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 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 TRP LYS; Similar ligands found: 128
No: Ligand ECFP6 Tc MDL keys Tc
1 LYS TRP LYS 1 1
2 LYS TRP 0.797101 0.933333
3 GLU ASP ASN ASP TRP ASN 0.6375 0.764706
4 ASP TRP ASN 0.6375 0.764706
5 LYS ALN LYS 0.632911 0.869565
6 LYS ALC LYS 0.6 0.822222
7 ASP GLU ASP LYS TRP ASP ASP PHE 0.59375 0.897959
8 ARG LEU TRP SER 0.578947 0.716667
9 ALA LEU ASP LYS TRP ASP 0.578947 0.846154
10 SER ARG ARG TRP ARG ARG TRP ASN ARG 0.565657 0.709677
11 LYS TYR LYS 0.564103 0.77551
12 LYS HIS LYS 0.5625 0.893617
13 GLY SER ASP PRO TRP LYS 0.560748 0.75
14 MET ASN TRP ASN ILE 0.56044 0.709091
15 ACE GLU TRP TRP TRP 0.55814 0.836735
16 GLU LEU GLU LYS TRP ALA SER 0.548077 0.833333
17 ARG ARG LYS TRP ARG ARG TRP HIS LEU 0.546296 0.75
18 PCA LYS TRP 0.542553 0.9375
19 GLU ALA ASP LYS TRP GLN SER 0.537037 0.833333
20 ASP ASN ARG LEU GLY LEU VAL TYR TRP PHE 0.536842 0.735849
21 LYS DAB LYS 0.528571 0.73913
22 GLU ASN ASP LYS TRP ALA SER 0.527778 0.785714
23 GLU LEU ASP LYS TRP ALA SER 0.527778 0.785714
24 ARG ARG ARG TRP HIS ARG TRP ARG LEU 0.523364 0.733333
25 GLU LEU ASP LYS TRP ALA ASN 0.522936 0.8
26 GLU GLN ASP LYS TRP ALA SER 0.522936 0.833333
27 LYS LYS 0.515152 0.688889
28 ASP TRP GLU ILE VAL 0.514852 0.769231
29 LYS LYS LYS 0.514286 0.755556
30 ALA LEU ASP LYS TRP ALA SER 0.514286 0.785714
31 TYR GLU TRP 0.510638 0.784314
32 GLU LEU ASP LYS TRP ALA GLY 0.509259 0.830189
33 ASP SER TRP LYS ASP GLY CYS TYR 0.508929 0.758621
34 LYS DPP LYS 0.507042 0.723404
35 TRP GLU GLU LEU 0.505495 0.82
36 GLU LEU ASP ORN TRP ALA SER 0.504505 0.767857
37 LYS ARG TRP ILE ILE LEU GLY LEU ASN LYS 0.503937 0.714286
38 LYS HPE LYS 0.5 0.822222
39 ARG ARG ARG TRP ARG ARG LEU THR VAL 0.5 0.698413
40 ASP ASP TRP ASN TRP GLU VAL GLU ASP 0.495146 0.745455
41 LYS SER LYS 0.493151 0.666667
42 LYS CYS LYS 0.493151 0.708333
43 R38 0.487805 0.705882
44 R59 0.487805 0.705882
45 LYS GLN LYS 0.486842 0.723404
46 LYS ASP LYS 0.486486 0.723404
47 TYR TRP ALA ALA ALA ALA 0.484848 0.730769
48 ILE ASP TRP PHE ASP GLY LYS GLU 0.483333 0.8
49 ILE ASP TRP PHE GLU GLY LYS GLU 0.483333 0.833333
50 TRP GLY 0.481013 0.770833
51 SER TRP PHE PRO 0.480769 0.762712
52 LYS LEU LYS 0.48 0.693878
53 LYS ASN LYS 0.48 0.68
54 LYS NVA LYS 0.48 0.708333
55 ALA ASN SER ARG TRP GLN ASP THR ARG LEU 0.478992 0.6875
56 ILE ASP TRP PHE ASP GLY LYS ASP 0.478632 0.8
57 LEU GLU LEU ASP LYS TRP ALA SER LEU 0.474576 0.77193
58 LYS MET LYS 0.474359 0.666667
59 LYS ARG TRP ILE ILE MET GLY LEU ASN LYS 0.474074 0.671642
60 LYS NLE LYS 0.473684 0.693878
61 LYS GLU LYS 0.473684 0.73913
62 ALA LEU ASP LYS TRP GLN ASN 0.470588 0.862745
63 LYS VAL LYS 0.460526 0.708333
64 ASP SER LYS ASP VAL LYS GLU TRP TYR VAL ZN 0.459677 0.714286
65 ARG ARG ARG ARG SER TRP TYR 0.459459 0.68254
66 LYS ORN LYS 0.455696 0.723404
67 GLU GLU TYR LEU LYS ALA TRP THR PHE 0.453846 0.775862
