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 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 ARG LYS; Similar ligands found: 107
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 LYS NVA LYS 0.66129 0.8
6 LYS GLN LYS 0.65625 0.837209
7 LYS GLU LYS 0.640625 0.837209
8 LYS DPP LYS 0.612903 0.8
9 ARG SER ARG 0.61194 0.833333
10 LYS MET LYS 0.61194 0.75
11 LYS ORN LYS 0.61194 0.904762
12 LYS ASN LYS 0.6 0.782609
13 LYS CYS LYS 0.59375 0.818182
14 LYS SER LYS 0.59375 0.765957
15 LYS ASP LYS 0.584615 0.818182
16 PAC DLY DLY DAR 0.582278 0.893617
17 ALA ARG TPO LYS 0.573171 0.763636
18 ARG ARG ALA ALA 0.569444 0.888889
19 LYS HPE LYS 0.567568 0.8
20 LYS LEU LYS 0.567164 0.782609
21 ALA ARG LYS LEU ASP 0.5625 0.875
22 LYS LYS LYS ALA 0.552239 0.837209
23 2UE DLY LYS DAR 0.534884 0.875
24 LYS ALA LYS 0.522388 0.837209
25 LYS GLY LYS 0.514706 0.818182
26 LYS VAL LYS 0.507246 0.8
27 LYS ILE LYS 0.507042 0.782609
28 LYS ARG ARG LYS SEP VAL 0.505747 0.75
29 LYS ALC LYS 0.5 0.8
30 ARG ARG ALA THR LYS MET NH2 0.494737 0.745455
31 ARG ASP ARG ALA ALA LYS LEU 0.494118 0.913043
32 LYS HIS LYS 0.493671 0.72549
33 LYS THR LYS 0.492958 0.75
34 ALA ARG 0.492308 0.906977
35 LYS TYR LYS 0.487179 0.72
36 ARG ARG GLY CYS NH2 0.486842 0.808511
37 LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG 0.481481 0.930233
38 ALA ARG ALA ALA ALA ALA ALA ALA ALA 0.48 0.909091
39 ARG ARG GLY LEU NH2 0.474359 0.77551
40 MET ALA ARG 0.474359 0.816327
41 ARG ARG GLY ILE NH2 0.468354 0.77551
42 VAL ALA ARG SER 0.468354 0.833333
43 LYS ALA ALA ARG M3L SER ALA 0.463918 0.672131
44 GLU LEU ARG ARG LYS MET MET TYR MET 0.462963 0.7
45 ARG GLU ALA ALA 0.4625 0.888889
46 PHE ARG SER LYS GLY GLU GLU LEU PHE THR 0.457447 0.788462
47 LYS GLY GLY ALA ALY ARG HIS ARG 0.45614 0.724138
48 GLN ARG ALA THR LYS MET NH2 0.455446 0.745455
49 ALA LYS 0.453125 0.767442
50 ILE LYS ARG SER LYS LYS ASN SER LEU ALA 0.452381 0.854167
51 ALA ARG 9AT 0.452055 0.795918
52 ACE LYS ARG ARG LYS SEP VAL 0.451613 0.75
53 ARG ARG GLY MET NH2 0.451219 0.764706
54 GLU ALY ARG 0.448276 0.913043
55 LYS ALN LYS 0.447059 0.734694
56 LEU GLY GLY ALA LYS GLN ARG GLY ASP VAL 0.444444 0.875
57 ALA ARG THR MLY GLN 0.44086 0.711864
58 SER C0F GLY LYS ARG LYS 0.440678 0.666667
59 LYS ASN LEU 0.44 0.7
60 LYS LYS 0.439394 0.833333
61 GLY ARG PHE ALA ALA ALA ILE ALA LYS 0.439252 0.823529
62 PHE ALN ARG ARG ARG ARG SLL ARG 00S 0.438202 0.833333
63 SER PRO LYS ARG ILE ALA 0.436893 0.688525
64 ARG ASP ALA ALA 0.435897 0.888889
65 ALA ARG THR LYS GLN THR ALA ARG 0.434783 0.82
66 VAL LYS 0.432836 0.733333
67 ARG ARG LYS TRP ARG ARG TRP HIS LEU 0.431034 0.7
68 LYS THR LYS LEU LEU 0.428571 0.705882
69 LYS ARG TRP ILE ILE LEU GLY LEU ASN LYS 0.427481 0.666667
70 LYS TRP LYS 0.426966 0.679245
71 PRO ALA ALA LYS ARG VAL LYS LEU ASP 0.425287 0.888889
72 LYS ALA THR LYS MLY 0.425 0.62069
73 ARG ARG ARG VAL ARG 00S 0.423913 0.764706
74 GLY GLY LYS LYS LYS TYR ARG LEU 0.423077 0.75
75 GLY GLY LYS LYS ARG TYR LYS LEU 0.423077 0.75
76 GLY GLY ARG LYS LYS TYR LYS LEU 0.423077 0.75
77 LYS ARG ARG ARG HIS PRO SER 0.421053 0.66129
78 5JP PRO LYS ARG ILE ALA 0.420561 0.666667
79 ALA ARG M3L SER 0.418605 0.694915
80 DAS DLY 0.41791 0.702128
81 ALA LYS PHE ARG HIS ASP 0.416667 0.75
82 ARG ARG LYS TRP CIR ARG TRP HIS LEU 0.416667 0.688525
83 GLU LEU LYS ARG LYS MET ILE TYR MET 0.416667 0.7
84 LEU LYS 0.414286 0.717391
85 GLN LYS 0.414286 0.813953
86 VAL LYS VAL VAL ALA LYS LYS TYR ARG ASN 0.413462 0.736842
87 ASN ARG LEU LEU LEU THR GLY 0.413043 0.740741
88 ARG PRO LYS ARG ILE ALA 0.412844 0.711864
89 SER SER ARG LYS GLU TYR TYR ALA 0.411765 0.763636
90 VAL ARG SER ARG ARG ABA LEU ARG LEU 0.410526 0.773585
91 SER GLU LEU GLU ILE LYS ARG TYR 0.408696 0.7
92 ALA ARG LYS ILE ASP ASN LEU ASP 0.407407 0.792453
93 ALA ARG THR M3L GLN THR ALA ALA LYS ALA 0.407407 0.677419
94 ALA ILE ARG SER 0.406977 0.795918
95 ALA PTR ARG 0.406593 0.689655
96 GLU ARG GLY MET THR 0.40625 0.740741
97 SER ARG ARG TRP ARG ARG TRP ASN ARG 0.40566 0.66129
98 GLN ILE LYS VAL ARG VAL ASP MET VAL 0.405405 0.792453
99 SER ARG LYS ILE ASP ASN LEU ASP 0.405405 0.75
100 ARG ARG LEU ILE PHE NH2 0.40404 0.745098
101 GLU LEU LYS TPO GLU ARG TYR 0.403361 0.646154
102 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.401961 0.773585
103 GLN ARG SER THR SEP THR 0.401961 0.677966
104 ALA ARG THR M3L GLN THR ALA ARG 0.401961 0.677419
105 GLY HIS LYS ILE LEU HIS ARG LEU LEU GLN 0.401709 0.711864
106 ALA MET ARG VAL 0.4 0.76
107 LYS ARG TRP ILE ILE MET GLY LEU ASN LYS 0.4 0.626866
Similar Ligands (3D)
Ligand no: 1; Ligand: LYS ARG 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
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