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Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
LYS NLE LYS B:1;
Valid;
none;
Kd = 0.0095 uM
389.541 n/a O=C([...
U1 A:518;
A:519;
Invalid;
Invalid;
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 209 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 (40)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 175 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 6DQT - LEU GLY GLY n/a n/a
33 6DTG - TYR LEU GLY ALA ASN GLY n/a n/a
34 6DQR - MET GLY GLY n/a n/a
35 6DTH - ARG PRO PRO GLY PHE n/a n/a
36 6DQQ - ALA ALA ALA ALA n/a n/a
37 6DQU - GLY ILE ILE ASN THR LEU n/a n/a
38 6DTF - LYS LYS LYS n/a n/a
39 3TCG Kd = 0.00000145 M LYS GLY GLU n/a n/a
40 2Z23 - LYS LYS LYS n/a n/a
50% Homology Family (41)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 149 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 6DQT - LEU GLY GLY n/a n/a
34 6DTG - TYR LEU GLY ALA ASN GLY n/a n/a
35 6DQR - MET GLY GLY n/a n/a
36 6DTH - ARG PRO PRO GLY PHE n/a n/a
37 6DQQ - ALA ALA ALA ALA n/a n/a
38 6DQU - GLY ILE ILE ASN THR LEU n/a n/a
39 6DTF - LYS LYS LYS n/a n/a
40 3TCG Kd = 0.00000145 M LYS GLY GLU n/a n/a
41 2Z23 - LYS LYS LYS n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: LYS NLE LYS; Similar ligands found: 46
No: Ligand ECFP6 Tc MDL keys Tc
1 LYS NLE LYS 1 1
2 LYS LYS LYS 0.857143 0.9
3 LYS NVA LYS 0.826923 0.975
4 LYS DAB LYS 0.788462 0.857143
5 LYS LYS 0.734694 0.875
6 LYS GLU LYS 0.732143 0.878049
7 LYS MET LYS 0.724138 0.906977
8 LYS GLN LYS 0.719298 0.878049
9 LYS DPP LYS 0.703704 0.837209
10 LYS ORN LYS 0.694915 0.857143
11 LYS SER LYS 0.678571 0.8
12 LYS CYS LYS 0.678571 0.857143
13 LYS ARG LYS 0.677419 0.782609
14 LYS LEU LYS 0.672414 0.904762
15 LYS ASP LYS 0.666667 0.857143
16 LYS LYS LYS ALA 0.655172 0.925
17 LYS ASN LYS 0.655172 0.818182
18 LYS ALA LYS 0.62069 0.925
19 LYS HPE LYS 0.61194 0.837209
20 LYS VAL LYS 0.6 0.880952
21 ALA LYS 0.584906 0.875
22 LYS THR LYS 0.580645 0.822222
23 LYS ILE LYS 0.571429 0.951219
24 GLN LYS 0.568965 0.853659
25 LYS ALC LYS 0.558824 0.837209
26 LYS GLY LYS 0.557377 0.857143
27 LYS TYR LYS 0.542857 0.75
28 VAL LYS 0.535714 0.833333
29 LYS HIS LYS 0.527778 0.72
30 LYS ALA THR LYS MLY 0.507246 0.735849
31 LYS ALN LYS 0.493506 0.765957
32 LYS THR LYS LEU LEU 0.493333 0.808511
33 LYS ASN LEU 0.492537 0.804348
34 DAS DLY 0.474576 0.733333
35 LYS TRP LYS 0.469136 0.705882
36 PRO PRO LYS LYS LYS ARG LYS VAL 0.454545 0.729167
37 HIS GLU GLU LEU ALA LYS LEU 0.448718 0.860465
38 LYS CYS VAL VAL MET 0.435897 0.826087
39 LEU LYS THR LYS LEU LEU 0.425 0.808511
40 ARG ASP ARG ALA ALA LYS LEU 0.421687 0.791667