68 MET TYR TRP TYR PRO TYR 0.453782 0.714286
69 LYS ALA LYS 0.453333 0.73913
70 MET LEU ILE TYR SER MET TRP GLY LYS 0.451852 0.681818
71 ALA TRP LEU PHE GLU ALA 0.449541 0.784314
72 SER VAL TYR ASP PHE PHE VAL TRP LEU 0.449153 0.655738
73 GLU LEU ASP HOX TRP ALA SER 0.449153 0.683333
74 GLU LEU ASP HIS TRP ALA SER 0.445378 0.724138
75 LYS ARG LYS 0.444444 0.641509
76 PCA GLN TRP 0.444444 0.857143
77 ARG ARG LYS TRP CIR ARG TRP HIS LEU 0.443609 0.737705
78 GLN GLU GLU TRP SEP THR VAL MET 0.442623 0.608696
79 LEU LEU GLU LEU ASP LYS TRP ALA NH2 0.440678 0.862745
80 GLN ALA SER GLN ASP VAL LYS ASN TRP 0.439024 0.775862
81 GLN ALA SER GLN GLU VAL LYS ASN TRP 0.439024 0.775862
82 SER SER VAL VAL GLY VAL TRP TYR LEU 0.438017 0.672131
83 ASP ASN TRP GLN ASN GLY THR SER 0.436975 0.724138
84 SER ARG TYR TRP ALA ILE ARG THR ARG 0.435115 0.656716
85 PCA ASN TRP 0.434343 0.788462
86 LSW 0.434343 0.84
87 X95 0.434343 0.84
88 LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG 0.433735 0.62963
89 ALA SER ASN GLU ASN TRP GLU THR MET 0.432203 0.666667
90 TRP LEU PHE VAL GLN ARG ASP SER LYS GLU 0.431818 0.765957
91 LYS THR LYS 0.43038 0.666667
92 MET ASP TRP ASN MET HIS ALA ALA 0.429752 0.728814
93 TRP PRO TRP 0.428571 0.830189
94 LYS GLY LYS 0.428571 0.708333
95 ALA ALA TRP LEU PHE GLU ALA 0.426087 0.784314
96 ACE ASN TRP GLU THR PHE 0.423729 0.689655
97 ACE TRP ARG VAL PRO 0.422414 0.703125
98 ASN GLN LEU ALA TRP PHE ASP THR ASP LEU 0.421875 0.689655
99 ALA ASN SER ARG TRP GLN THR SER ILE ILE 0.420635 0.661538
100 GLY GLU GLU TRP GLY PRO TRP VAL NH2 0.420168 0.775862
101 LYS ILE LYS 0.419753 0.693878
102 LYS VAL PRO ARG ASN GLN ASP TRP LEU 0.41958 0.652174
103 GLN LYS 0.418919 0.680851
104 LTN 0.418919 0.673913
105 THR SER THR THR SER VAL ALA SER SER TRP 0.418182 0.714286
106 MET TRP ARG PRO TRP 0.416 0.641791
107 0ZN 0.414141 0.730769
108 GLY LEU MET TRP LEU SER TYR PHE VAL 0.414062 0.646154
109 MET LEU TRP GLY TYR LEU GLN TYR VAL 0.414062 0.693548
110 SER SER VAL ILE GLY VAL TRP TYR LEU 0.414062 0.66129
111 SER LEU LEU MET TRP ILE THR GLN LEU 0.41129 0.65625
112 LYS LYS LYS ALA 0.410256 0.73913
113 ACE ASN PRO ASP TRP ASP PHE ASN NH2 0.410256 0.849057
114 ALA VAL PRO TRP 0.409524 0.8
115 LYS SER HIS GLN GLU 0.409524 0.763636
116 VAL ASP SER LYS ASN THR SER SER TRP 0.408333 0.745763
117 ACE TRP HIS THR ALA NH2 NH2 0.407407 0.709091
118 ARG PHE MET ASP TYR TRP GLU GLY LEU 0.407143 0.623188
119 SER ASN TRP SER HIS PRO GLN PHE GLU LYS 0.405594 0.714286
120 SER LEU LEU MET TRP ILE THR GLN SER 0.404762 0.65625
121 GLY LYS ILE SER LYS HIS TRP THR GLY ILE 0.404412 0.737705
122 VAL LYS 0.402778 0.625
123 LYS ARG LYS SER ARG TRP ASP GLU THR PRO 0.402778 0.642857
124 TRP 0.402597 0.638298
125 DTR 0.402597 0.638298
126 LYS PHE LYS 0.402299 0.755556
127 PHE LEU GLU LYS 0.402062 0.72
128 GLU PRO GLN ALA PRO TRP MET GLU GLN 0.401515 0.714286
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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