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 13 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 13 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 12 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 Ka = 51900 M^-1 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 (2D)
Ligand no: 1; Ligand: ARG GLU ALA ALA; Similar ligands found: 63
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 ASP ALA ALA 0.519481 0.954545
5 VAL LEU ARG ASP ASP LEU LEU GLU ALA 0.516484 0.895833
6 ARG ALA ARG 0.506667 0.863636
7 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.494949 0.826923
8 ARG SER ARG 0.486842 0.816327
9 HIS GLY ALA ALA ARG ALA GLU VAL HIS LEU 0.484536 0.955556
10 MET ALA ARG 0.481481 0.875
11 ARG ILE MET GLU NH2 0.478261 0.877551
12 ALA GLU ALA VAL PRO TRP LYS SER GLU 0.473684 0.75
13 GLU GLU PHE GLY ARG ALA PHE SER PHE 0.469027 0.777778
14 ASP ALA GLU PHE ARG HIS ASP 0.466019 0.914894
15 GLU ALA GLN THR ARG LEU 0.465347 0.86
16 ALA GLU ALA ALA GLN ALA 0.463415 0.790698
17 LYS ARG LYS 0.4625 0.888889
18 VAL ALA ARG SER 0.457831 0.893617
19 GLU ALY ARG 0.455556 0.893617
20 ACE GLU ALA GLN THR ARG LEU 0.455446 0.843137
21 ARG ARG ARG ARG TRP ARG GLU ARG GLN 0.453704 0.75
22 LYS ALA ARG VAL LEU ALA GLU ALA MET SER 0.453704 0.877551
23 ARG GLY THR 0.45 0.893617
24 ARG ARG ARG GLU THR GLN VAL 0.446809 0.843137
25 ARG ARG GLY LEU NH2 0.445783 0.87234
26 ARG LEU GLY GLU SER 0.443038 0.869565
27 C0O DAL DAL 0.442857 0.767442
28 ACE GLY ALA ALA GLN GLU GLU 0.44186 0.822222
29 ARG ARG ALA THR LYS MET NH2 0.441176 0.732143
30 ARG ARG GLY ILE NH2 0.440476 0.87234
31 ARG GLU 0.44 0.953488
32 ARG GLN ALA SEP LEU SER ILE SER VAL 0.439655 0.728814
33 SER GLU ILE GLU PHE ALA ARG LEU 0.434783 0.796296
34 LYS LYS LYS ALA 0.434211 0.777778
35 SER SER ARG LYS GLU TYR TYR ALA 0.432692 0.781818
36 VAL LEU CIR ASP ASP LEU LEU GLU ALA 0.431579 0.816327
37 LYS GLU LYS 0.428571 0.777778
38 GLU ARG GLY MET THR 0.428571 0.826923
39 ALA ARG THR M3L GLN THR ALA ALA LYS ALA 0.427273 0.693548
40 ARG ARG GLY CYS NH2 0.421687 0.829787
41 CYS ALA ARG ALA TYR 0.419753 0.844444
42 ILE GLN GLN SER ILE GLU ARG ILE 0.417476 0.843137
43 ARG GLY ASP 0.414634 0.911111
44 ARG SER ALA SEP GLU PRO SER LEU 0.412698 0.605634
45 SER SER ILE GLU PHE ALA ARG LEU 0.411765 0.781818
46 ARG GLU ARG SER PRO THR ARG 0.41 0.688525
47 THR ARG ARG GLU THR GLN LEU 0.41 0.826923
48 ARG ARG GLY MET NH2 0.409091 0.784314
49 ALA ARG THR ALA ALA THR ALA ARG LYS SER 0.408602 0.836735
50 ARG ILE ALA ALA ALA 0.407407 0.866667
51 ARG ABA PHE ILE PHE ALA ASN ILE 0.40708 0.811321
52 ASP ALA GLU PHE ARG HIS ASP SER 0.40678 0.75
53 PHE ALA GLY LEU ARG GLN ALA VAL THR GLN 0.40566 0.843137
54 ALA GLN PHE SER ALA SER ALA SER ARG 0.40566 0.826923
55 ALA ARG 9AT 0.405063 0.854167
56 ARG VAL ALA GLN LEU GLU GLN VAL TYR ILE 0.404959 0.796296
57 ARG ARG ILE TYR ASP LEU ILE GLU LEU 0.404959 0.754386
58 ARG ASP ARG ALA ALA LYS LEU 0.404255 0.893617
59 ILE GLU ILE 0.402597 0.733333
60 GLU ARG GLY SER GLY ARG 0.402062 0.803922
61 ARG ARG ARG VAL ARG 00S 0.402062 0.784314
62 ALA ALA ALA ALA SER ALA ALA 0.4 0.666667
63 LYS ALA ALA ARG M3L SER ALA 0.4 0.66129
Similar Ligands (3D)
Ligand no: 1; Ligand: ARG GLU ALA ALA; 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 : 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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