41 GLY THR LEU SER ASN ARG ALA SER LYS LEU 0.410256 0.787234
42 ALA LYS GLU LYS SER ASP 0.410256 0.787234
43 LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG 0.405063 0.723404
44 ILE LYS LEU GLU THR LYS LYS THR LYS LEU 0.402439 0.78
45 PRO ALA ALA LYS ARG VAL LYS LEU ASP 0.402439 0.729167
46 PRO LYS THR PRO LYS LYS ALA LYS LYS LEU 0.4 0.857143
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 with APoc: 94
This union binding pocket(no: 1) in the query (biounit: 1b7h.bio1) has 34 residues
No: Leader PDB Ligand Sequence Similarity
1 5O0J GLC 1.10375
2 2ZBA ZBA 1.30719
3 5FPE 3TR 1.55039
4 5AO7 NAG 1.90476
5 3SUC ATP 1.93424
6 4KQR VPP 1.95035
7 4GNC ASO 2.00669
8 5MRH Q9Z 2.12766
9 4C2C ALA ALA ALA 2.24215
10 6EK3 OUL 2.26244
11 1MJT ITU 2.30548
12 2JFN UMA 2.45614
13 4TQK NAG 2.46305
14 5VKM GAL SIA 2.46914
15 4RF7 ARG 2.51451
16 4KBA 1QM 2.71903
17 5MUY MGT 2.7439
18 1W55 GPP 2.96496
19 3CH8 PRO GLN PRO VAL ASP SER TRP VAL 3.07692
20 1GAW FAD 3.18471
21 2Z3U CRR 3.29412
22 2Y91 98J 3.39623
23 1UI0 URA 3.41463
24 2UVO NAG 3.50877
25 4AML GYU 3.50877
26 5CSS G3P 3.53982
27 1UUY PPI 3.59281
28 5WHT SIA 3.62319
29 5WHT SIA GAL GLC 3.62319
30 5WHT SIA GAL 3.62319
31 1RL4 BRR 3.7234
32 3BY9 SIN 3.84615
33 3GDN MXN 3.86847
34 1S17 GNR 3.88889
35 5K62 ASN VAL 3.92157
36 2HZY DHJ 4.038
37 4JE7 BB2 4.06091
38 4RHS SIA SIA GAL 4.09836
39 4DR9 BB2 4.16667
40 1G27 BB1 4.16667
41 2OJW ADP 4.42708
42 4O08 PO6 4.6729
43 1BKC INN 4.6875
44 4UP4 GAL NAG 4.73815
45 4UP4 NAG 4.73815
46 4UP4 NDG 4.73815
47 5OF1 SAL 4.7619
48 4LO6 SIA GAL 4.84988
49 5JY4 ISC 4.85933
50 5JXZ ISC 4.85933
51 5JXZ ISJ 4.85933
52 3H9A PPY 4.93827
53 4B9E FAH 4.98339
54 1WS1 BB2 5.12821
55 3UWB BB2 5.19481
56 3SJK LYS PRO VAL LEU ARG THR ALA 5.26316
57 2F6D ACR 5.28455
58 2Z48 NGA 5.32407
59 2Z49 AMG 5.32407
60 3DWQ NGC GAL NGA POL AZI 5.55556
61 3QPB URA 5.67376
62 5MTE BB2 5.83942
63 1RM8 BAT 5.91716
64 4D06 X8W 6.00707
65 2UZH IPE 6.06061
66 3BU1 HSM 6.08108
67 2G36 TRP 6.18956
68 4XCP PLM 7.05882
69 2AK3 AMP 7.07965
70 3M6P BB2 7.25389
71 5A04 BGC 7.37463
72 1R55 097 7.94393
73 2FDW D3G 7.98319
74 2EW5 Y12 8.28729
75 2BVE PH5 8.40336
76 4A9C B5F 8.5443
77 3KP6 SAL 8.60927
78 1LQY BB2 8.69565
79 6MB9 NMY 8.75912
80 2JLD ALA GLY GLY ALA ALA ALA ALA ALA 9.52381
81 2V5E SCR 9.90099
82 6GR0 F8W 10.3448
83 6MJ7 ARG 10.9091
84 1SQL GUN 11.6438
85 3HQ9 OXL 12.4638
86 3RDV ASP SER TRP LYS ASP GLY CYS TYR 12.5
87 5KIQ SIA GAL NAG FUC 13.198
88 3G5K BB2 13.6612
89 3KO0 TFP 16.8317
90 3IWD M2T 17.6471
91 3H0L ADP 25.5319
92 3DRG ARG PRO PRO GLY PHE SER PRO PHE ALA 39.6518
93 6HLX G9Z 43.4959
94 4FAJ LEU VAL THR LEU VAL PHE VAL 46.2282
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