Receptor
PDB id Resolution Class Description Source Keywords
1QKA 1.8 Å NON-ENZYME: TRANSPORT OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KRK SALMONELLA TYPHIMURIUM PROTEIN TRANSPORT COMPLEX (PEPTIDE TRANSPORT-PEPTIDE) PEPTTRANSPORT
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:608;
A:603;
A:607;
A:610;
A:601;
A:611;
A:609;
A:605;
A:606;
A:602;
A:604;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
270.028 O2 U [O-][...
LYS ARG LYS B:1;
Valid;
none;
Kd = 1200 nM
433.578 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 220 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 186 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 157 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 ARG LYS; Similar ligands found: 110
No: Ligand ECFP6 Tc MDL keys Tc
1 LYS ARG LYS 1 1
2 LYS LYS LYS 0.736842 0.857143
3 LYS DAB LYS 0.683333 0.818182
4 LYS NLE LYS 0.677419 0.782609
5 PRO PRO LYS LYS LYS ARG LYS VAL 0.666667 0.888889
6 LYS NVA LYS 0.66129 0.8
7 LYS GLN LYS 0.65625 0.837209
8 LYS GLU LYS 0.640625 0.837209
9 LYS LYS 0.631579 0.833333
10 LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG 0.630137 0.930233
11 LYS DPP LYS 0.612903 0.8
12 LYS ORN LYS 0.61194 0.904762
13 ARG SER ARG 0.61194 0.833333
14 LYS MET LYS 0.61194 0.75
15 LYS ASN LYS 0.6 0.782609
16 PRO ALA ALA LYS ARG VAL LYS LEU ASP 0.597403 0.888889
17 LYS CYS LYS 0.59375 0.818182
18 LYS SER LYS 0.59375 0.765957
19 LYS ASP LYS 0.584615 0.818182
20 PAC DLY DLY DAR 0.582278 0.893617
21 ARG ASP ARG ALA ALA LYS LEU 0.575 0.913043
22 ARG ARG ALA ALA 0.569444 0.888889
23 LYS HPE LYS 0.567568 0.8
24 LYS LEU LYS 0.567164 0.782609
25 ALA ARG LYS LEU ASP 0.5625 0.875
26 ALA PRO ALA LEU ARG VAL VAL LYS 0.559524 0.913043
27 ALA ARG 0.555556 0.906977
28 LYS LYS LYS ALA 0.552239 0.837209
29 ARG ARG ARG ARG ARG ARG ARG ARG 0.541667 0.906977
30 ARG ARG ARG ARG ARG ARG ARG ARG ARG ARG 0.541667 0.906977
31 ARG GLU 0.537313 0.930233
32 2UE DLY LYS DAR 0.534884 0.875
33 GLN LYS 0.523077 0.813953
34 LYS ALA LYS 0.522388 0.837209
35 LYS GLY LYS 0.514706 0.818182
36 LYS VAL LYS 0.507246 0.8
37 LYS ILE LYS 0.507042 0.782609
38 LYS ARG ARG LYS SEP VAL 0.505747 0.75
39 LYS ALC LYS 0.5 0.8
40 ARG ARG ALA THR LYS MET NH2 0.494737 0.745455
41 LYS HIS LYS 0.493671 0.72549
42 LYS THR LYS 0.492958 0.75
43 ILE LYS ARG SER LYS LYS ASN SER LEU ALA 0.487805 0.854167
44 LYS TYR LYS 0.487179 0.72
45 ARG ARG GLY CYS NH2 0.486842 0.808511
46 ALA LYS 0.483871 0.790698
47 ALA ARG ALA ALA ALA ALA ALA ALA ALA 0.48 0.909091
48 ARG ARG GLY LEU NH2 0.474359 0.77551
49 MET ALA ARG 0.474359 0.816327
50 LEU GLY GLY ALA LYS GLN ARG GLY ASP VAL 0.474227 0.875
51 VAL ALA ARG SER 0.468354 0.833333
52 ARG ARG GLY ILE NH2 0.468354 0.77551
53 LYS ALA ALA ARG M3L SER ALA 0.463918 0.672131
