Receptor
PDB id Resolution Class Description Source Keywords
1B9J 1.8 Å NON-ENZYME: TRANSPORT OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KLK 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:521;
A:522;
A:523;
A:524;
A:525;
A:526;
A:527;
A:528;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
270.028 O2 U [O-][...
LYS LEU LYS B:1;
Valid;
none;
Kd = 1100 nM
389.541 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 LEU LYS; Similar ligands found: 74
No: Ligand ECFP6 Tc MDL keys Tc
1 LYS LEU LYS 1 1
2 LYS LYS LYS 0.74 0.894737
3 LYS LYS 0.723404 0.815789
4 LYS DAB LYS 0.692308 0.871795
5 LYS DPP LYS 0.692308 0.85
6 LYS NVA LYS 0.672727 0.923077
7 LYS CYS LYS 0.666667 0.829268
8 LYS ALA LYS 0.666667 0.921053
9 LYS SER LYS 0.666667 0.772727
10 LYS NLE LYS 0.660714 0.9
11 LYS ASP LYS 0.654545 0.85
12 LYS ASN LYS 0.642857 0.790698
13 LYS GLU LYS 0.631579 0.871795
14 LYS MET LYS 0.627119 0.857143
15 LYS GLN LYS 0.62069 0.85
16 LYS VAL LYS 0.614035 0.973684
17 LYS THR LYS LEU LEU 0.61194 0.883721
18 LYS ASN LEU 0.6 0.860465
19 LYS ORN LYS 0.6 0.85
20 LYS LYS LYS ALA 0.596491 0.921053
21 LYS THR LYS 0.59322 0.813953
22 LYS ARG LYS 0.580645 0.73913
23 LYS ILE LYS 0.57377 0.948718
24 HIS GLU GLU LEU ALA LYS LEU 0.573529 0.948718
25 ALA LYS 0.568627 0.815789
26 GLN LYS 0.563636 0.8
27 ALA ARG LYS LEU ASP 0.56338 0.791667
28 LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG 0.5625 0.723404
29 PHE LEU GLU LYS 0.56 0.880952
30 LYS ALC LYS 0.553846 0.829268
31 VAL LYS 0.54717 0.868421
32 LEU LEU LEU 0.545455 0.815789
33 LYS TYR LYS 0.537313 0.73913
34 LYS HIS LYS 0.536232 0.708333
35 LYS HPE LYS 0.529412 0.829268
36 LYS GLY LYS 0.516667 0.829268
37 LYS LEU LEU PHE 0.513889 0.853659
38 LEU LYS THR LYS LEU LEU 0.506849 0.883721
39 ARG ASP ARG ALA ALA LYS LEU 0.506667 0.826087
40 PHE LEU ALA TYR LYS 0.5 0.770833
41 SER LEU LEU LYS LYS LEU LEU LEU ALA 0.5 0.840909
42 SER LEU LEU LYS LYS LEU LEU ASP 0.5 0.826087
43 PHE LEU SER TYR LYS 0.5 0.698113
44 LYS LEU VAL GLN LEU LEU THR THR THR 0.493827 0.804348
45 PRO LEU SER LYS 0.493333 0.76
46 LYS ALN LYS 0.486486 0.755556
47 LYS SER LEU LEU GLN GLN LEU LEU THR GLU 0.482353 0.791667
48 ALA PRO ALA LEU ARG VAL VAL LYS 0.481013 0.826087
49 LYS TRP LYS 0.48 0.693878
50 PHE GLU ALA LYS LYS LEU VAL 0.478873 1
51 LYS ILE LEU GLY PRV VAL PHE PRQ VAL 0.473684 0.840909
52 LYS ALA THR LYS MLY 0.463768 0.76
53 GLY THR LEU SER ASN ARG ALA SER LYS LEU 0.452055 0.840909
54 ALA LYS GLU LYS SER ASP 0.445946 0.73913
55 SER LEU LYS LEU MET THR THR VAL 0.445783 0.74
56 ARG LEU GLY GLU SER 0.441176 0.6875
57 LYS CYS VAL VAL MET 0.44 0.840909
58 ALA LEU ALA LEU 0.435484 0.815789
59 ALA LEU ASP LEU PHE 0.430556 0.72093
60 ASN LEU LEU GLN LYS LYS 0.43038 0.857143
61 ARG ARG ARG ARG ARG ARG ARG ARG ARG ARG 0.424242 0.702128
62 LEU GLU 0.423729 0.769231
63 GLN LEU ALA 0.421875 0.775
64 GLU LEU ARG ARG LYS MET MET TYR MET 0.42 0.633333
65 LYS TRP 0.418919 0.632653
66 GLU ASP LEU 0.415385 0.825
67 GLU LEU ASP LYS TYR ALA SER 0.412371 0.711538
68 ARG SER ARG 0.411765 0.615385
69 LYS VAL LEU PHE LEU ASP GLY 0.408602 0.822222
70 ALA LEU 0.407407 0.684211
71 LYS LEU VAL ALA LEU GLY ILE ASN ALA VAL 0.40404 0.804348
72 GLY ILE ASP ASP GLY MET ASN LEU ASN ILE 0.402778 0.673913
73 LYS ALA SER VAL GLY 0.402597 0.8
74 LYS ARG LYS ARG LYS ARG LYS ARG 0.4 0.680851
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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