Receptor
PDB id Resolution Class Description Source Keywords
1B58 1.8 Å NON-ENZYME: TRANSPORT OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KYK 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 TYR LYS B:1;
Valid;
none;
Kd = 260 nM
439.557 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 TYR LYS; Similar ligands found: 107
No: Ligand ECFP6 Tc MDL keys Tc
1 LYS TYR LYS 1 1
2 LYS ALC LYS 0.75 0.880952
3 PHE LEU ALA TYR LYS 0.609195 0.854167
4 PHE LEU SER TYR LYS 0.609195 0.773585
5 LYS LYS 0.586207 0.738095
6 LYS LYS LYS 0.580645 0.809524
7 LYS SER LYS 0.578125 0.744681
8 LYS DAB LYS 0.571429 0.790698
9 LYS DPP LYS 0.571429 0.772727
10 LYS TRP LYS 0.564103 0.77551
11 LYS HIS LYS 0.56 0.755102
12 LYS CYS LYS 0.553846 0.755556
13 LYS GLU LYS 0.552239 0.790698
14 LYS ALN LYS 0.551282 0.844444
15 LYS ASP LYS 0.545455 0.772727
16 LYS GLN LYS 0.544118 0.772727
17 GLY GLY LYS LYS LYS TYR LYS LEU 0.54023 0.857143
18 LYS NVA LYS 0.537313 0.755556
19 LYS ASN LYS 0.537313 0.723404
20 LYS LEU LYS 0.537313 0.73913
21 THR ASN GLU TYR LYS VAL 0.533333 0.836735
22 LYS HPE LYS 0.533333 0.880952
23 LYS NLE LYS 0.529412 0.73913
24 THR TYR LYS PHE PHE GLU GLN 0.526882 0.84
25 GLU ASN PRO THR TYR LYS PHE PHE GLU GLN 0.526882 0.84
26 GLU ASN GLN LYS GLU TYR PHE PHE 0.521277 0.875
27 GLU LEU ARG ARG LYS MET MET TYR MET 0.514852 0.7
28 LYS VAL LYS 0.514706 0.755556
29 GLU GLU GLN GLU GLU TYR 0.513514 0.883721
30 LYS ALA LYS 0.507463 0.790698
31 LYS ORN LYS 0.507042 0.772727
32 LYS MET LYS 0.507042 0.708333
33 VAL TYR 0.5 0.711111
34 LYS PHE LYS 0.5 0.809524
35 LYS THR LYS 0.5 0.782609
36 THR LYS ASN TYR LYS GLN THR SER VAL 0.495146 0.777778
37 GLU LEU ASP LYS TYR ALA SER 0.494949 0.788462
38 GLY GLY LYS LYS LYS TYR GLN LEU 0.494737 0.84
39 LYS ARG LYS 0.493151 0.68
40 GLN LYS 0.492308 0.727273
41 GLU GLN TYR LYS PHE TYR SER VAL 0.49 0.777778
42 SER SER ARG LYS GLU TYR TYR ALA 0.489362 0.763636
43 GLY TYR 0.484848 0.772727
44 VAL LYS VAL VAL ALA LYS LYS TYR ARG ASN 0.479592 0.736842
45 GLY GLY ARG LYS LYS TYR LYS LEU 0.479592 0.75
46 GLY GLY LYS LYS ARG TYR LYS LEU 0.479592 0.75
47 GLY GLY LYS LYS LYS TYR ARG LEU 0.479592 0.75
48 GLU ASN LEU TYR PHE GLN 0.479167 0.716981
49 LYS GLY LYS 0.478261 0.755556
50 THR ASN GLU PHE TYR PHE 0.477273 0.770833
51 ASP ASN ARG LEU GLY LEU VAL TYR GLN PHE 0.476744 0.755102
52 THR ASN GLU TYR TYR VAL 0.471264 0.72549
53 SER ASP TYR GLN ARG LEU 0.46875 0.714286
54 THR GLU ASP ASN ASP ASP ASP LEU TYR GLY 0.467532 0.755102
55 LYS ILE LYS 0.465753 0.73913