54 THR ALA ARG M3L SER THR 0.463415 0.694915
55 GLU LEU ARG ARG LYS MET MET TYR MET 0.462963 0.7
56 ARG GLU ALA ALA 0.4625 0.888889
57 THR LYS PRO ARG 0.45977 0.759259
58 PHE ARG SER LYS GLY GLU GLU LEU PHE THR 0.457447 0.788462
59 LYS GLY GLY ALA ALY ARG HIS ARG 0.45614 0.724138
60 GLN ARG ALA THR LYS MET NH2 0.455446 0.745455
61 ALA ARG 9AT 0.452055 0.795918
62 ARG ARG GLY MET NH2 0.451219 0.764706
63 ARG VAL 0.449275 0.866667
64 GLU ALY ARG 0.448276 0.913043
65 LYS ALN LYS 0.447059 0.734694
66 VAL LYS 0.446154 0.755556
67 ALA ARG THR MLY GLN 0.44086 0.711864
68 SER SER ARG LYS GLU TYR TYR ALA 0.44 0.763636
69 LYS ASN LEU 0.44 0.7
70 GLY ARG PHE ALA ALA ALA ILE ALA LYS 0.439252 0.823529
71 SER PRO LYS ARG ILE ALA 0.436893 0.688525
72 LYS ALA THR LYS MLY 0.435897 0.62069
73 ARG ASP ALA ALA 0.435897 0.888889
74 ALA ARG THR LYS GLN THR ALA ARG 0.434783 0.82
75 ARG ARG LYS TRP ARG ARG TRP HIS LEU 0.431034 0.7
76 LYS THR LYS LEU LEU 0.428571 0.705882
77 LYS ARG TRP ILE ILE LEU GLY LEU ASN LYS 0.427481 0.666667
78 LYS TRP LYS 0.426966 0.679245
79 ARG ARG ARG VAL ARG 00S 0.423913 0.764706
80 GLY GLY ARG LYS LYS TYR LYS LEU 0.423077 0.75
81 GLY GLY LYS LYS ARG TYR LYS LEU 0.423077 0.75
82 GLY GLY LYS LYS LYS TYR ARG LEU 0.423077 0.75
83 VAL LYS VAL VAL ALA LYS LYS TYR ARG ASN 0.423077 0.736842
84 LYS ARG ARG ARG HIS PRO SER 0.421053 0.66129
85 ALA ARG M3L SER 0.418605 0.694915
86 DAS DLY 0.41791 0.702128
87 GLU LEU LYS ARG LYS MET ILE TYR MET 0.416667 0.7
88 ALA LYS PHE ARG HIS ASP 0.416667 0.75
89 ARG ARG LYS TRP CIR ARG TRP HIS LEU 0.416667 0.688525
90 ARG ASP 0.416667 0.909091
91 ARG PRO LYS ARG ILE ALA 0.412844 0.711864
92 VAL ARG SER ARG ARG ABA LEU ARG LEU 0.410526 0.773585
93 ASN ARG LEU LEU LEU THR GLY 0.409091 0.735849
94 SER GLU LEU GLU ILE LYS ARG TYR 0.408696 0.7
95 ALA ARG LYS ILE ASP ASN LEU ASP 0.407407 0.792453
96 ALA ARG THR M3L GLN THR ALA ALA LYS ALA 0.407407 0.677419
97 ALA ILE ARG SER 0.406977 0.795918
98 ALA PTR ARG 0.406593 0.689655
99 GLU ARG GLY MET THR 0.40625 0.740741
100 SER ARG ARG TRP ARG ARG TRP ASN ARG 0.40566 0.66129
101 GLN ILE LYS VAL ARG VAL ASP MET VAL 0.405405 0.792453
102 SER ARG LYS ILE ASP ASN LEU ASP 0.405405 0.75
103 ARG ARG LEU ILE PHE NH2 0.40404 0.745098
104 GLU LEU LYS TPO GLU ARG TYR 0.403361 0.646154
105 ALA ARG THR M3L GLN THR ALA ARG 0.401961 0.677419
106 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.401961 0.773585
107 GLY HIS LYS ILE LEU HIS ARG LEU LEU GLN 0.401709 0.711864
108 ALA LYS ARG HIS ARG MLZ VAL LEU ARG ASP 0.401709 0.666667
109 ALA MET ARG VAL 0.4 0.76
110 LYS ARG TRP ILE ILE MET GLY LEU ASN LYS 0.4 0.626866
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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