Receptor
PDB id Resolution Class Description Source Keywords
6WZZ 1.6 Å NON-ENZYME: OTHER GID4 IN COMPLEX WITH VGLWKS PEPTIDE HOMO SAPIENS GID4 STRUCTURAL GENOMICS STRUCTURAL GENOMICS CONSORTIUM SPEPTIDE BINDING PROTEIN
Ref.: RECOGNITION OF NONPROLINE N-TERMINAL RESIDUES BY TH PRO/N-DEGRON PATHWAY. PROC.NATL.ACAD.SCI.USA V. 117 14158 2020
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
UNX A:307;
A:309;
A:306;
A:301;
A:312;
A:313;
A:310;
A:302;
A:305;
A:311;
A:304;
A:303;
A:308;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
n/a X *
VAL GLY LEU TRP LYS SER B:1;
 Valid;
 Atoms found LESS than expected: % Diff = 0.102;
 submit data
616.808 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6CDG 1.6 Å NON-ENZYME: OTHER GID4 FRAGMENT IN COMPLEX WITH A PEPTIDE HOMO SAPIENS STRUCTURAL GENOMICS CONSORTIUM SGC PEPTIDE BINDING PROTEIN
Ref.: MOLECULAR BASIS OF GID4-MEDIATED RECOGNITION OF DEG THE PRO/N-END RULE PATHWAY. NAT. CHEM. BIOL. V. 14 466 2018
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 6CD8 Kd = 19.4 uM PRO SER ARG VAL n/a n/a
2 6CDG Kd = 1.9 uM PRO GLY LEU TRP LYS SER n/a n/a
3 6WZZ - VAL GLY LEU TRP LYS SER n/a n/a
4 6CD9 - PRO SER ARG TRP n/a n/a
5 6WZX - ILE GLY LEU TRP LYS SER n/a n/a
6 6CDC Kd = 2.5 uM PRO GLY LEU TRP n/a n/a
7 6CCT - PRO THR LEU VAL n/a n/a
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 6CCU Kd = 35.2 uM PRO HIS ARG VAL n/a n/a
2 6CD8 Kd = 19.4 uM PRO SER ARG VAL n/a n/a
3 6CDG Kd = 1.9 uM PRO GLY LEU TRP LYS SER n/a n/a
4 6WZZ - VAL GLY LEU TRP LYS SER n/a n/a
5 6CD9 - PRO SER ARG TRP n/a n/a
6 6WZX - ILE GLY LEU TRP LYS SER n/a n/a
7 6CDC Kd = 2.5 uM PRO GLY LEU TRP n/a n/a
8 6CCT - PRO THR LEU VAL 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 1144 families.
1 6CCU Kd = 35.2 uM PRO HIS ARG VAL n/a n/a
2 6CD8 Kd = 19.4 uM PRO SER ARG VAL n/a n/a
3 6CDG Kd = 1.9 uM PRO GLY LEU TRP LYS SER n/a n/a
4 6WZZ - VAL GLY LEU TRP LYS SER n/a n/a
5 6CD9 - PRO SER ARG TRP n/a n/a
6 6WZX - ILE GLY LEU TRP LYS SER n/a n/a
7 6CDC Kd = 2.5 uM PRO GLY LEU TRP n/a n/a
8 6CCT - PRO THR LEU VAL n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: VAL GLY LEU TRP LYS SER; Similar ligands found: 68
No: Ligand ECFP6 Tc MDL keys Tc
1 VAL GLY LEU TRP LYS SER 1 1
2 PRO GLY LEU TRP LYS SER 0.630252 0.909091
3 ALA LEU ASP LYS TRP ASP 0.59292 0.875
4 GLU LEU ASP LYS TRP ALA GLY 0.560976 0.909091
5 LYS TRP LYS 0.553398 0.8
6 GLU LEU GLU LYS TRP ALA SER 0.536 0.844828
7 GLU LEU ASP LYS TRP ALA ASN 0.53125 0.844828
8 LYS ARG TRP ILE ILE LEU GLY LEU ASN LYS 0.527778 0.769231
9 ALA LEU ASP LYS TRP ALA SER 0.524194 0.830508
10 GLU LEU ASP LYS TRP ALA SER 0.523438 0.830508
11 ILE ASP TRP PHE ASP GLY LYS ASP 0.522727 0.844828
12 ARG LEU TRP SER 0.521368 0.746032
13 ARG ARG LYS TRP ARG ARG TRP HIS LEU 0.519084 0.75
14 LYS GLN TRP LEU VAL TRP LEU PHE LEU 0.507463 0.875
15 ARG ARG LYS TRP CIR ARG TRP HIS LEU 0.503704 0.738462
16 PRO GLY LEU TRP 0.5 0.909091
