Receptor
PDB id Resolution Class Description Source Keywords
5THA 1.8 Å NON-ENZYME: OTHER GEMIN5 WD40 REPEATS IN COMPLEX WITH A GUANOSYL MOIETY HOMO SAPIENS WD40 REPEAT STRUCTURAL GENOMICS STRUCTURAL GENOMICS CONSORSGC RNA BINDING PROTEIN
Ref.: STRUCTURAL INSIGHTS INTO GEMIN5-GUIDED SELECTION OF PRE-SNRNAS FOR SNRNP ASSEMBLY. GENES DEV. V. 30 2376 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
UNX A:802;
A:814;
A:810;
A:808;
A:803;
A:811;
A:821;
A:815;
A:817;
A:818;
A:812;
A:805;
A:804;
A:813;
A:807;
A:809;
A:816;
A:819;
A:806;
A:820;
A:801;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data n/a n/a X n/a
GP3 A:822;
Valid;
Atoms found LESS than expected: % Diff = 0.529;
Kd = 140 uM
788.406 C20 H27 N10 O18 P3 c1nc2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5TEF 1.95 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF GEMIN5 WD40 REPEATS IN COMPLEX WITH M7G HOMO SAPIENS STRUCTURAL GENOMICS STRUCTURAL GENOMICS CONSORTIUM SGC SP
Ref.: STRUCTURAL INSIGHTS INTO GEMIN5-GUIDED SELECTION OF PRE-SNRNAS FOR SNRNP ASSEMBLY. GENES DEV. V. 30 2376 2016
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 5H1M - M7G C11 H19 N5 O11 P2 CN1CN(C2=C....
2 5THA Kd = 140 uM GP3 C20 H27 N10 O18 P3 c1nc2c(n1[....
3 5TEF Kd = 4 uM GTG C21 H30 N10 O18 P3 C[n+]1cn(c....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 5H1M - M7G C11 H19 N5 O11 P2 CN1CN(C2=C....
2 5THA Kd = 140 uM GP3 C20 H27 N10 O18 P3 c1nc2c(n1[....
3 5TEF Kd = 4 uM GTG C21 H30 N10 O18 P3 C[n+]1cn(c....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 5H1M - M7G C11 H19 N5 O11 P2 CN1CN(C2=C....
2 5THA Kd = 140 uM GP3 C20 H27 N10 O18 P3 c1nc2c(n1[....
3 5TEF Kd = 4 uM GTG C21 H30 N10 O18 P3 C[n+]1cn(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GP3; Similar ligands found: 148
No: Ligand ECFP6 Tc MDL keys Tc
1 GP3 1 1
2 GTP 0.921053 0.973684
3 GSP 0.897436 0.925
4 GDP 0.881579 0.973684
5 GNH 0.87013 0.961039
6 G1R 0.860759 0.961039
7 GCP 0.8375 0.948718
8 GNP 0.82716 0.948718
9 G 0.815789 0.960526
10 5GP 0.815789 0.960526
11 GTG 0.806818 0.962025
12 GMV 0.802469 0.948718
13 G2R 0.8 0.936709
14 G3A 0.797753 1
15 G5P 0.788889 1
16 GP2 0.765432 0.936709
17 GAV 0.764706 0.936709
18 Y9Z 0.755556 0.880952
19 GKE 0.755556 0.961538
20 GDD 0.755556 0.961538
21 GDC 0.755556 0.961538
22 GFB 0.747253 0.961538
23 GDR 0.747253 0.961538
24 GDP MG 0.746988 0.9
25 G2P 0.741176 0.936709
26 6CK 0.73913 0.9375
27 GDP BEF 0.738095 0.878049
28 GPG 0.730337 0.987013
29 GCP G 0.724138 0.911392
30 GKD 0.723404 0.961538
31 JB2 0.723404 0.961538
32 ALF 5GP 0.717647 0.86747
33 GPD 0.715789 0.925926
34 GDX 0.715789 0.974026
35 BEF GDP 0.712644 0.86747
36 GTP MG 0.712644 0.9
37 YGP 0.706522 0.902439
38 GDP ALF 0.688889 0.86747
39 GDP AF3 0.688889 0.86747
40 CAG 0.682692 0.904762
41 JB3 0.68 0.949367
42 0O2 0.673913 0.960526
43 NGD 0.673267 0.987013
44 GMP 0.671053 0.857143
45 2MD 0.653846 0.892857
46 G G 0.648936 0.961039
