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 209 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 175 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 = 0.00000145 M 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 149 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 = 0.00000145 M LYS GLY GLU n/a n/a
41 2Z23 - LYS LYS LYS n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: LYS TYR LYS; Similar ligands found: 87
No: Ligand ECFP6 Tc MDL keys Tc
1 LYS TYR LYS 1 1
2 PHE LEU SER TYR LYS 0.593407 0.796296
3 PHE LEU ALA TYR LYS 0.593407 0.86
4 LYS LYS 0.590164 0.795455
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 NVA LYS 0.550725 0.765957
13 LYS ASP LYS 0.550725 0.782609
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 THR ASN GLU TYR LYS VAL 0.521277 0.843137
23 THR TYR LYS PHE PHE GLU GLN 0.520833 0.862745
24 GLU ASN PRO THR TYR LYS PHE PHE GLU GLN 0.520833 0.862745
25 GLU ASN GLN LYS GLU TYR PHE PHE 0.515464 0.88
26 LYS MET LYS 0.513514 0.72
27 LYS ORN LYS 0.513514 0.782609
28 LYS THR LYS 0.506849 0.791667
29 LYS PHE LYS 0.506329 0.818182
30 THR LYS ASN TYR LYS GLN THR SER VAL 0.504673 0.814815
31 GLU LEU ARG ARG LYS MET MET TYR MET 0.5 0.733333
32 GLU GLU GLN GLU GLU TYR 0.5 0.866667
33 GLU LEU ASP LYS TYR ALA SER 0.495146 0.811321
34 LYS ALA LYS 0.492958 0.8
35 GLN LYS 0.492754 0.777778
36 LYS ARG LYS 0.487179 0.72
37 LYS GLY LYS 0.486111 0.782609
38 GLU GLN TYR LYS PHE TYR SER VAL 0.485714 0.814815
39 GLY GLY LYS LYS LYS TYR GLN LEU 0.484848 0.88
40 SER SER ARG LYS GLU TYR TYR ALA 0.48 0.8
41 LYS VAL LYS 0.479452 0.765957
42 ALA LYS 0.476923 0.755556
43 LYS ALC LYS 0.475 0.844444
44 GLY TYR 0.463768 0.804348
45 TYR GLN SER LYS LEU 0.463158 0.811321
46 THR ASN GLU PHE TYR PHE 0.461538 0.76
47 GLY GLY LYS LYS LYS TYR ARG LEU 0.461538 0.785714
48 LYS ALA VAL TYR ASN PHE ALA THR MET 0.461538 0.716667
49 GLY GLY ARG LYS LYS TYR LYS LEU 0.461538 0.785714
50 VAL LYS VAL VAL ALA LYS LYS TYR ARG ASN 0.461538 0.77193
51 GLY GLY LYS LYS ARG TYR LYS LEU 0.461538 0.785714
52 LYS ILE LYS 0.460526 0.75
53 VAL TYR 0.458333 0.723404
54 GLU ASN LEU TYR PHE GLN 0.455446 0.722222
55 LYS ALA LEU TYR ASN PHE ALA THR MET 0.453782 0.716667
56 LYS ALA VAL TYR ASN LEU ALA THR MET 0.452991 0.741379
57 GLU LEU LYS ARG LYS MET ILE TYR MET 0.45 0.733333
58 THR LYS ASN TYR LYS GLN PHE SER VAL 0.444444 0.767857
59 LYS LYS LYS ALA 0.44 0.8
60 THR ASN GLU TYR TYR VAL 0.43956 0.716981
61 ALA ALA SER LEU TYR GLU LYS LYS ALA ALA 0.435185 0.830189
62 TYR GLY GLY PHE MET 0.434343 0.777778
63 TYR GLN PHE 0.430233 0.808511
64 SER ASP TYR GLN ARG LEU 0.427184 0.75
65 ASN GLY TYR GLU ASN PRO THR TYR LYS 0.426357 0.6875
66 CYS THR PHE LYS THR LYS THR ASN 0.425743 0.773585
67 TI2 0.421687 0.708333
68 VAL LYS 0.42029 0.723404
69 ASP ASN ARG LEU GLY LEU VAL TYR GLN PHE 0.42 0.745098
70 GLU LEU ASN ARG LYS MET ILE TYR MET 0.418605 0.698413
71 ASP PHE GLU ASP TYR GLU PHE ASP 0.418367 0.75
72 GLY LEU TYR ALA SER LYS LEU ALA 0.417476 0.777778
73 LEU ALA ILE TYR SER 0.416667 0.764706
74 SER GLN ASN TYR 0.41573 0.784314
75 LYS TRP 0.413793 0.745098
76 ASP ALA ASP GLU TYR LEU 0.41 0.745098
77 TYR GLY GLY PHE LEU 0.408163 0.788462
78 GLY SER ASP PRO PHE LYS 0.407407 0.655738
79 ASP ARG VAL TYR 0.406593 0.745098
80 GLU VAL TYR GLU SER 0.40625 0.8
81 SER GLN TYR TYR TYR ASN SER LEU 0.405941 0.701754
82 TYR GLU LEU ASP GLU LYS PHE ASP ARG LEU 0.404959 0.745763
83 THR PHE LYS LYS THR ASN 0.40404 0.788462
84 LYS LEU PRO ALA GLN PHE TYR ILE LEU 0.402985 0.698413
85 GLN SER TYR TPO VAL 0.401961 0.655738
86 ASP GLU LEU GLU ILE LYS ALA TYR 0.4 0.862745
87 LYS ASN LEU 0.4 0.673077
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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