Receptor
PDB id Resolution Class Description Source Keywords
5TDA 0.79 Å EC: 6.3.2.- CRYSTAL STRUCTURE OF THE UBR-BOX DOMAIN FROM UBR2 IN COMPLEX N-DEGRON HOMO SAPIENS ZN-FINGER N-END RULE UBR-BOX N-DEGRON LIGASE
Ref.: BOUND WATERS MEDIATE BINDING OF DIVERSE SUBSTRATES UBIQUITIN LIGASE. STRUCTURE V. 25 719 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN A:202;
A:203;
A:201;
 Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
 submit data
65.409 Zn [Zn+2...
ARG LEU TRP SER B:1;
 Valid;
 Atoms found MORE than expected: % Diff = 1.35;
 submit data
561.664 n/a O=C([...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5TDB 1.1 Å EC: 6.3.2.- CRYSTAL STRUCTURE OF THE HUMAN UBR-BOX DOMAIN FROM UBR2 IN C WITH ASYMMETRICALLY DOUBLE METHYLATED ARGININE PEPTIDE HOMO SAPIENS UBR-BOX N-END RULE ASYMMETRICALLY DOUBLE METHYLATED ARGINILIGASE
Ref.: BOUND WATERS MEDIATE BINDING OF DIVERSE SUBSTRATES UBIQUITIN LIGASE. STRUCTURE V. 25 719 2017
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 41 families.
1 5TDB Kd = 1.45 uM DA2 ILE PHE SER n/a n/a
2 3NY3 Ka = 51900 M^-1 ARG ILE PHE SER n/a n/a
3 5TDA - ARG LEU TRP SER n/a n/a
4 5TDD Kd = 34 uM HIS ILE PHE SER n/a n/a
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 27 families.
1 5TDC Kd = 12.88 uM NMM ILE PHE SER n/a n/a
2 5TDB Kd = 1.45 uM DA2 ILE PHE SER n/a n/a
3 3NY3 Ka = 51900 M^-1 ARG ILE PHE SER n/a n/a
4 5TDA - ARG LEU TRP SER n/a n/a
5 5TDD Kd = 34 uM HIS ILE PHE 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 LEU TRP SER; Similar ligands found: 134
No: Ligand ECFP6 Tc MDL keys Tc
1 ARG LEU TRP SER 1 1
2 ARG ARG ARG TRP ARG ARG LEU THR VAL 0.707965 0.904762
3 ARG ARG ARG TRP HIS ARG TRP ARG LEU 0.690265 0.887097
4 ARG ARG LYS TRP ARG ARG TRP HIS LEU 0.658333 0.873016
5 ARG ARG LYS TRP CIR ARG TRP HIS LEU 0.637097 0.859375
6 ARG ARG ARG ARG TRP ARG GLU ARG GLN 0.622807 0.852459
7 SER ARG ARG TRP ARG ARG TRP ASN ARG 0.610619 0.830769
8 GLU LEU ARG SER ARG TYR TRP ALA ILE 0.602941 0.852941
9 GLU LEU GLU LYS TRP ALA SER 0.6 0.852459
10 GLU LEU ASP ORN TRP ALA SER 0.590164 0.852459
11 GLU LEU ASP HOX TRP ALA SER 0.58871 0.78125
12 GLU LEU ASP NRG TRP ALA SER 0.587786 0.816901
13 GLU LEU ASP LYS TRP ALA SER 0.585366 0.83871
14 GLU LEU ASP HIS TRP ALA SER 0.584 0.809524
15 ALA LEU ASP LYS TRP ALA SER 0.561983 0.83871
16 ALA ASN SER ARG TRP GLN ASP THR ARG LEU 0.543478 0.892308
17 SER LEU LEU MET TRP ILE THR GLN SER 0.541985 0.75
18 LYS ARG TRP ILE ILE LEU GLY LEU ASN LYS 0.538462 0.833333
19 LYS TRP LYS 0.538462 0.75
20 ALA LEU ASP LYS TRP ASP 0.538462 0.790323
21 SER SER THR ARG GLY ILE SER GLN LEU TRP 0.535211 0.892308
22 PRO SER ARG TRP 0.533898 0.857143
23 ARG PHE MET ASP TYR TRP GLU GLY LEU 0.530612 0.811594
24 GLU ALA ASP LYS TRP GLN SER 0.523438 0.777778
25 VAL GLY LEU TRP LYS SER 0.521368 0.746032
26 GLU LEU ASP LYS TRP ALA ASN 0.51938 0.765625
27 LYS GLN TRP LEU VAL TRP LEU PHE LEU 0.518797 0.790323
