN ARG LYS MET ILE TYR MET 0.418605 0.698413
61 ASP PHE GLU ASP TYR GLU PHE ASP 0.418367 0.75
62 GLU TYR GLY PRO LYS TRP ASN LYS 0.418182 0.785714
63 THR LYS ASN TYR LYS GLN PHE SER VAL 0.418182 0.767857
64 GLY LEU TYR ALA SER LYS LEU ALA 0.417476 0.777778
65 LEU ALA ILE TYR SER 0.416667 0.764706
66 SER GLN ASN TYR 0.41573 0.784314
67 LYS LYS 0.414286 0.795455
68 VAL TYR 0.413333 0.723404
69 ASP PHE GLU LYS GLU GLY TYR SER LEU 0.413223 0.77193
70 TYR SER ALA 0.4125 0.77551
71 DLY DTY DLY DLY DAL DLE ZDC 0.411215 0.741379
72 GLN LYS 0.410959 0.777778
73 ASP ALA ASP GLU TYR LEU 0.41 0.745098
74 THR ASN GLU PHE TYR PHE 0.408602 0.76
75 TYR GLY GLY PHE LEU 0.408163 0.788462
76 ASP ARG VAL TYR 0.406593 0.745098
77 GLU VAL TYR GLU SER 0.40625 0.8
78 SER GLN TYR TYR TYR ASN SER LEU 0.405941 0.701754
79 ALA LYS 0.405797 0.733333
80 TYR GLU LEU ASP GLU LYS PHE ASP ARG LEU 0.404959 0.745763
81 PHE TYR ARG TYR GLY PHE VAL ALA ASN PHE 0.40404 0.788462
82 THR PHE LYS LYS THR ASN 0.40404 0.788462
83 LYS LEU PRO ALA GLN PHE TYR ILE LEU 0.402985 0.698413
84 GLN SER TYR TPO VAL 0.401961 0.655738
85 LYS ASN LEU 0.4 0.673077
86 ASP GLU LEU GLU ILE LYS ALA TYR 0.4 0.862745
Similar Ligands (3D)
Ligand no: 1; Ligand: LYS TYR LYS; 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
APoc FAQ
Feedback