Receptor
PDB id Resolution Class Description Source Keywords
5LXI 1.44 Å NON-ENZYME: SIGNAL_HORMONE GABARAP-L1 ATG4B LIR COMPLEX HOMO SAPIENS LIR GABARAP ATG8 LC3 SIGNALING PROTEIN
Ref.: ATG4B CONTAINS A C-TERMINAL LIR MOTIF IMPORTANT FOR AND EFFICIENT CLEAVAGE OF MAMMALIAN ORTHOLOGS OF YE AUTOPHAGY V. 13 834 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GLU ASP GLU ASP PHE GLU ILE LEU SEP LEU E:386;
C:384;
Valid;
Valid;
Atoms found LESS than expected: % Diff = 0.225;
Atoms found MORE than expected: % Diff = 1.034;
submit data
1239.19 n/a [P+](...
PER D:206;
D:205;
Invalid;
Invalid;
none;
none;
submit data
31.999 O2 [O-][...
PGE D:203;
D:202;
Invalid;
Invalid;
none;
none;
submit data
150.173 C6 H14 O4 C(COC...
PEG B:203;
Invalid;
none;
submit data
106.12 C4 H10 O3 C(COC...
MG D:201;
B:202;
B:201;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
EDO D:204;
Invalid;
none;
submit data
62.068 C2 H6 O2 C(CO)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5LXI 1.44 Å NON-ENZYME: SIGNAL_HORMONE GABARAP-L1 ATG4B LIR COMPLEX HOMO SAPIENS LIR GABARAP ATG8 LC3 SIGNALING PROTEIN
Ref.: ATG4B CONTAINS A C-TERMINAL LIR MOTIF IMPORTANT FOR AND EFFICIENT CLEAVAGE OF MAMMALIAN ORTHOLOGS OF YE AUTOPHAGY V. 13 834 2017
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 263 families.
1 5LXI - GLU ASP GLU ASP PHE GLU ILE LEU SEP LEU n/a n/a
2 5LXH - GLU ASP GLU ASP PHE GLU ILE LEU SER LEU n/a n/a
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 5AZG Kd = 2.9 uM TYR GLN GLU SER THR ASP PHE THR PHE LEU n/a n/a
2 5AZF Kd = 36.1 uM TRP GLU GLU LEU n/a n/a
3 5L83 - ASP TRP GLU ILE VAL n/a n/a
4 5LXI - GLU ASP GLU ASP PHE GLU ILE LEU SEP LEU n/a n/a
5 5LXH - GLU ASP GLU ASP PHE GLU ILE LEU SER LEU n/a n/a
50% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 5AZG Kd = 2.9 uM TYR GLN GLU SER THR ASP PHE THR PHE LEU n/a n/a
2 5AZF Kd = 36.1 uM TRP GLU GLU LEU n/a n/a
3 5E6O Kd = 76.9 uM TRP GLU GLU LEU n/a n/a
4 5GMV Kd = 1.78 uM ASP SEP TYR GLU VAL LEU ASP LEU n/a n/a
5 5L83 - ASP TRP GLU ILE VAL n/a n/a
6 5LXI - GLU ASP GLU ASP PHE GLU ILE LEU SEP LEU n/a n/a
7 5LXH - GLU ASP GLU ASP PHE GLU ILE LEU SER LEU n/a n/a
8 4EOY - ASN ASP TRP LEU LEU PRO SER TYR n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GLU ASP GLU ASP PHE GLU ILE LEU SEP LEU; Similar ligands found: 103
No: Ligand ECFP6 Tc MDL keys Tc
1 GLU ASP GLU ASP PHE GLU ILE LEU SEP LEU 1 1
2 GLU ASP GLU ASP PHE GLU ILE LEU SER LEU 0.733871 0.785714
3 GLU ARG GLU SEP GLU PHE ASP ILE GLU ASP 0.654676 0.836066
4 LYS MET ASP SEP PHE LEU ASP MET GLN LEU 0.625899 0.836066
5 GLU ILE ILE ASN PHE GLU LYS LEU 0.606061 0.706897
6 SER GLU ILE GLU PHE ALA ARG LEU 0.583942 0.709677
7 GLN PHE LYS ASP ASN VAL ILE LEU LEU 0.571429 0.724138
8 SER SER ILE GLU PHE ALA ARG LEU 0.560284 0.725806
9 SER ILE ILE ASN PHE GLU LYS LEU 0.558824 0.745763