17 LYS ARG TRP ILE ILE MET GLY LEU ASN LYS 0.496732 0.75
18 ILE ASP TRP PHE GLU GLY LYS GLU 0.492754 0.844828
19 ILE ASP TRP PHE ASP GLY LYS GLU 0.492754 0.844828
20 ALA LEU ASP LYS TRP GLN ASN 0.491667 0.890909
21 ARG ARG ARG TRP ARG ARG LEU THR VAL 0.484615 0.701493
22 LEU GLU LEU ASP LYS TRP ALA SER LEU 0.481752 0.816667
23 GLU LEU ASP ORN TRP ALA SER 0.480916 0.813559
24 MET LEU ILE TYR SER MET TRP GLY LYS 0.480263 0.75
25 VAL CYS TRP GLY GLU LEU MET ASN LEU 0.475177 0.819672
26 MET LEU TRP GLY TYR LEU GLN TYR VAL 0.468085 0.806452
27 GM6 0.46729 0.704918
28 GLU ASN ASP LYS TRP ALA SER 0.466165 0.754098
29 GLU ALA ASP LYS TRP GLN SER 0.466165 0.766667
30 ASP SER TRP LYS ASP GLY CYS TYR 0.464789 0.707692
31 ALA TRP LEU PHE GLU ALA 0.464 0.8
32 GLU GLN ASP LYS TRP ALA SER 0.462687 0.766667
33 ARG ARG ARG TRP HIS ARG TRP ARG LEU 0.458015 0.734375
34 ASP GLU ASP LYS TRP ASP ASP PHE 0.456 0.789474
35 PCA LYS TRP 0.452991 0.821429
36 LYS TRP 0.447619 0.777778
37 GLU GLU TYR LEU LYS ALA TRP THR PHE 0.447368 0.777778
38 ALA ALA TRP LEU PHE GLU ALA 0.442748 0.8
39 SER SER VAL VAL GLY VAL TRP TYR LEU 0.442029 0.71875
40 PHE GLN TRP MET GLY TYR GLU LEU TRP 0.44 0.793651
41 ALA LEU TRP GLY PHE PHE PRO VAL LEU 0.44 0.806452
42 GLY LEU MET TRP LEU SER TYR PHE VAL 0.43662 0.742424
43 GLU LEU ASP NRG TRP ALA SER 0.434483 0.64
44 ARG ARG ARG ARG TRP ARG GLU ARG GLN 0.434109 0.725806
45 TRP GLU GLU LEU 0.433628 0.833333
46 GLY ILE TRP GLY PHE VAL PHE THR LEU 0.432624 0.770492
47 MET SER LEU PRO GLY ARG TRP LYS PRO LYS 0.431953 0.671053
48 TRP LEU PHE VAL GLN ARG ASP SER LYS GLU 0.429825 0.792453
49 GLY LYS ILE SER LYS HIS TRP THR GLY ILE 0.428571 0.753846
50 ALA LEU TRP GLY PHE VAL PRO VAL LEU 0.427632 0.806452
51 ASP TRP ASN 0.427273 0.672414
52 ACE GLU TRP TRP TRP 0.423423 0.732143
53 GLU LEU ASP HOX TRP ALA SER 0.417266 0.741935
54 GLU LEU ASP HIS TRP ALA SER 0.414286 0.741935
55 SER SER VAL ILE GLY VAL TRP TYR LEU 0.413793 0.707692
56 0ZN 0.413793 0.732143
57 TYR TRP ALA ALA ALA ALA 0.413223 0.689655
58 THR SER THR LEU GLN GLU GLN ILE GLY TRP 0.412162 0.790323
59 SER ARG ARG TRP ARG ARG TRP ASN ARG 0.410853 0.637681
60 THR SER ASN LEU GLN GLU GLN ILE GLY TRP 0.406667 0.777778
61 GLU LEU ARG SER ARG TYR TRP ALA ILE 0.406452 0.666667
62 ARG PHE MET ASP TYR TRP GLU GLY LEU 0.40625 0.724638
63 ARG VAL LYS GLU LYS TYR GLN HIS LEU TRP 0.404762 0.77193
64 LYS VAL PRO ARG ASN GLN ASP TRP LEU 0.403614 0.704225
65 ASP TRP GLU ILE VAL 0.401575 0.785714
66 LEU LEU TRP ALA GLY PRO MET ALA VAL 0.401316 0.8125
67 PHE PRO ARG PRO TRP LEU HIS GLY LEU 0.401198 0.714286
68 ASP ASN TRP GLN ASN GLY THR SER 0.4 0.725806
Similar Ligands (3D)
Ligand no: 1; Ligand: VAL GLY LEU TRP LYS SER; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6CDG; Ligand: PRO GLY LEU TRP LYS SER; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 6cdg.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
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