47 TPG 0.645455 0.842697
48 G3D 0.644444 0.960526
49 MGD 0.635514 0.892857
50 G4P 0.630435 0.960526
51 GDP 7MG 0.626263 0.936709
52 U2G 0.625 0.9375
53 FEG 0.625 0.903614
54 GH3 0.619565 0.948052
55 ZGP 0.619048 0.892857
56 CG2 0.613208 0.9375
57 PGD 0.612613 0.925926
58 MD1 0.612613 0.892857
59 3GP 0.6 0.922078
60 DGT 0.597826 0.9
61 DBG 0.587719 0.974359
62 FE9 0.575221 0.778947
63 6G0 0.569892 0.936709
64 G1G 0.566372 0.95
65 2GP 0.563218 0.935065
66 MGP 0.55914 0.936709
67 I2C FE2 CMO CMO 0.557522 0.811111
68 GPX 0.556701 0.922078
69 DGI 0.554348 0.9
70 G4M 0.552846 0.904762
71 IDP 0.549451 0.947368
72 U A G G 0.539823 0.961039
73 G A A A 0.530973 0.948718
74 GTA 0.528302 0.962025
75 BGO 0.522523 0.949367
76 G1R G1R 0.521008 0.949367
77 BA3 0.516854 0.921053
78 PGD O 0.516667 0.852273
79 P2G 0.516484 0.860759
80 AP5 0.511111 0.921053
81 B4P 0.511111 0.921053
82 GGM 0.508772 0.925926
83 DGP 0.505495 0.8875
84 DG 0.505495 0.8875
85 P1G 0.505376 0.85
86 G G U 0.5 0.961039
87 IMP 0.494505 0.934211
88 G2Q 0.490196 0.936709
89 AQP 0.489362 0.921053
90 5FA 0.489362 0.921053
91 GPC 0.483051 0.880952
92 G C 0.482759 0.901235
93 ATP 0.478723 0.921053
94 A2D 0.477778 0.921053
95 G7M 0.473118 0.924051
96 AGS 0.46875 0.875
97 SAP 0.46875 0.875
98 01G 0.46729 0.903614
99 A4P 0.46087 0.892857
100 G G G RPC 0.457627 0.9
101 APC G U 0.454545 0.911392
102 SGP 0.452632 0.807229
103 ITT 0.452632 0.87013
104 U G A 0.451128 0.91358
105 PCG 0.44898 0.934211
106 C2E 0.44898 0.947368
107 35G 0.44898 0.934211
108 UP5 0.447368 0.898734
109 G G G C 0.447154 0.9375
110 ADP 0.446809 0.921053
111 MGO 0.445545 0.843373
112 ANP 0.444444 0.897436
113 5GP 5GP 0.444444 0.909091
114 A G C C 0.443548 0.9125
115 AR6 0.443299 0.896104
116 APR 0.443299 0.896104
117 AN2 0.442105 0.909091
118 G U34 0.440678 0.890244
119 AD9 0.438776 0.897436
120 M33 0.4375 0.884615
121 ACP 0.43299 0.897436
122 ACQ 0.43 0.897436
123 G C C C 0.429688 0.925
124 A1R 0.428571 0.841463
125 7DT 0.428571 0.907895
126 T5A 0.428571 0.825581
127 DG DG 0.425926 0.890244
128 CA0 0.42268 0.897436
129 UCG 0.421875 0.9125
130 ATF 0.421569 0.886076
131 ADQ 0.415094 0.897436
132 MGQ 0.415094 0.961538
133 93A 0.412371 0.813953
134 A G U 0.411765 0.91358
135 6AD 0.411765 0.843373
136 A22 0.409524 0.934211
137 25L 0.409091 0.934211
138 ADX 0.408163 0.811765
139 AGO 0.406504 0.91358
140 AVV 0.40566 0.831325
141 50T 0.40404 0.884615
142 MGV 0.40367 0.914634
143 4TC 0.403361 0.876543
144 4AD 0.401869 0.875
145 RGT 0.401786 0.910256
146 CGP 0.401639 0.869048
147 JBT 0.4 0.8
148 PRX 0.4 0.82716
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5TEF; Ligand: GTG; Similar sites found: 2
This union binding pocket(no: 1) in the query (biounit: 5tef.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2OVR SER LEU ILE PRO TPO PRO ASP LYS 0.001474 0.44919 14.094
2 5MWJ EBU 0.0004891 0.42974 19.2878
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