10 ARG ARG ILE TYR ASP LEU ILE GLU LEU 0.552448 0.651515
11 VAL ASN ASP ILE PHE GLU ALA ILE 0.551471 0.714286
12 SER GLU ASP GLU PHE TYR ASP ALA LEU SER 0.55 0.716667
13 ASP ALA ASP GLU TYR LEU 0.535433 0.684211
14 ASP SEP TYR GLU VAL LEU ASP LEU 0.527397 0.877193
15 GLU GLU TYR LEU GLN ALA PHE THR TYR 0.524476 0.655738
16 GLU GLU ASN LEU LEU ASP PHE VAL ARG PHE 0.520548 0.646154
17 TYR GLU LEU ASP GLU LYS PHE ASP ARG LEU 0.517007 0.608696
18 GLU THR LEU LEU ASP LEU ASP PHE LEU GLU 0.512 0.716981
19 GLY ILE LEU GLU PHE VAL PHE THR LEU 0.510791 0.706897
20 LEU ASP GLU GLU THR GLY GLU PHE LEU 0.510791 0.724138
21 ILE LEU ALA LYS PHE LEU HIS GLU LEU 0.5 0.625
22 ASP PHE GLU GLU ILE 0.5 0.75
23 ASN GLN LEU ALA TRP PHE ASP THR ASP LEU 0.496774 0.615385
24 ASP GLU LEU GLU ILE LYS ALA TYR 0.496504 0.683333
25 MET PHE SER ILE ASP ASN ILE LEU ALA 0.489796 0.693548
26 LYS VAL ILE THR PHE ILE ASP LEU 0.489362 0.754386
27 SER SER LEU GLU ASN PHE ALA ALA TYR VAL 0.486667 0.666667
28 SER ILE ILE GLY PHE GLU LYS LEU 0.486111 0.741379
29 GLU LEU ASP 1OL VAL GLU PHE 0.486111 0.709091
30 PRO GLU GLY ASP PM3 GLU GLU VAL LEU 0.485915 0.872727
31 PHE GLU ALA ASN GLY ASN LEU ILE 0.482759 0.694915
32 GLU LEU ASP LYS TYR ALA SER 0.482014 0.716667
33 SER LEU PHE ASN THR ILE ALA VAL LEU 0.479167 0.724138
34 ARG ABA GLN ILE PHE ALA ASN ILE 0.479167 0.701754
35 ILE ARG LYS ILE LEU PHE LEU ASP GLY ILE 0.477419 0.65625
36 MET GLU ASP TPO GLN ALA ILE ASP 0.475524 0.79661
37 SER ILE TYR PHE TPO PRO GLU LEU TYR ASP 0.473684 0.712329
38 GLU ASN LEU TYR PHE GLN 0.470588 0.629032
39 TYR ASP GLN ILE LEU 0.470149 0.672414
40 GLY ALA PHE THR PHE ASN GLU ASP PHE 0.463768 0.616667
41 ACE ASP ALA ASP GLU FTY LEU NH2 0.460993 0.821429
42 ARG VAL LEU PHE GLU ALA MET 0.46 0.606061
43 PRO GLU SEP LEU GLU SER CYS PHE 0.457746 0.892857
44 THR ASN GLU PHE ALA PHE 0.457364 0.625
45 GLU VAL ASN 1OL ALA GLU PHE 0.456376 0.672414
46 SER LEU ASN TYR ILE ILE LYS VAL LYS GLU 0.451613 0.6875
47 ARG GLN ALA SEP LEU SER ILE SER VAL 0.447368 0.790323
48 ARG ABA PHE ILE PHE ALA ASN ILE 0.445205 0.640625
49 GLU LEU ASP HOX TRP ALA SER 0.444444 0.636364
50 ACE VAL PHE PHE ALA GLU ASP NH2 0.440298 0.685185
51 GLU LEU ASP LYS TRP ALA ASN 0.44 0.630769
52 TYR GLN GLU SER THR ASP PHE THR PHE LEU 0.439394 0.666667
53 LYS GLN GLU PRO GLN GLU ILE ASP PHE 0.438272 0.621212
54 GLU LEU LYS TPO GLU ARG TYR 0.437909 0.746269
55 SER LEU LYS ILE ASP ASN GLU ASP 0.4375 0.683333
56 SER SER LEU GLU ASN PHE ARG ALA TYR VAL 0.436364 0.637681
57 LEU GLU LEU ASP LYS TRP ALA SER LEU 0.435897 0.661538
58 SER LEU PHE ASN THR VAL ALA THR LEU 0.434483 0.689655
59 SER GLU LEU GLU ILE LYS ARG TYR 0.434211 0.647059
60 SER GLN LEU LYS ASN ASN ALA LYS GLU ILE 0.433566 0.672131
61 LYS ALA LEU TYR ASN PHE ALA THR MET 0.433121 0.617647
62 ASP PHE GLU GLU ILE PRO GLY GLU TYS LEU 0.431953 0.620253
