Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ARG ARG ALA ALA X:1;
Valid;
none;
Kd = 17.7 uM
474.567 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 ARG ALA ALA; Similar ligands found: 87
No: Ligand ECFP6 Tc MDL keys Tc
1 ARG ARG ALA ALA 1 1
2 ARG GLU ALA ALA 0.815385 0.954545
3 ALA ARG ALA ALA ALA ALA ALA ALA ALA 0.806452 0.976744
4 LYS ARG LYS 0.569444 0.888889
5 VAL ALA ARG SER 0.56 0.893617
6 ARG SER ARG 0.557143 0.854167
7 MET ALA ARG 0.546667 0.875
8 ARG ALA ARG 0.535211 0.906977
9 ARG ASP ALA ALA 0.527027 0.911111
10 ARG ARG GLY LEU NH2 0.526316 0.87234
11 ARG ARG ALA THR LYS MET NH2 0.521277 0.763636
12 ARG ARG GLY ILE NH2 0.519481 0.87234
13 LYS LYS LYS ALA 0.5 0.777778
14 ARG ARG GLY CYS NH2 0.5 0.829787
15 ALA ARG THR ALA ALA THR ALA ARG LYS SER 0.494118 0.875
16 ALA ARG 9AT 0.486111 0.854167
17 ARG ARG GLY MET NH2 0.481481 0.784314
18 VAL LEU ARG ASP ASP LEU LEU GLU ALA 0.472527 0.895833
19 C0O DAL DAL 0.469697 0.767442
20 ARG ARG ARG VAL ARG 00S 0.466667 0.82
21 ARG LEU GLY GLU SER 0.466667 0.829787
22 ALA ARG 0.462687 0.930233
23 LYS ALA ALA ARG M3L SER ALA 0.459184 0.688525
24 ALA ARG THR M3L GLN THR ALA ARG LYS 0.457447 0.688525
25 ALA ARG THR M3L GLN THR ALA ALA LYS ALA 0.457143 0.693548
26 GLU ALA GLN THR ARG LEU 0.454545 0.823529
27 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.454545 0.826923
28 ARG ASP ARG ALA ALA LYS LEU 0.454545 0.893617
29 ARG GLY THR 0.454545 0.854167
30 GLN ARG ALA THR LYS MET NH2 0.45098 0.732143
31 ALA ALA LEU THR ARG ALA 0.450549 0.82
32 ALA ARG LYS LEU ASP 0.448276 0.857143
33 HIS GLY ALA ALA ARG ALA GLU VAL HIS LEU 0.443299 0.913043
34 GLU ALY ARG 0.443182 0.854167
35 CYS ALA ARG ALA TYR 0.441558 0.844444
36 ASN ARG LEU LEU LEU THR GLY 0.43956 0.826923
37 PHE ALA GLY LEU ARG GLN ALA VAL THR GLN 0.435644 0.807692
38 ALA ILE ARG SER 0.435294 0.854167
39 ARG ABA PHE ILE PHE ALA ASN ILE 0.435185 0.777778
40 MET ABA LEU ARG MET THR ALA VAL MET 0.435185 0.75
41 GLU ARG GLY MET THR 0.431579 0.792453
42 ALA MET ARG VAL 0.428571 0.816327
43 ARG ARG LEU ILE PHE NH2 0.428571 0.836735
44 ARG ILE ALA ALA ALA 0.428571 0.866667
45 ARG ARG ALA SEP ALA PRO LEU PRO 0.42735 0.6
46 ASP ALA GLU PHE ARG HIS ASP 0.427184 0.875
47 PTR LEU ARG VAL ALA 0.427184 0.728814
48 VAL ARG MET 0.426829 0.795918
49 ALA ARG THR M3L GLN THR ALA ARG 0.425743 0.693548
50 ARG ABA VAL ILE PHE ALA ASN ILE 0.423423 0.792453
51 ALA ALA ALA ALA SER ALA ALA 0.422535 0.666667
52 GLU GLU PHE GLY ARG ALA PHE SER PHE 0.421053 0.745455
53 ALA DA2 THR M3L GLN THR ALA ARG ALA 0.421053 0.693548
54 VAL ARG SER ARG ARG ABA LEU ARG LEU 0.421053 0.826923
55 MET ALA ALA 0.42029 0.6875
56 SER PRO LYS ARG ILE ALA 0.419048 0.677419
57 ARG GLY ASP 0.417722 0.869565
58 ALA ARG THR MLY GLN THR ALA ARG LYS SER 0.417582 0.82
59 GLY ALA ARG ALA HIS SER SER 0.417476 0.716667
60 ARG GLN ALA SEP LEU SER ILE SER VAL 0.417391 0.728814
61 LYS ALA ARG VAL LEU ALA GLU ALA MET SER 0.416667 0.84
62 ARG ARG ARG ARG TRP ARG GLU ARG GLN 0.416667 0.75
63 ACE GLU ALA GLN THR ARG LEU 0.415842 0.807692
64 ALA ARG M3L SER 0.413793 0.711864
65 ALA ARG TPO LYS 0.413043 0.781818
66 GLN ARG SER THR SEP THR 0.411765 0.754386
67 MET CYS LEU ARG MET THR ALA VAL MET 0.410714 0.781818
68 ALA ALA ALA 0.409836 0.604651
69 GLN THR ALA ARG M3L SER 0.409524 0.666667
70 ARG PRO LYS ARG ILE ALA 0.409091 0.728814
71 ARG SER MLZ SER ASP GLY 0.408163 0.736842
72 VAL ALA PHE ARG SER 0.408163 0.82
73 ALA GLN PHE SER ALA SER ALA SER ARG 0.407767 0.826923
74 ASN ALA LEU LEU ARG TYR LEU LEU ASP 0.407407 0.754386
75 PHE TYR ARG ALA LEU MET 0.40708 0.711864
76 ARG LEU PRO ALA LYS ALA PRO LEU LEU 0.405172 0.704918
77 GLU ARG GLY SER GLY ARG 0.404255 0.803922
78 ARG ILE MET GLU NH2 0.404255 0.84
79 ARG ARG ARG GLU THR GLN VAL 0.404255 0.843137
80 LYS ARG ARG LYS SEP VAL 0.404255 0.767857
81 5JP PRO LYS ARG ILE ALA 0.40367 0.65625
82 ALA ALA ALA ALA ALA ALA ALA 0.403226 0.604651
83 SER GLU ILE GLU PHE ALA ARG LEU 0.4 0.763636
84 VAL ARG SER ARG ARG CYS LEU ARG LEU 0.4 0.826923
85 PHE LEU ARG GLY ARG ALA TYR GLY LEU 0.4 0.754386
86 MET CYS LEU ARG NLE THR ALA VAL MET 0.4 0.767857
87 ASN ARG LEU ILE LEU THR GLY 0.4 0.8
Similar Ligands (3D)
Ligand no: 1; Ligand: ARG ARG 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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