Receptor
PDB id Resolution Class Description Source Keywords
1B3H 2 Å NON-ENZYME: TRANSPORT OLIGO-PEPTIDE BINDING PROTEIN COMPLEXED WITH LYSYL- CYCLOHEXYLALANYL-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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
LYS ALC LYS B:1;
Valid;
none;
Kd = 0.62 uM
423.558 n/a O=C([...
U1 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
238.029 U [U]
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 ALC LYS; Similar ligands found: 100
No: Ligand ECFP6 Tc MDL keys Tc
1 LYS ALC LYS 1 1
2 LYS TYR LYS 0.75 0.880952
3 LYS HPE LYS 0.686567 1
4 LYS PHE LYS 0.671642 0.918919
5 LYS ALN LYS 0.608108 0.902439
6 LYS LYS 0.607143 0.837838
7 LYS LYS LYS 0.6 0.918919
8 LYS TRP LYS 0.6 0.822222
9 LYS DPP LYS 0.590164 0.871795
10 LYS DAB LYS 0.590164 0.894737
11 PHE LEU SER TYR LYS 0.586207 0.679245
12 PHE LEU ALA TYR LYS 0.586207 0.75
13 LYS HIS LYS 0.575342 0.8
14 LYS CYS LYS 0.571429 0.85
15 LYS SER LYS 0.571429 0.790698
16 LYS ASP LYS 0.5625 0.871795
17 LYS GLN LYS 0.560606 0.871795
18 PHE LEU GLU LYS 0.555556 0.857143
19 LYS LEU LYS 0.553846 0.829268
20 LYS ASN LYS 0.553846 0.809524
21 LYS NVA LYS 0.553846 0.85
22 LYS NLE LYS 0.545455 0.829268
23 LYS GLU LYS 0.545455 0.894737
24 LYS VAL LYS 0.530303 0.85
25 LYS ALA LYS 0.523077 0.894737
26 LYS MET LYS 0.521739 0.790698
27 LYS ORN LYS 0.521739 0.871795
28 LYS LEU LEU PHE 0.512821 0.829268
29 CYS VAL PHE MET 0.512195 0.680851
30 LYS ARG LYS 0.507042 0.755556
31 CYS THR PHE LYS THR LYS THR ASN 0.505495 0.74
32 LYS VAL LEU PHE LEU ASP GLY 0.505376 0.8
33 GLU ASN PRO THR TYR LYS PHE PHE GLU GLN 0.505376 0.74
34 THR TYR LYS PHE PHE GLU GLN 0.505376 0.74
35 GLY SER ASP PRO PHE LYS 0.505155 0.660714
36 ALA PHE 0.5 0.657895
37 GLU ASN GLN LYS GLU TYR PHE PHE 0.5 0.770833
38 THR PHE LYS LYS THR ASN 0.494382 0.770833
39 LYS THR LYS 0.492754 0.790698
40 ASP PHE 0.492537 0.717949
41 LYS GLY LYS 0.492537 0.85
42 GLN LYS 0.484375 0.820513
43 GLU THR LEU LEU ASP LEU ASP PHE LEU GLU 0.482759 0.688889
44 LYS TRP 0.480519 0.755556
45 LYS ILE LYS 0.478873 0.829268
46 THR LYS CYS VAL PHE MET 0.474227 0.692308
47 LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG 0.472973 0.73913
48 LYS ALA VAL PHE ASN PHE ALA THR MET 0.471698 0.642857
49 PHE LEU 0.470588 0.634146
50 LYS VAL ILE THR PHE ILE ASP LEU 0.470588 0.734694
51 GLU GLN TYR LYS PHE TYR SER VAL 0.47 0.685185
52 ASP PHE SER ILE 0.46988 0.632653
53 GLY PHE 0.46875 0.692308
54 GLY ARG PHE ALA ALA ALA ILE ALA LYS 0.465347 0.72549
55 ASP PHE GLU GLU ILE 0.465116 0.767442
56 ASP GLU ASP LYS TRP ASP ASP PHE 0.459184 0.734694
57 ALA LYS 0.459016 0.789474
58 GLU ASN LEU TYR PHE GLN 0.458333 0.622642
59 ALA LEU ASP LEU PHE 0.454545 0.697674
60 TI1 0.454545 0.717391
61 THR ASN GLU PHE TYR PHE 0.454545 0.666667
62 ASP ASN ARG LEU GLY LEU VAL TYR GLN PHE 0.453488 0.653061
63 LYS LYS LYS ALA 0.449275 0.894737
64 LEU SER PRO ASP SER PHE LEU ASN ASP 0.448718 0.638298
65 GLU ILE ILE ASN PHE GLU LYS LEU 0.447619 0.787234
66 VAL LYS 0.444444 0.75
67 LYS ALA VAL TYR ASN PHE ALA THR MET 0.442478 0.610169
68 THR ASN GLU PHE ALA PHE 0.438202 0.727273
69 GLU PHE SER PRO 0.438202 0.666667
70 GLN VAL ASN PHE LEU GLY LYS 0.438095 0.770833
71 LYS ALA LEU TYR ASN PHE ALA THR MET 0.434783 0.610169
72 SER ILE ILE ASN PHE GLU LYS LEU 0.433962 0.692308
73 TYR GLN PHE 0.433735 0.695652
74 TYR GLY GLY PHE MET 0.431579 0.660377
75 ARG ILE PHE SER 0.431579 0.653846
76 ALA GLN PHE SER ALA SER ALA SER ARG 0.428571 0.648148
77 GLN PHE LYS ASP ASN VAL ILE LEU LEU 0.428571 0.734694
78 ALA LYS PHE ARG HIS ASP 0.427184 0.660714
79 OIR 0.426667 0.674419
80 ALA PHE THR 0.426667 0.690476
81 SER ILE ILE GLY PHE GLU LYS LEU 0.425926 0.72
82 LEU GLU PHE GLN GLY 0.423913 0.777778
83 ALA ILE PHE GLN SER SER MET THR LYS 0.423423 0.672727
84 THR LYS ASN TYR LYS GLN PHE SER VAL 0.423077 0.642857
85 LYS ASN LEU 0.418919 0.717391
86 LYS MET ASP SEP PHE LEU ASP MET GLN LEU 0.418803 0.616667
87 ASP PHE M3L THR ASP 0.418367 0.62069
88 GLU THR LEU GLU ASP SER VAL PHE 0.416667 0.645833
89 LYS MET ASN THR GLN PHE THR ALA VAL 0.415929 0.685185
90 TYR GLY GLY PHE LEU 0.414894 0.666667
91 TI2 0.4125 0.630435
92 GLY GLN VAL PRO PHE SER LYS GLU GLU CYS 0.411765 0.72549
93 ALA GLU THR PHE 0.411765 0.711111
94 ASP PHE GLU ASP TYR GLU PHE ASP 0.410526 0.702128
95 TYR GLU LEU ASP GLU LYS PHE ASP ARG LEU 0.405172 0.627119
96 GLY GLY LYS LYS LYS TYR LYS LEU 0.404255 0.755102
97 THR ASN GLU TYR LYS VAL 0.402062 0.734694
98 ILE ASP TRP PHE GLU GLY LYS GLU 0.4 0.685185
99 SER PHE ALA ASN GLY 0.4 0.653061
100 ILE ASP TRP PHE ASP GLY LYS GLU 0.4 0.654545
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
Feedback