28 GLU LEU ASP LYS TRP ALA GLY 0.511811 0.790323
29 GLU ASN ASP LYS TRP ALA SER 0.511628 0.765625
30 ARG PHE PRO LEU THR PHE GLY TRP 0.509934 0.791667
31 GLU GLN ASP LYS TRP ALA SER 0.507692 0.777778
32 ALA ASN SER ARG TRP GLN VAL THR ARG VAL 0.507576 0.876923
33 LYS ARG TRP ILE ILE MET GLY LEU ASN LYS 0.506579 0.785714
34 SER ARG TYR TRP ALA ILE ARG THR ARG 0.503497 0.850746
35 SER LEU LEU MET TRP ILE THR GLN LEU 0.5 0.75
36 ALA ASN SER ARG TRP GLN THR SER ILE ILE 0.5 0.876923
37 ASP TRP ASN 0.495238 0.634921
38 PHE LEU TRP GLY PRO ARG ALA LEU VAL 0.493421 0.797101
39 LEU GLU LEU ASP LYS TRP ALA SER LEU 0.492647 0.825397
40 PHE PRO ARG PRO TRP LEU HIS GLY LEU 0.490446 0.774648
41 MET LEU TRP GLY TYR LEU GLN TYR VAL 0.489209 0.735294
42 ALA TRP LEU PHE GLU ALA 0.487805 0.75
43 ARG PHE PRO LEU THR PHE GLY TRP CYS PHE 0.487654 0.77027
44 ARG VAL LYS GLU LYS TYR GLN HIS LEU TRP 0.487395 0.754098
45 ARG TYR PRO LEU THR PHE GLY TRP 0.487342 0.77027
46 SER LEU LEU MET TRP ILE THR GLN CYS 0.485507 0.75
47 MET SER LEU PRO GLY ARG TRP LYS PRO LYS 0.484663 0.773333
48 GLU GLY PRO ARG ASN GLN ASP TRP LEU 0.48366 0.763889
49 SER LEU LEU MET TRP ILE THR GLN ALA 0.481752 0.75
50 PRO ARG PRO ILE LEU LEU PRO TRP ARG NH2 0.479167 0.768116
51 LYS VAL PRO ARG ASN GLN ASP TRP LEU 0.474684 0.763889
52 SER SER VAL VAL GLY VAL TRP TYR LEU 0.474074 0.757576
53 ASP ASN TRP GLN ASN GLY THR SER 0.473684 0.738462
54 TRP GLU GLU LEU 0.472727 0.779661
55 MET LEU ILE TYR SER MET TRP GLY LYS 0.470588 0.712329
56 ARG TYR PRO LEU THR LEU GLY TRP CYS PHE 0.470238 0.75
57 TRP LEU PHE VAL GLN ARG ASP SER LYS GLU 0.468468 0.711864
58 SER PRO LEU ASP SER LEU TRP TRP ILE 0.468085 0.712329
59 ABA SER LEU TRP ASN GLY PRO HIS LEU 0.466667 0.726027
60 ASN ASP TRP LEU LEU PRO SER TYR 0.466667 0.684211
61 LYS ARG LYS SER ARG TRP ASP GLU THR PRO 0.465409 0.777778
62 ALA ALA TRP LEU PHE GLU ALA 0.465116 0.75
63 ACE TRP ARG VAL PRO 0.465116 0.794118
64 SER SER VAL ILE GLY VAL TRP TYR LEU 0.464286 0.746269
65 MET TRP ARG PRO TRP 0.464286 0.708333
66 01W ARG TRP THR DAB MET LEU GLY 0.464052 0.674699
67 ALA ASN SER ARG TRP ALY THR SER ILE ILE 0.463087 0.811594
68 ACE GLU TRP TRP TRP 0.462963 0.66129
69 GLU ASP ASN ASP TRP ASN 0.462264 0.634921
70 THR SER THR LEU GLN GLU GLN ILE GLY TRP 0.461538 0.8
71 ARG GLY TYR LEU TYR GLN GLY LEU 0.460938 0.78125
72 ARG GLN TRP GLY PRO ASP PRO ALA ALA VAL 0.459627 0.771429
73 PRO GLY LEU TRP LYS SER 0.458647 0.790323
74 GLY LEU MET TRP LEU SER TYR PHE VAL 0.457143 0.728571
75 ALA ASN SER ARG TRP PRO THR THR ARG LEU 0.456376 0.794521
76 SER VAL TYR ASP PHE PHE VAL TRP LEU 0.455882 0.742424
77 THR SER ASN LEU GLN GLU GLN ILE GLY TRP 0.455172 0.787879
78 PRO GLY LEU TRP 0.45 0.790323
79 PHE GLN TRP MET GLY TYR GLU LEU TRP 0.449664 0.724638
80 MET ASN TRP ASN ILE 0.447368 0.671875
81 VAL CYS TRP GLY GLU LEU MET ASN LEU 0.444444 0.720588
82 ARG GLN PHE GLY PRO ASP TRP ILE VAL ALA 0.443787 0.774648
