Receptor
PDB id Resolution Class Description Source Keywords
3NIK 1.85 Å EC: 6.-.-.- THE STRUCTURE OF UBR BOX (REAA) SACCHAROMYCES CEREVISIAE E3 UBIQUITIN LIGASE UBR BOX ZINC-BINDING PROTEIN N-END RULIGASE METAL BINDING PROTEIN
Ref.: STRUCTURAL BASIS FOR THE RECOGNITION OF N-END RULE SUBSTRATES BY THE UBR BOX OF UBIQUITIN LIGASES NAT.STRUCT.MOL.BIOL. V. 17 1175 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ARG GLU ALA ALA X:1;
Valid;
none;
Kd = 358.8 uM
445.477 n/a O=C([...
ZN A:1;
A:2;
A:3;
B:1;
B:2;
B:3;
D:1;
D:2;
D:3;
F:1;
F:2;
F:3;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3NIM 2 Å EC: 6.-.-.- THE STRUCTURE OF UBR BOX (RRAA) SACCHAROMYCES CEREVISIAE E3 UBIQUITIN LIGASE UBR BOX ZINC-BINDING PROTEIN N-END RULIGASE METAL BINDING PROTEIN
Ref.: STRUCTURAL BASIS FOR THE RECOGNITION OF N-END RULE SUBSTRATES BY THE UBR BOX OF UBIQUITIN LIGASES NAT.STRUCT.MOL.BIOL. V. 17 1175 2010
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 12 families.
1 3NIL - ARG ASP ALA ALA n/a n/a
2 3NIJ - HIS ILE ALA ALA n/a n/a
3 3NIH - ARG ILE ALA ALA ALA n/a n/a
4 3NII - LYS ILE ALA ALA n/a n/a
5 3NIM Kd = 17.7 uM ARG ARG ALA ALA n/a n/a
6 3NIK Kd = 358.8 uM ARG GLU ALA ALA n/a n/a
7 3NIN - ARG LEU GLY GLU SER n/a n/a
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 12 families.
1 3NIL - ARG ASP ALA ALA n/a n/a
2 3NIJ - HIS ILE ALA ALA n/a n/a
3 3NIH - ARG ILE ALA ALA ALA n/a n/a
4 3NII - LYS ILE ALA ALA n/a n/a
5 3NIM Kd = 17.7 uM ARG ARG ALA ALA n/a n/a
6 3NIK Kd = 358.8 uM ARG GLU ALA ALA n/a n/a
7 3NIN - ARG LEU GLY GLU SER n/a n/a
50% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 5TDC Kd = 12.88 uM NMM ILE PHE SER n/a n/a
2 3NIL - ARG ASP ALA ALA n/a n/a
3 3NIJ - HIS ILE ALA ALA n/a n/a
4 3NIH - ARG ILE ALA ALA ALA n/a n/a
5 3NII - LYS ILE ALA ALA n/a n/a
6 3NIM Kd = 17.7 uM ARG ARG ALA ALA n/a n/a
7 3NIK Kd = 358.8 uM ARG GLU ALA ALA n/a n/a
8 3NIN - ARG LEU GLY GLU SER n/a n/a
9 5TDB Kd = 1.45 uM DA2 ILE PHE SER n/a n/a
10 3NY3 Kd = 19 uM ARG ILE PHE SER n/a n/a
11 5TDA - ARG LEU TRP SER n/a n/a
12 5TDD Kd = 34 uM HIS ILE PHE SER n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ARG GLU ALA ALA; Similar ligands found: 73
No: Ligand ECFP6 Tc MDL keys Tc
1 ARG GLU ALA ALA 1 1
2 ARG ARG ALA ALA 0.815385 0.954545
3 ALA ARG ALA ALA ALA ALA ALA ALA ALA 0.657143 0.976744
4 ARG GLU 0.636364 0.953488
5 ARG ASP ARG ALA ALA LYS LEU 0.523256 0.893617
6 ARG ASP ALA ALA 0.519481 0.954545
7 VAL LEU ARG ASP ASP LEU LEU GLU ALA 0.516484 0.895833
8 ARG ALA ARG 0.506667 0.863636
9 ARG VAL 0.5 0.931818
10 HIS GLY ALA ALA ARG ALA GLU VAL HIS LEU 0.5 0.955556
11 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.494949 0.826923
12 ARG SER ARG 0.486842 0.816327
13 MET ALA ARG 0.481481 0.875
14 ARG ILE MET GLU NH2 0.478261 0.877551
15 ALA GLU ALA VAL PRO TRP LYS SER GLU 0.473684 0.75
16 GLU GLU PHE GLY ARG ALA PHE SER PHE 0.469027 0.777778