56 TYR GLN SER LYS LEU 0.462366 0.773585
57 LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG 0.460526 0.666667
58 LYS ALA VAL TYR ASN PHE ALA THR MET 0.460177 0.694915
59 LYS ALA VAL TYR ASN LEU ALA THR MET 0.460177 0.719298
60 GLU LEU LYS ARG LYS MET ILE TYR MET 0.45614 0.7
61 ASP ASN ARG LEU GLY LEU VAL TYR TRP PHE 0.452632 0.679245
62 LYS ALA LEU TYR ASN PHE ALA THR MET 0.452174 0.694915
63 LYS TRP 0.45 0.714286
64 ALA LYS 0.444444 0.697674
65 THR LYS ASN TYR LYS GLN PHE SER VAL 0.442308 0.732143
66 ASP ALA ASP GLU TYR LEU 0.442105 0.755102
67 LEU ALA ILE TYR SER 0.44086 0.74
68 TYR GLN PHE 0.440476 0.804348
69 PHE LEU GLU LYS 0.438202 0.765957
70 TI2 0.4375 0.73913
71 SER GLN TYR TYR TYR ASN SER LEU 0.4375 0.666667
72 TYR GLY GLY PHE MET 0.4375 0.754717
73 LYS LYS LYS ALA 0.43662 0.790698
74 ALA TYR ARG 0.435294 0.764706
75 ASP PHE GLU ASP TYR GLU PHE ASP 0.431579 0.808511
76 VAL LYS 0.430769 0.666667
77 SER GLN ASN TYR 0.430233 0.745098
78 ALA ALA SER LEU TYR GLU LYS LYS ALA ALA 0.428571 0.807692
79 SER LEU ASN TYR ILE ILE LYS VAL LYS GLU 0.42735 0.75
80 PHE TYR ARG ALA LEU MET 0.427273 0.666667
81 GLY LEU TYR ALA SER LYS LEU ALA 0.424242 0.754717
82 ASN GLY TYR GLU ASN PRO THR TYR LYS 0.424 0.65625
83 GLU LEU ASN ARG LYS MET ILE TYR MET 0.422764 0.666667
84 GLN SER TYR TPO VAL 0.42268 0.622951
85 TYR GLY GLY PHE LEU 0.421053 0.764706
86 ARG GLY TYR LEU TYR GLN GLY LEU 0.420561 0.689655
87 GLU VAL TYR GLU SER 0.419355 0.77551
88 CYS THR PHE LYS THR LYS THR ASN 0.418367 0.735849
89 ASP SER TRP LYS ASP GLY CYS TYR 0.412281 0.706897
90 ALA PTR ARG 0.411111 0.661017
91 TYR GLU LEU ASP GLU LYS PHE ASP ARG LEU 0.410256 0.711864
92 MET ASN TYR ASP ILE 0.409639 0.729167
93 ALA MLE TYR TYR AHY 0.409524 0.677966
94 GLY SER ASP PRO PHE LYS 0.409524 0.633333
95 LYS ASN LEU 0.407895 0.647059
96 ASP ASP LEU TYR GLY 0.406593 0.745098
97 THR PHE LYS LYS THR ASN 0.40625 0.764706
98 ASN ALA LEU LEU ARG TYR LEU LEU ASP 0.40625 0.686275
99 SER LEU TYR LEU THR VAL ALA THR LEU 0.405941 0.692308
100 ASP GLU LEU GLU ILE LYS ALA TYR 0.405405 0.857143
101 ALA LYS GLU LYS SER ASP 0.404762 0.714286
102 PHE ARG TYR LEU GLY 0.403846 0.689655
103 MET LEU ILE TYR SER MET TRP GLY LYS 0.402985 0.636364
104 PHE TYR ARG TYR GLY PHE VAL ALA ASN PHE 0.401786 0.689655
105 ARG GLY TYR VAL TYR GLN GLY LEU 0.401786 0.689655
106 CYS VAL PHE MET 0.4 0.615385
107 LYS SER HIS GLN GLU 0.4 0.678571
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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