83 ALA LEU ASP LYS TRP GLN ASN 0.443548 0.803279
84 SER LEU LEU MET TRP ILE THR GLN VAL 0.440559 0.735294
85 ALA LEU TRP GLY PHE PHE PRO VAL LEU 0.44 0.710145
86 LEU LEU TRP ASN GLY PRO ILE ALA VAL 0.439189 0.680556
87 0ZN 0.438596 0.716667
88 GLU GLU TYR LEU LYS ALA TRP THR PHE 0.437909 0.761194
89 ALA SER ASN GLU ASN TRP GLU THR MET 0.437037 0.735294
90 ASP TRP GLU ILE VAL 0.435484 0.737705
91 ARG LEU GLY GLU SER 0.434343 0.683333
92 LYS TRP 0.433962 0.728814
93 ARG TYR PRO LEU THR PHE GLY TRP CYS PHE 0.433526 0.736842
94 ILE SER PRO ARG THR LEU ASP ALA TRP 0.432927 0.794521
95 ASP ASN ARG LEU GLY LEU VAL TYR TRP PHE 0.429752 0.709677
96 LEU LEU TRP ALA GLY PRO MET ALA VAL 0.42953 0.671233
97 ALA LEU TRP GLY PHE VAL PRO VAL LEU 0.427632 0.710145
98 LEU LEU TRP ASN GLY PRO MET ALA VAL 0.425806 0.653333
99 MET ASP TRP ASN MET HIS ALA ALA 0.425532 0.691176
100 ILE ASP TRP PHE ASP GLY LYS ASP 0.425532 0.738462
101 SER LEU ARG PHE LEU TYR GLU GLY 0.425373 0.787879
102 GLU LEU ARG ARG LYS MET MET TYR MET 0.425373 0.710145
103 TYR TRP ALA ALA ALA ALA 0.425 0.677419
104 ARG SER ARG 0.424242 0.704918
105 ASN GLN LEU ALA TRP PHE ASP THR ASP LEU 0.423611 0.734375
106 ALA TRP ARG HIS PRO GLN PHE GLY GLY 0.423313 0.742857
107 LEU LEU TRP ASN GLY PRO MET GLN VAL 0.423077 0.653333
108 GLY ILE TRP GLY PHE VAL PHE THR LEU 0.422535 0.753846
109 ASP GLU ASP LYS TRP ASP ASP PHE 0.421875 0.714286
110 SER TRP PHE PRO 0.420635 0.685714
111 ALA LEU TRP GLY PRO ASP PRO ALA ALA ALA 0.42 0.7
112 ACE TRP HIS THR ALA NH2 NH2 0.419355 0.6875
113 GLY SER HIS LEU GLU VAL GLN GLY TYR TRP 0.41875 0.779412
114 ARG ARG LEU LEU ARG GLY HIS ASN GLN TYR 0.417808 0.808824
115 THR SER THR THR SER VAL ALA SER SER TRP 0.417323 0.774194
116 GLY ASN PHE LEU GLN SER ARG 0.416667 0.78125
117 ALA ASN SER ARG TRP PRO ALY SER ILE ILE 0.415663 0.76
118 MET TYR TRP TYR PRO TYR 0.415493 0.626667
119 ASP SER TRP LYS ASP GLY CYS TYR 0.414966 0.695652
120 ALA SER LEU ASN LEU PRO ALA VAL SER TRP 0.414474 0.722222
121 ILE ASP TRP PHE GLU GLY LYS GLU 0.410959 0.738462
122 ILE ASP TRP PHE ASP GLY LYS GLU 0.410959 0.738462
123 GLY LYS ILE SER LYS HIS TRP THR GLY ILE 0.410256 0.764706
124 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.408 0.71875
125 ALA ASN SER ARG TRP PRO THR SER ALY ILE 0.407186 0.75
126 ALA PRO ALA TRP LEU PHE GLU ALA 0.406667 0.685714
127 GLY SER ASP PRO TRP LYS 0.405797 0.676056
128 PHE TYR ARG ALA LEU MET 0.404412 0.757576
129 R59 0.403846 0.666667
130 R38 0.403846 0.666667
131 PHE GLU ASP LEU ARG LEU LEU SER PHE 0.402985 0.809524
132 PRO ALA TRP LEU PHE GLU ALA 0.402778 0.777778
133 ASP ASP TRP ASN TRP GLU VAL GLU ASP 0.401575 0.676923
134 ARG GLY TYR VAL TYR GLN GLY LEU 0.40146 0.78125
Similar Ligands (3D)
Ligand no: 1; Ligand: ARG LEU TRP SER; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader) APoc FAQ
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