17 ARG ARG ARG ARG ARG ARG ARG ARG ARG ARG 0.468354 0.844444
18 ARG ARG ARG ARG ARG ARG ARG ARG 0.468354 0.844444
19 ASP ALA GLU PHE ARG HIS ASP 0.466019 0.914894
20 ARG ASP 0.465753 0.931818
21 GLU ALA GLN THR ARG LEU 0.465347 0.86
22 ALA GLU ALA ALA GLN ALA 0.463415 0.790698
23 LYS ARG LYS 0.4625 0.888889
24 SER SER ARG LYS GLU TYR TYR ALA 0.460784 0.781818
25 VAL ALA ARG SER 0.457831 0.893617
26 GLU ALY ARG 0.455556 0.893617
27 ACE GLU ALA GLN THR ARG LEU 0.455446 0.843137
28 LYS ALA ARG VAL LEU ALA GLU ALA MET SER 0.453704 0.877551
29 LYS ALA ARG VAL LEU ALA GLU ALA MET 0.453704 0.877551
30 THR ALA ARG M3L SER THR 0.453488 0.683333
31 ALA ARG 0.450704 0.930233
32 ARG GLY THR 0.45 0.893617
33 ARG ARG ARG GLU THR GLN VAL 0.446809 0.843137
34 ARG ARG GLY LEU NH2 0.445783 0.87234
35 ARG LEU GLY GLU SER 0.443038 0.869565
36 ACE GLY ALA ALA GLN GLU GLU 0.44186 0.822222
37 ARG ARG ALA THR LYS MET NH2 0.441176 0.732143
38 ARG ARG GLY ILE NH2 0.440476 0.87234
39 ARG GLN ALA SEP LEU SER ILE SER VAL 0.439655 0.728814
40 SER GLU ILE GLU PHE ALA ARG LEU 0.434783 0.796296
41 LYS LYS LYS ALA 0.434211 0.777778
42 VAL LEU CIR ASP ASP LEU LEU GLU ALA 0.431579 0.816327
43 GLU ARG GLY MET THR 0.428571 0.826923
44 LYS GLU LYS 0.428571 0.777778
45 ALA ARG THR M3L GLN THR ALA ALA LYS ALA 0.427273 0.693548
46 LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG 0.425287 0.826087
47 ARG ARG GLY CYS NH2 0.421687 0.829787
48 ARG GLY ARG ALA 2MR GLY GLN GLU 0.421569 0.854167
49 PRO PRO LYS LYS LYS ARG LYS VAL 0.420455 0.869565
50 CYS ALA ARG ALA TYR 0.419753 0.844444
51 ARG ARG ARG GLU ARG SER PRO THR ARG 0.418803 0.65625
52 ILE GLN GLN SER ILE GLU ARG ILE 0.417476 0.843137
53 ARG GLY ASP 0.414634 0.911111
54 SER SER ILE GLU PHE ALA ARG LEU 0.411765 0.781818
55 THR ASN GLU PHE ALA PHE 0.410526 0.627451
56 ARG GLU ARG SER PRO THR ARG 0.41 0.688525
57 THR ARG ARG GLU THR GLN LEU 0.41 0.826923
58 ARG ARG GLY MET NH2 0.409091 0.784314
59 ALA ARG THR ALA ALA THR ALA ARG LYS SER 0.408602 0.836735
60 ARG ILE ALA ALA ALA 0.407407 0.866667
61 ARG ABA PHE ILE PHE ALA ASN ILE 0.40708 0.811321
62 ASP ALA GLU PHE ARG HIS ASP SER 0.40678 0.75
63 PRO ALA ALA LYS ARG VAL LYS LEU ASP 0.406593 0.869565
64 ALA GLN PHE SER ALA SER ALA SER ARG 0.40566 0.826923
65 ALA ARG 9AT 0.405063 0.854167
66 ARG VAL ALA GLN LEU GLU GLN VAL TYR ILE 0.404959 0.796296
67 ARG ARG ILE TYR ASP LEU ILE GLU LEU 0.404959 0.754386
68 ILE GLU ILE 0.402597 0.733333
69 ARG ARG ARG VAL ARG 00S 0.402062 0.784314
70 GLU ARG GLY SER GLY ARG 0.402062 0.803922
71 ALA ALA ALA ALA SER ALA ALA 0.4 0.666667
72 LYS ARG HIS ARG MLY VAL LEU ARG ASP ASN 0.4 0.666667
73 LYS ALA ALA ARG M3L SER ALA 0.4 0.66129
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3NIM; Ligand: ARG ARG ALA ALA; 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: 3nim.bio4) has 17 residues
No: Leader PDB Ligand Sequence Similarity
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