Receptor
PDB id Resolution Class Description Source Keywords
3NIL 1.75 Å EC: 6.-.-.- THE STRUCTURE OF UBR BOX (RDAA) 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
ACT F:195;
F:196;
Invalid;
Invalid;
none;
none;
submit data
59.044 C2 H3 O2 CC(=O...
ARG ASP ALA ALA X:1;
Valid;
none;
submit data
345.38 n/a O=C(N...
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 ASP ALA ALA; Similar ligands found: 40
No: Ligand ECFP6 Tc MDL keys Tc
1 ARG ASP ALA ALA 1 1
2 ARG ILE ALA ALA ALA 0.57971 0.826087
3 ARG ARG ALA ALA 0.527027 0.911111
4 ARG GLY ASP 0.520548 0.954545
5 ARG GLU ALA ALA 0.519481 0.954545
6 ARG LEU GLY GLU SER 0.513889 0.829787
7 ARG SER MLZ SER ASP GLY 0.505495 0.767857
8 ARG SER ARG 0.5 0.854167
9 ARG GLY ASP ILE ASN ASN ASN VAL 0.489583 0.826923
10 ARG ALA ARG 0.479452 0.863636
11 GLU ALY ARG 0.465116 0.893617
12 ARG ARG ARG ARG TRP ARG GLU ARG GLN 0.461538 0.75
13 ARG ARG GLY ILE NH2 0.45 0.833333
14 ASP ALA GLU PHE ARG HIS ASP 0.445545 0.914894
15 ARG GLY THR 0.441558 0.893617
16 ARG ARG GLY LEU NH2 0.4375 0.833333
17 LYS ARG LYS 0.435897 0.888889
18 ACE ARG LYS VAL ARG MET 5XU 0.433735 0.78
19 ALA ARG THR ALA ALA THR ALA ARG LYS SER 0.431818 0.836735
20 GLY ARG GLY ASP SER PRO 0.426966 0.893617
21 ALA ALA LEU THR ARG ALA 0.423913 0.82
22 ALA ARG ALA ALA ALA ALA ALA ALA ALA 0.423077 0.931818
23 LYS ALA ALA ARG M3L SER ALA 0.42 0.66129
24 GLU ARG GLU SEP GLU PHE ASP ILE GLU ASP 0.418033 0.716667
25 ARG ASP 0.416667 0.976744
26 VAL LEU ARG ASP ASP LEU LEU GLU ALA 0.414894 0.895833
27 ARG ARG GLY CYS NH2 0.4125 0.829787
28 LYS ASP LYS 0.410959 0.8
29 GLU ASP LEU 0.410959 0.717391
30 ILE GLU ILE 0.410959 0.695652
31 GLN LEU ALA 0.410959 0.652174
32 PRO ALA ALA LYS ARG VAL LYS LEU ASP 0.409091 0.829787
33 ARG ILE MET GLU NH2 0.408602 0.84
34 MET ARG THR GLY ASN ALA XSN 0.407895 0.770833
35 SER LYS SER MLZ ASP ARG LYS TYR THR LEU 0.406593 0.672727
36 ALA ARG 0.405797 0.930233
37 ALA ARG LYS LEU ASP 0.404494 0.895833
38 MET ALA ARG 0.402439 0.836735
39 ILE LYS ARG SER MLZ LYS ASN SER LEU ALA 0.4 0.745455
40 ARG ARG GLY MET NH2 0.4 0.784314
Similar Ligands (3D)
Ligand no: 1; Ligand: ARG ASP 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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