Receptor
PDB id Resolution Class Description Source Keywords
1JEV 1.3 Å NON-ENZYME: TRANSPORT OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KWK SALMONELLA TYPHIMURIUM COMPLEX (PEPTIDE TRANSPORT/PEPTIDE) PEPTIDE TRANSPORT
Ref.: THE ROLE OF WATER IN SEQUENCE-INDEPENDENT LIGAND BINDING BY AN OLIGOPEPTIDE TRANSPORTER PROTEIN. NAT.STRUCT.BIOL. V. 3 998 1996
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 TRP LYS B:1;
 Valid;
 none;
 Kd = 130 nM
462.595 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 TRP LYS; Similar ligands found: 101
No: Ligand ECFP6 Tc MDL keys Tc
1 LYS TRP LYS 1 1
2 LYS ALN LYS 0.623529 0.875
3 LYS TRP 0.614458 0.93617
4 ASP TRP ASN 0.597701 0.769231
5 ALA LEU ASP LYS TRP ASP 0.588235 0.851852
6 GLU LEU GLU LYS TRP ALA SER 0.553571 0.854545
7 VAL GLY LEU TRP LYS SER 0.553398 0.8
8 PCA LYS TRP 0.55102 0.94
9 ASP GLU ASP LYS TRP ASP ASP PHE 0.54717 0.901961
10 ARG ARG LYS TRP ARG ARG TRP HIS LEU 0.547009 0.783333
11 LYS HIS LYS 0.546512 0.897959
12 LYS GLN TRP LEU VAL TRP LEU PHE LEU 0.546219 0.886792
13 LYS TYR LYS 0.541176 0.784314
14 GLU LEU ASP LYS TRP ALA SER 0.53913 0.807018
15 GLU ALA ASP LYS TRP GLN SER 0.53913 0.87037
16 GLU ASN ASP LYS TRP ALA SER 0.53913 0.821429
17 ARG LEU TRP SER 0.538462 0.75
18 GLU LEU ASP LYS TRP ALA ASN 0.534483 0.821429
19 GLU GLN ASP LYS TRP ALA SER 0.534483 0.87037
20 SER ARG ARG TRP ARG ARG TRP ASN ARG 0.53271 0.741935
21 GLY SER ASP PRO TRP LYS 0.530435 0.770492
22 ARG ARG LYS TRP CIR ARG TRP HIS LEU 0.528926 0.770492
23 ALA LEU ASP LYS TRP ALA SER 0.526786 0.807018
24 GLU LEU ASP LYS TRP ALA GLY 0.526316 0.851852
25 GLU ASP ASN ASP TRP ASN 0.522222 0.769231
26 ACE GLU TRP TRP TRP 0.521739 0.803922
27 LYS ARG TRP ILE ILE LEU GLY LEU ASN LYS 0.518797 0.746032
28 ILE ASP TRP PHE ASP GLY LYS GLU 0.516129 0.821429
29 ILE ASP TRP PHE GLU GLY LYS GLU 0.516129 0.854545
30 ILE ASP TRP PHE ASP GLY LYS ASP 0.512397 0.821429
31 LYS LYS LYS 0.5 0.765957
32 LYS DPP LYS 0.493506 0.72
33 GLU LEU ASP ORN TRP ALA SER 0.491525 0.789474
34 PRO GLY LEU TRP LYS SER 0.491525 0.886792
35 ARG ARG ARG TRP HIS ARG TRP ARG LEU 0.491379 0.766667
36 ARG ARG ARG ARG TRP ARG GLU ARG GLN 0.491071 0.821429
37 LYS HPE LYS 0.488636 0.829787
38 LYS DAB LYS 0.487179 0.734694
39 LYS ARG TRP ILE ILE MET GLY LEU ASN LYS 0.485915 0.701493
40 ASP SER TRP LYS ASP GLY CYS TYR 0.484375 0.766667
41 ASP TRP GLU ILE VAL 0.481481 0.759259
42 LYS CYS LYS 0.481013 0.734694
43 LYS SER LYS 0.481013 0.692308
44 LEU GLU LEU ASP LYS TRP ALA SER LEU 0.48 0.793103