63 SER LEU TYR ASN THR ILE ALA THR LEU 0.431507 0.688525
64 LYS VAL LEU PHE LEU ASP GLY 0.428571 0.714286
65 GLN LEU SER PRO PHE PRO PHE ASP LEU 0.427673 0.628571
66 ASP PHE GLU ASP TYR GLU PHE ASP 0.426471 0.610169
67 LYS GLN TRP ASP ASN TYR GLU PTR ILE TRP 0.426136 0.695652
68 ILE LEU ALA LYS PHE LEU HIS THR LEU 0.424051 0.61194
69 GLU LEU ASP LYS TRP ALA SER 0.423841 0.671875
70 FME TYR PHE ILE ASN ILE LEU THR LEU 0.423077 0.636364
71 ALA TYR ASP GLU SEP TPO ASP GLU GLU 0.422819 0.842105
72 LEU ALA ILE TYR SER 0.422222 0.672414
73 GLU ALA GLN THR ARG LEU 0.421429 0.619048
74 ARG ARG LEU ILE PHE NH2 0.421429 0.65
75 SER ALA LYS ILE ASP ASN LEU ASP 0.42069 0.683333
76 PHE LEU GLU LYS 0.419847 0.722222
77 TYR ALA GLY SEP TPO ASP GLU ASN 0.419753 0.75
78 ACE PRO ASP PTR GLU ASN LEU 0.418301 0.671233
79 GLU LEU ASP ORN TRP ALA SER 0.418301 0.68254
80 TYR LEU ASP SEP GLY ILE HIS SER GLY ALA 0.417647 0.704225
81 ARG ABA VAL ILE PHE ALA ASN ILE 0.417219 0.677419
82 SER VAL TYR ASP PHE PHE VAL TRP LEU 0.416667 0.61194
83 GLU GLU PHE GLY ARG ALA PHE SER PHE 0.415584 0.615385
84 LEU GLN ARG VAL LEU SEP ALA PRO PHE 0.414634 0.694444
85 PHE ARG SER LYS GLY GLU GLU LEU PHE THR 0.41358 0.666667
86 ACE GLN LEU ASP ALA PHE 0.413043 0.703704
87 ACE GLN ALA ASP LEU PHE 0.413043 0.703704
88 GLU ALA ASP LYS TRP GLN SER 0.411765 0.606061
89 ALA ARG THR GLU LEU TYR ARG SER LEU 0.409091 0.656716
90 LEU PRO PHE ASP LYS THR THR ILE MET 0.408284 0.611111
91 HIS GLU GLU LEU ALA LYS LEU 0.408 0.666667
92 ALA ALA TRP LEU PHE GLU ALA 0.407895 0.606557
93 SER ASP ILE LEU PHE PRO ALA ASP SER 0.407643 0.671642
94 GLU THR LEU LEU ASP LEU ASP PHE ASP PRO 0.406667 0.632353
95 GLY ARG PHE ALA ALA ALA ILE ALA LYS 0.405405 0.634921
96 LEU GLU PHE GLN GLY 0.404412 0.696429
97 LYS LYS ALA THR GLN ALA SEP GLN GLU TYR 0.404412 0.827586
98 THR GLU ASN LEU TYR PHE GLN SER GLY THR 0.403727 0.661538
99 THR ASN GLU PHE TYR ALA 0.401408 0.612903
100 ILE ASN PHE ASP PHE ASN THR ILE 0.4 0.65
101 CYS THR GLU LEU LYS LEU ASN ASP TYR 0.4 0.65625
102 PHE VAL PHE LEU GLU ILE NH2 0.4 0.703704
103 GLY ASN TYR SER PHE TYR ALA LEU 0.4 0.615385
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5LXI; Ligand: GLU ASP GLU ASP PHE GLU ILE LEU SEP LEU; Similar sites found: 9
This union binding pocket(no: 1) in the query (biounit: 5lxi.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1SS4 GSH 0.00004596 0.53086 None
2 1R1Q ACE ARG GLU PTR VAL ASN VAL 0.02548 0.4027 None
3 1Y7P RIP 0.02297 0.40877 4.06504
4 1N13 AG2 0.01957 0.4097 4.42478
5 2QQC AG2 0.02407 0.40468 4.46429
6 2BVE PH5 0.002041 0.46327 5.04202
7 4DS0 A2G GAL NAG FUC 0.0004684 0.48588 10.5691
8 1LCK GLU GLY GLN PTR GLN PRO GLN PRO ALA 0.006803 0.41348 10.5691
9 5LFV SIA GAL NAG 0.01386 0.42739 22.7642
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