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 C:1;
C:10;
C:11;
C:2;
C:3;
C:4;
C:5;
C:6;
C:7;
C:8;
C:9;
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 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 ARG LYS; Similar ligands found: 102
No: Ligand ECFP6 Tc MDL keys Tc
1 LYS ARG LYS 1 1
2 LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG 0.927273 0.976744
3 ARG ARG ARG ARG ARG ARG ARG ARG ARG ARG 0.785714 0.953488
4 LYS LYS LYS 0.754717 0.809524
5 LYS DAB LYS 0.709091 0.790698
6 LYS ARG LYS ARG LYS ARG LYS ARG 0.681818 0.930233
7 LYS NLE LYS 0.677966 0.73913
8 LYS GLN LYS 0.666667 0.813953
9 LYS NVA LYS 0.661017 0.755556
10 LYS GLU LYS 0.65 0.790698
11 LYS LYS 0.641509 0.738095
12 ALA ARG LYS LEU ASP 0.625 0.875
13 LYS DPP LYS 0.62069 0.772727
14 LYS MET LYS 0.619048 0.708333
15 ARG SER ARG 0.619048 0.833333
16 LYS ORN LYS 0.619048 0.857143
17 LYS ASN LYS 0.606557 0.76087
18 LYS SER LYS 0.6 0.744681
19 LYS CYS LYS 0.6 0.795455
20 PRO ALA ALA LYS ARG VAL LYS LEU ASP 0.597222 0.888889
21 ARG ARG ALA ALA 0.597015 0.888889
22 LYS ASP LYS 0.590164 0.772727
23 ARG ASP ARG ALA ALA LYS LEU 0.586667 0.913043
24 LYS LEU LYS 0.580645 0.73913
25 LYS HPE LYS 0.571429 0.755556
26 ARG ARG ARG ARG ARG ARG ARG ARG 0.567164 0.906977
27 LYS LYS LYS ALA 0.564516 0.790698
28 ALA ARG 0.559322 0.883721
29 ALA ARG TPO LYS 0.551282 0.763636
30 LYS ALA LYS 0.548387 0.790698
31 ARG GLU 0.539683 0.906977
32 ALA PRO ALA LEU ARG VAL VAL LYS 0.5375 0.913043
33 GLN LYS 0.533333 0.767442
34 ARG ASP 0.532258 0.886364
35 LYS VAL LYS 0.53125 0.755556
36 LYS ILE LYS 0.522388 0.73913
37 LYS THR LYS 0.515152 0.708333
38 LYS ALC LYS 0.507042 0.755556
39 MET ALA ARG 0.5 0.816327
40 LYS HIS LYS 0.493333 0.686275
41 LYS TYR LYS 0.493151 0.68
42 LYS GLY LYS 0.492308 0.795455
43 ARG ARG ALA THR LYS MET NH2 0.488889 0.745455
44 LYS ARG ARG LYS SEP VAL 0.487805 0.75
45 VAL ALA ARG SER 0.486486 0.833333
46 ARG VAL 0.484375 0.844444
47 ALA LYS 0.482759 0.697674
48 ILE LYS ARG SER LYS LYS ASN SER LEU ALA 0.480519 0.854167
49 ARG GLU ALA ALA 0.48 0.888889
50 ALA ARG ALA ALA ALA ALA ALA ALA ALA 0.478873 0.909091
51 THR ALA ARG M3L SER THR 0.468354 0.694915
52 ALA LYS GLU LYS SER ASP 0.467532 0.714286
53 VAL LYS 0.466667 0.666667
54 GLU LEU ARG ARG LYS MET MET TYR MET 0.465347 0.7
55 LYS ALA ALA ARG M3L SER ALA 0.462366 0.672131
56 ARG ARG GLY ILE NH2 0.461538 0.77551
57 ARG ARG GLY LEU NH2 0.461538 0.77551
58 ARG ARG GLY CYS NH2 0.460526 0.826087
59 LYS ASN LEU 0.457143 0.68
60 ALA ARG THR MLZ GLN THR ALA ARG LYS 0.454545 0.75
61 ARG ASP ALA ALA 0.452055 0.888889
62 LYS ALN LYS 0.45 0.693878
63 SER ARG ARG TRP ARG ARG TRP ASN ARG 0.44898 0.66129
64 THR LYS PRO ARG 0.445783 0.759259
65 ARG LEU GLY GLU SER 0.444444 0.770833
66 LYS TRP LYS 0.444444 0.641509
67 LYS THR LYS LEU LEU 0.443038 0.666667
68 GLN ARG ALA THR LYS MET NH2 0.442105 0.745455
69 ARG ARG LYS TRP ARG ARG TRP HIS LEU 0.439252 0.7
70 ALA ARG THR MLY GLN 0.438202 0.711864
71 LYS ARG HIS ARG MLY VAL LEU ARG ASP ASN 0.43662 0.660377
72 SER SER ARG LYS GLU TYR TYR ALA 0.43617 0.763636
73 LYS GLY GLY ALA ALY ARG HIS ARG 0.435185 0.724138
74 ARG ARG GLY MET NH2 0.432099 0.764706
75 GLU ALY ARG 0.432099 0.913043
76 VAL LYS VAL VAL ALA LYS LYS TYR ARG ASN 0.428571 0.736842
77 ACE ALA ARG THR LYS GLN 0.425287 0.836735
78 ALA ARG M3L SER 0.421687 0.694915
79 GLY ARG PHE ALA ALA ALA ILE ALA LYS 0.421569 0.823529
80 LEU GLY GLY ALA LYS GLN ARG GLY ASP VAL 0.421053 0.875
81 ACE ARG LYS VAL ARG MET 5XU 0.419753 0.76
82 LYS ALA ALA ARG ALY SER ALA PRO ALA 0.416667 0.803922
83 ARG ARG ARG TRP HIS ARG TRP ARG LEU 0.415094 0.683333
84 GLY GLY ARG LYS LYS TYR LYS LEU 0.414141 0.75
85 GLY GLY LYS LYS LYS TYR ARG LEU 0.414141 0.75
86 GLY GLY LYS LYS ARG TYR LYS LEU 0.414141 0.75
87 ARG ARG ARG GLU THR GLN VAL 0.413793 0.784314
88 LYS ARG TRP ILE ILE LEU GLY LEU ASN LYS 0.412698 0.666667
89 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.412371 0.773585
90 GLU LEU LYS ARG LYS MET ILE TYR MET 0.412281 0.7
91 LYS ARG ARG ARG HIS PRO SER 0.409091 0.66129
92 SER GLU LEU GLU ILE LYS ARG TYR 0.409091 0.7
93 ALA MET ARG VAL 0.407407 0.76
94 ARG PRO LYS ARG ILE ALA 0.403846 0.711864
95 ALA PTR ARG 0.402299 0.689655
96 GLU ALA GLN THR ARG LEU 0.402062 0.769231
97 GLN ARG SER THR SEP THR 0.402062 0.677966
98 SER ASP TYR GLN ARG LEU 0.402062 0.714286
99 ARG ARG LEU ILE PHE NH2 0.402062 0.745098
100 GLU LEU LYS TPO GLU ARG TYR 0.401786 0.646154
101 VAL ARG SER ARG ARG CYS LEU ARG LEU 0.4 0.773585
102 ARG GLY THR 0.4 0.833333
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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