45 ALA LEU ASP LYS TRP GLN ASN 0.477064 0.867925
46 LYS GLN LYS 0.47561 0.75
47 LYS NVA LYS 0.475 0.72
48 LYS ASP LYS 0.475 0.734694
49 ARG ARG ARG TRP ARG ARG LEU THR VAL 0.470588 0.730159
50 MET ASN TRP ASN ILE 0.47 0.714286
51 TRP GLU GLU LEU 0.469388 0.807692
52 LYS NLE LYS 0.469136 0.705882
53 LYS ASN LYS 0.469136 0.705882
54 LYS MET LYS 0.464286 0.679245
55 SER TRP PHE PRO 0.463636 0.783333
56 LYS LEU LYS 0.463415 0.705882
57 LYS GLU LYS 0.463415 0.75
58 GLU GLU TYR LEU LYS ALA TRP THR PHE 0.453237 0.783333
59 ASP ASN ARG LEU GLY LEU VAL TYR TRP PHE 0.448598 0.727273
60 MET LEU ILE TYR SER MET TRP GLY LYS 0.447552 0.701493
61 LYS ORN LYS 0.447059 0.734694
62 TYR TRP ALA ALA ALA ALA 0.443396 0.722222
63 GLN ALA SER GLN ASP VAL LYS ASN TRP 0.442748 0.810345
64 GLN ALA SER GLN GLU VAL LYS ASN TRP 0.442748 0.810345
65 ALA TRP LEU PHE GLU ALA 0.434783 0.773585
66 LYS ALC LYS 0.433333 0.791667
67 GLU LEU ASP HOX TRP ALA SER 0.432 0.716667
68 MET TYR TRP TYR PRO TYR 0.429688 0.707692
69 GLU LEU ASP HIS TRP ALA SER 0.428571 0.745763
70 LYS ARG LYS 0.426966 0.679245
71 LYS ALA LYS 0.426829 0.75
72 TRP GLY 0.425287 0.836735
73 GAL TRP LYS TYR LEU PHB 0.425197 0.770492
74 LYS VAL PRO ARG ASN GLN ASP TRP LEU 0.423841 0.681159
75 PCA GLN TRP 0.423077 0.86
76 TYR GLU TRP 0.423077 0.773585
77 GLY LYS ILE SER LYS HIS TRP THR GLY ILE 0.422535 0.758065
78 R38 0.422222 0.711538
79 R59 0.422222 0.711538
80 LYS GLY LYS 0.421687 0.734694
81 ALA SER ASN GLU ASN TRP GLU THR MET 0.419355 0.698413
82 GLU LEU ASP NRG TRP ALA SER 0.41791 0.616438
83 LYS VAL LYS 0.416667 0.72
84 LYS ARG LYS SER ARG TRP ASP GLU THR PRO 0.414474 0.671429
85 PCA ASN TRP 0.413462 0.792453
86 TRP PRO TRP 0.413462 0.818182
87 ALA ALA TRP LEU PHE GLU ALA 0.413223 0.773585
88 LYS PHE LYS 0.413043 0.765957
89 ASP ASN TRP GLN ASN GLY THR SER 0.412698 0.758621
90 CYS ASP PTR ALA ASN PHE LYS 0.412371 0.730769
91 LSW 0.409524 0.88
92 X95 0.409524 0.88
93 ACE ASN TRP GLU THR PHE 0.408333 0.694915
94 MET ASP TRP ASN MET HIS ALA ALA 0.407692 0.733333
95 ARG VAL LYS GLU LYS TYR GLN HIS LEU TRP 0.40708 0.777778
96 LYS THR LYS 0.406977 0.679245
97 SER VAL TYR ASP PHE PHE VAL TRP LEU 0.40625 0.677419
98 ASP ASP TRP ASN TRP GLU VAL GLU ASP 0.403509 0.75
99 SER SER VAL VAL GLY VAL TRP TYR LEU 0.403101 0.693548
100 LYS ILE LYS 0.402299 0.705882
101 LYS LYS LYS ALA 0.4 0.75
Similar Ligands (3D)
Ligand no: 1; Ligand: LYS TRP 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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