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 199 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 (33)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 166 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 3TCG Kd = 0.00000145 M LYS GLY GLU n/a n/a
33 2Z23 - LYS LYS LYS n/a n/a
50% Homology Family (34)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 141 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 3TCG Kd = 0.00000145 M LYS GLY GLU n/a n/a
34 2Z23 - LYS LYS LYS n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: LYS HIS LYS; Similar ligands found: 77
No: Ligand ECFP6 Tc MDL keys Tc
1 LYS HIS LYS 1 1
2 LYS SER HIS GLN GLU 0.643678 0.846154
3 ALA HIS HIS 0.585714 0.847826
4 LYS ALC LYS 0.575342 0.8
5 LYS TRP LYS 0.5625 0.893617
6 LYS TYR LYS 0.56 0.755102
7 GLU LYS VAL HIS VAL GLN 0.55914 0.897959
8 LYS LYS 0.557377 0.704545
9 LYS LYS LYS 0.553846 0.772727
10 LYS DAB LYS 0.545455 0.795455
11 LYS DPP LYS 0.545455 0.777778
12 LYS LEU LYS 0.536232 0.708333
13 LYS ASN LYS 0.536232 0.729167
14 LYS SER LYS 0.529412 0.68
15 LYS CYS LYS 0.529412 0.723404
16 LYS ASP LYS 0.521739 0.73913
17 LYS GLY HIS HIS HIS HIS HIS HIS 0.515789 0.857143
18 LYS NVA LYS 0.514286 0.723404
19 LYS ALN LYS 0.512195 0.770833
20 LYS GLY GLY ALA ALY ARG HIS ARG 0.509259 0.758621
21 LYS GLU LYS 0.507042 0.755556
22 LYS NLE LYS 0.507042 0.708333
23 LYS GLN LYS 0.5 0.73913
24 ALA HIS ALA LYS ALA 0.5 0.913043
25 ARG ARG LYS TRP ARG ARG TRP HIS LEU 0.5 0.733333
26 ASP HIS ASP ALA HIS ALA 0.494253 0.78
27 LYS ARG LYS 0.493333 0.686275
28 LYS VAL LYS 0.492958 0.723404
29 LYS MET LYS 0.486486 0.68
30 LYS ORN LYS 0.486486 0.73913
31 LYS ALA LYS 0.485714 0.755556
32 LYS PRO HIS SER ASP 0.480769 0.745763
33 ARG ARG ARG TRP HIS ARG TRP ARG LEU 0.476636 0.716667
34 ALA LYS PHE ARG HIS ASP 0.475728 0.785714
35 LYS HPE LYS 0.475 0.8
36 ALA HIS ALA 0.473684 0.782609
37 GLN GLY HIS GLY GLU 0.466667 0.895833
38 LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG 0.461538 0.673077
39 LYS THR LYS 0.459459 0.68
40 LYS GLY LYS 0.458333 0.723404
41 ALA LYS ARG HIS ARG MLZ VAL LEU ARG ASP 0.455357 0.7
42 GLY HIS LYS ILE LEU HIS ARG LEU LEU GLN 0.451327 0.745763
43 LYS TRP 0.451219 0.829787
44 HIS HIS HIS HIS HIS GLY SER 0.449438 0.784314
45 GLN LYS 0.449275 0.695652
46 ARG HIS LYS FDL 0.448276 0.619718
47 LYS ILE LYS 0.447368 0.708333
48 GLY HIS GLY 0.447368 0.808511
49 LYS GLY GLY ALA ALY ARG HIS ARG LYS VAL 0.444444 0.758621
50 GLY SER SER HIS HIS HIS HIS HIS 0.44186 0.727273
51 ALA ILE HIS 0.439024 0.8125
52 PHE ASN GLU LEU SER HIS LEU 0.43299 0.745455
53 SER HIS LYS ILE ASP ASN LEU ASP 0.431034 0.758621
54 GLY ALA ARG ALA HIS SER SER 0.427184 0.704918
55 ALA LYS 0.424242 0.666667
56 ARG HIS LYS ALY LEU MET PHE LYS 0.422764 0.677419
57 ILE LEU MET GLU HIS ILE HIS LYS LEU 0.422414 0.8
58 LYS LYS LYS ALA 0.418919 0.755556
