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 10 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 10 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 (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 5TDC Kd = 12.88 uM NMM ILE PHE SER n/a n/a
2 3NIJ - HIS ILE ALA ALA n/a n/a
3 3NII - LYS ILE ALA ALA n/a n/a
4 3NIM Kd = 17.7 uM ARG ARG ALA ALA n/a n/a
5 3NIK Kd = 358.8 uM ARG GLU ALA ALA n/a n/a
6 3NIN - ARG LEU GLY GLU SER n/a n/a
7 5TDB Kd = 1.45 uM DA2 ILE PHE SER n/a n/a
8 3NY3 Kd = 19 uM ARG ILE PHE SER n/a n/a
9 5TDA - ARG LEU TRP SER n/a n/a
10 5TDD Kd = 34 uM HIS ILE PHE SER n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ARG ARG ALA ALA; Similar ligands found: 71
No: Ligand ECFP6 Tc MDL keys Tc
1 ARG ARG ALA ALA 1 1
2 ARG GLU ALA ALA 0.809524 0.954545
3 ALA ARG ALA ALA ALA ALA ALA ALA ALA 0.770492 0.976744
4 ARG ARG ARG ARG ARG ARG ARG ARG ARG ARG 0.66129 0.931818
5 ARG ASP ARG ALA ALA LYS LEU 0.605263 0.893617
6 LYS ARG LYS 0.597015 0.888889
7 ARG ARG ARG ARG ARG ARG ARG ARG 0.588235 0.886364
8 LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG 0.57971 0.911111
9 THR GLY 2MR ALA ARG ALA ARG ALA 0.5625 0.895833
10 ARG ALA ARG 0.558824 0.906977
11 VAL ALA ARG SER 0.547945 0.893617
12 ARG SER ARG 0.544118 0.854167
13 MET ALA ARG 0.541667 0.875
14 ARG ARG ALA THR LYS MET NH2 0.539326 0.763636
15 ALA ARG LYS LEU ASP 0.538462 0.857143
16 LYS LYS LYS ALA 0.538462 0.733333
17 ARG ASP 0.53125 0.866667
18 ARG VAL 0.53125 0.909091
19 LYS ARG LYS ARG LYS ARG LYS ARG 0.52 0.866667
20 ARG GLU 0.515152 0.886364
21 ARG ASP ALA ALA 0.513889 0.911111
22 PRO ALA ALA LYS ARG VAL LYS LEU ASP 0.512821 0.869565
23 ARG ARG GLY ILE NH2 0.5 0.87234
24 ARG ARG GLY LEU NH2 0.5 0.87234
25 THR ALA ARG M3L SER THR 0.4875 0.711864
26 ALA ARG 0.484375 0.906977
27 ARG ARG GLY CYS NH2 0.480519 0.847826
28 LYS ALA ALA ARG M3L SER ALA 0.478723 0.688525
29 ARG ARG GLY MET NH2 0.469136 0.784314
30 ARG LEU GLY GLU SER 0.465753 0.829787
31 VAL LEU ARG ASP ASP LEU LEU GLU ALA 0.460674 0.895833
32 GLN ARG ALA THR LYS MET NH2 0.458333 0.732143
33 LYS ARG HIS ARG MLY VAL LEU ARG ASP ASN 0.458333 0.648148
34 ARG ARG ARG GLU THR GLN VAL 0.448276 0.84
35 GLU ALA GLN THR ARG LEU 0.447917 0.823529
36 HIS GLY ALA ALA ARG ALA GLU VAL HIS LEU 0.446809 0.913043
37 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.443299 0.826923
38 ARG GLY THR 0.44 0.854167
39 LYS ALA LYS 0.434783 0.733333
40 ARG ILE ALA ALA ALA 0.434211 0.866667
41 GLU ALY ARG 0.433735 0.854167
42 ARG ARG LEU ILE PHE NH2 0.43299 0.836735
43 ALA ARG THR M3L GLN THR ALA ALA LYS ALA 0.432692 0.693548
44 ALA ALA LEU THR ARG ALA 0.428571 0.82
45 ARG ARG ALA SEP ALA PRO LEU PRO 0.426087 0.6
46 SER SER ARG LYS GLU TYR TYR ALA 0.42268 0.75
47 ACE ARG LYS VAL ARG MET 5XU 0.421687 0.816327
48 ARG PRO LYS ARG ILE ALA 0.419048 0.728814
49 VAL ALA PHE ARG SER 0.416667 0.82
50 ALA ALA ALA ALA SER ALA ALA 0.414286 0.645833
51 LYS LYS LYS 0.411765 0.711111
52 ARG GLY ARG ALA 2MR GLY GLN GLU 0.411765 0.854167
53 PTR LEU ARG VAL ALA 0.411765 0.728814
54 ARG ABA PHE ILE PHE ALA ASN ILE 0.411215 0.777778
55 ALA MET ARG VAL 0.409639 0.816327
56 ILE LYS ARG SER LYS LYS ASN SER LEU ALA 0.409639 0.8
57 PHE TYR ARG ALA LEU MET 0.409091 0.711864
58 MET ARG THR GLY ASN ALA XSN 0.406593 0.823529
59 GLY ALA ARG ALA HIS SER SER 0.405941 0.716667
60 PHE ALA GLY LEU ARG GLN ALA VAL THR GLN 0.405941 0.807692
61 MET ABA LEU ARG MET THR ALA VAL MET 0.40566 0.75
62 ARG GLN ALA SEP LEU SER ILE SER VAL 0.403509 0.728814
63 ALA ALA LEU ALA ALA LEU LEU ALA ALA 0.402778 0.644444
64 ARG GLY ASP 0.402597 0.869565
65 LYS ALA ALA ARG ALY SER ALA PRO ALA 0.402299 0.788462
66 VAL LYS VAL VAL ALA LYS LYS TYR ARG ASN 0.401961 0.724138
67 GLN LEU ALA THR M3L ALA ALA ARG LYS SER 0.401786 0.677419
68 ALA ARG MLZ SER ALA PRO ALA THR 0.4 0.626866
69 ARG ABA VAL ILE PHE ALA ASN ILE 0.4 0.792453
70 ALA PRO ALA LEU ARG VAL VAL LYS 0.4 0.893617
71 ALA ILE ARG SER 0.4 0.854167
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: 13
This union binding pocket(no: 1) in the query (biounit: 3nim.bio4) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1T5C ADP 0.002279 0.44478 None
2 1H3F TYE 0.007101 0.42759 None
3 2VVG ADP 0.007295 0.41548 2.43902
4 2XT3 ADP 0.006909 0.4215 3.65854
5 1GOJ ADP 0.006567 0.41801 3.65854
6 4WOE 3S5 0.009699 0.41289 4.87805
7 3H4S ADP 0.009445 0.41388 6.09756
8 1F9V ADP 0.01561 0.40428 6.09756
9 3R96 AMP 0.03715 0.40198 9.7561
10 3R96 ACO 0.03715 0.40198 9.7561
11 3LRE ADP 0.003734 0.43438 12.1951
12 2AWN ADP 0.007697 0.41064 12.1951
13 4BQS ADP 0.01641 0.40189 13.4146
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