Receptor
PDB id Resolution Class Description Source Keywords
1B3F 1.8 Å NON-ENZYME: TRANSPORT OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KHK 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 HIS LYS B:1;
Valid;
none;
Kd = 130 nM
413.523 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 HIS LYS; Similar ligands found: 68
No: Ligand ECFP6 Tc MDL keys Tc
1 LYS HIS LYS 1 1
2 LYS SER HIS GLN GLU 0.640449 0.884615
3 HIS HIS HIS HIS HIS HIS 0.589041 0.851064
4 LYS LYS 0.571429 0.76087
5 ALA HIS HIS 0.569444 0.833333
6 LYS LYS LYS 0.567164 0.782609
7 LYS TYR LYS 0.564103 0.764706
8 LYS DPP LYS 0.558824 0.770833
9 GLU LYS VAL HIS VAL GLN 0.556701 0.92
10 LYS DAB LYS 0.550725 0.787234
11 LYS ASN LYS 0.549296 0.755102
12 LYS TRP LYS 0.546512 0.897959
13 LYS SER LYS 0.542857 0.705882
14 LYS CYS LYS 0.542857 0.75
15 LYS LEU LYS 0.541667 0.72
16 LYS NVA LYS 0.535211 0.734694
17 LYS ASP LYS 0.535211 0.75
18 LYS NLE LYS 0.527778 0.72
19 LYS GLU LYS 0.520548 0.765957
20 LYS ALN LYS 0.517647 0.78
21 LYS GLN LYS 0.513514 0.765957
22 ALA HIS ALA LYS ALA 0.511111 0.916667
23 LYS GLY GLY ALA ALY ARG HIS ARG 0.508772 0.793103
24 LYS MET LYS 0.5 0.692308
25 LYS ORN LYS 0.5 0.75
26 LYS ARG LYS 0.493671 0.72549
27 LYS HPE LYS 0.487805 0.808511
28 LYS ALA LYS 0.479452 0.765957
29 LYS GLY LYS 0.472973 0.75
30 ALA LYS PHE ARG HIS ASP 0.472222 0.821429
31 ARG ARG LYS TRP ARG ARG TRP HIS LEU 0.470085 0.766667
32 LYS PRO HIS SER ASP 0.46729 0.766667
33 LYS VAL LYS 0.466667 0.734694
34 LYS ALC LYS 0.463415 0.770833
35 ASP HIS ASP ALA HIS ALA 0.461538 0.769231
36 ALA HIS ALA 0.461538 0.770833
37 GLN LYS 0.458333 0.744681
38 GLN GLY HIS GLY GLU 0.456522 0.9375
39 ARG ARG LYS TRP CIR ARG TRP HIS LEU 0.454545 0.754098
40 LYS THR LYS 0.454545 0.692308
41 GLY HIS LYS ILE LEU HIS ARG LEU LEU GLN 0.452991 0.779661
42 HIS HIS HIS HIS HIS GLY SER 0.449438 0.807692
43 LYS ILE LYS 0.448718 0.72
44 ALA ILE HIS 0.445783 0.8
45 ARG HIS LYS FDL 0.441667 0.647887
46 ALA LYS 0.441176 0.723404
47 ALA LYS ARG HIS ARG MLZ VAL LEU ARG ASP 0.440678 0.733333
48 ILE LEU MET GLU HIS ILE HIS LYS LEU 0.439655 0.807018
49 SER HIS LYS ILE ASP ASN LEU ASP 0.432203 0.793103
50 ILE LEU ALA LYS PHE LEU HIS GLU LEU 0.432203 0.851852
51 ILE LEU GLY LYS PHE LEU HIS ARG LEU 0.430894 0.766667
52 SER HIS MET ALA GLU ILE 0.430108 0.724138
53 LYS LYS LYS ALA 0.428571 0.765957
54 LYS ILE LEU HIS ARG LEU LEU GLN ASP 0.426087 0.846154
55 PHE ASN GLU LEU SER HIS LEU 0.424242 0.767857
56 ALA LYS ARG HIS ARG MLY VAL LEU ARG ASP 0.422764 0.698413
57 ILE LEU ALA LYS PHE LEU HIS THR LEU 0.421488 0.793103
58 LYS TRP 0.420455 0.857143
59 GLY HIS GLY 0.417722 0.833333
60 ARG ARG ARG TRP HIS ARG TRP ARG LEU 0.413793 0.75
61 LYS ARG ARG ARG HIS PRO SER 0.411765 0.725806
62 GLY SER SER HIS HIS HIS HIS HIS 0.411111 0.763636
63 ARG HIS LYS ALY LEU MET PHE LYS 0.409449 0.709677
64 LYS ILE LEU HIS ARG LEU LEU GLN ASP SER 0.409091 0.754098
65 VAL LYS 0.408451 0.693878
66 LYS ASN LEU 0.407407 0.679245
67 HIS LYS LEU VAL GLN LEU LEU THR THR THR 0.40708 0.807018
68 HIS SER LYS LYS LYS CYS ASP GLU LEU 0.4 0.793103
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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