59 LYS ARG ARG ARG HIS PRO SER 0.417391 0.693548
60 ILE LEU ALA LYS PHE LEU HIS GLU LEU 0.415254 0.846154
61 LYS ILE LEU HIS ARG LEU LEU GLN ASP SER 0.414062 0.721311
62 HIS LYS LEU VAL GLN LEU LEU THR THR THR 0.412844 0.785714
63 ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP 0.412281 0.758621
64 VAL LYS 0.411765 0.638298
65 LYS ASN LEU 0.410256 0.653846
66 ACE PHE HIS ALA ALA NH2 0.408602 0.755102
67 SER HIS PHE ASN GLU TYR GLU 0.40678 0.711864
68 LYS ARG ARG ARG HIS PRO SER GLY 0.40678 0.661538
69 ILE LEU GLY LYS PHE LEU HIS ARG LEU 0.406504 0.733333
70 ARG ARG LYS TRP CIR ARG TRP HIS LEU 0.406015 0.721311
71 VAL LEU HIS ASP ASP LEU LEU GLU ALA 0.405941 0.784314
72 ILE LEU ALA LYS PHE LEU HIS THR LEU 0.404959 0.785714
73 SER HIS MET ALA GLU ILE 0.40367 0.711864
74 ASP ALA GLU PHE ARG HIS ASP 0.40367 0.767857
75 LYS GLY GLY ALA ALY ARG HIS ARG LYS ILE 0.403361 0.724138
76 GLU LEU ASP HIS TRP ALA SER 0.403361 0.706897
77 HIS SER LYS LYS LYS CYS ASP GLU LEU 0.401786 0.77193
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: 43
This union binding pocket(no: 1) in the query (biounit: 1b7h.bio1) has 34 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2ZBA ZBA 0.01811 0.41015 1.30719
2 5MRH Q9Z 0.03101 0.40923 2.12766
3 4C2C ALA ALA ALA 0.01987 0.42954 2.24215
4 2JFN UMA 0.01036 0.42589 2.45614
5 4KBA 1QM 0.01796 0.42176 2.71903
6 1W55 GPP 0.01624 0.43916 2.96496
7 2Y91 98J 0.02565 0.41916 3.39623
8 1UUY PPI 0.00007649 0.55479 3.59281
9 1RL4 BRR 0.02852 0.4152 3.7234
10 3BY9 SIN 0.04042 0.40875 3.84615
11 1S17 GNR 0.01463 0.40477 3.88889
12 2HZY DHJ 0.0158 0.40635 4.038
13 4JE7 BB2 0.01243 0.40802 4.06091
14 4RHS SIA SIA GAL 0.004474 0.47573 4.09836
15 4DR9 BB2 0.01092 0.41731 4.16667
16 1G27 BB1 0.01702 0.40174 4.16667
17 1BKC INN 0.03047 0.40235 4.6875
18 4UP4 NDG 0.02729 0.40426 4.73815
19 4UP4 NAG 0.02729 0.40426 4.73815
20 3H9A PPY 0.04068 0.40767 4.93827
21 4B9E FAH 0.04206 0.41044 4.98339
22 4NFD SIA 0.02378 0.40314 5
23 1WS1 BB2 0.01749 0.40749 5.12821
24 3SJK LYS PRO VAL LEU ARG THR ALA 0.02384 0.41999 5.26316
25 2Z48 NGA 0.02264 0.41988 5.32407
26 3DWQ NGC GAL NGA POL AZI 0.0115 0.44023 5.55556
27 3QPB URA 0.0411 0.41476 5.67376
28 1RM8 BAT 0.004767 0.45708 5.91716
29 2UZH IPE 0.01742 0.42885 6.06061
30 3BU1 HSM 0.02055 0.42309 6.08108
31 2G36 TRP 0.02953 0.41646 6.18956
32 1R55 097 0.03412 0.40702 7.94393
33 2FDW D3G 0.0406 0.40301 7.98319
34 2BVE PH5 0.003963 0.45357 8.40336
35 4A9C B5F 0.03203 0.41612 8.5443
36 1LQY BB2 0.0162 0.40584 8.69565
37 2V5E SCR 0.01382 0.41679 9.90099
38 3RDV ASP SER TRP LYS ASP GLY CYS TYR 0.02796 0.41161 12.5
39 3G5K BB2 0.02311 0.40167 13.6612
40 3KO0 TFP 0.01907 0.41871 16.8317
41 3IWD M2T 0.04847 0.40553 17.6471
42 3H0L ADP 0.02636 0.41296 25.5319
43 4FAJ LEU VAL THR LEU VAL PHE VAL 0.000007879 0.49272 46.2282
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