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 X *
GP3 A:822;
Valid;
Atoms found LESS than expected: % Diff = 0;
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 1443 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 1205 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 1039 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: 155
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 9GM 0.82716 0.948718
9 GNP 0.82716 0.948718
10 G 0.815789 0.960526
11 5GP 0.815789 0.960526
12 GTG 0.806818 0.962025
13 GMV 0.802469 0.948718
14 G2R 0.8 0.936709
15 G3A 0.797753 1
16 G5P 0.788889 1
17 GP2 0.765432 0.936709
18 GAV 0.764706 0.936709
19 GDD 0.755556 0.961538
20 Y9Z 0.755556 0.880952
21 GDC 0.755556 0.961538
22 GKE 0.755556 0.961538
23 GFB 0.747253 0.961538
24 GDR 0.747253 0.961538
25 G2P 0.741176 0.936709
26 6CK 0.73913 0.9375
27 GPG 0.730337 0.987013
28 GKD 0.723404 0.961538
29 JB2 0.723404 0.961538
30 ALF 5GP 0.717647 0.86747
31 GPD 0.715789 0.925926
32 GDX 0.715789 0.974026
33 YGP 0.706522 0.902439
34 ALF GDP 0.688889 0.86747
35 GDP ALF 0.688889 0.86747
36 GDP AF3 0.688889 0.86747
37 CAG 0.682692 0.904762
38 JB3 0.68 0.949367
39 0O2 0.673913 0.960526
40 NGD 0.673267 0.987013
41 GMP 0.671053 0.857143
42 2MD 0.653846 0.892857
43 TPG 0.645455 0.842697
44 G3D 0.644444 0.960526
45 MGD 0.635514 0.892857
46 G4P 0.630435 0.960526
47 GDP 7MG 0.626263 0.936709
48 FEG 0.625 0.903614
49 U2G 0.625 0.9375
50 G G 0.622449 0.974026
51 GH3 0.619565 0.948052
52 ZGP 0.619048 0.892857
53 CG2 0.613208 0.9375
54 MD1 0.612613 0.892857
55 PGD 0.612613 0.925926
56 3GP 0.6 0.922078
57 DGT 0.597826 0.9
58 DBG 0.587719 0.974359
59 FE9 0.575221 0.778947
60 6G0 0.569892 0.936709
61 G1G 0.566372 0.95
62 GCP G 0.565657 0.897436
63 2GP 0.563218 0.935065
64 MGP 0.55914 0.936709
65 GPX 0.556701 0.922078
66 DGI 0.554348 0.9
67 G4M 0.552846 0.904762
68 IDP 0.549451 0.947368
69 A G 0.544643 0.961039
70 R7I 0.542553 0.922078
71 R5I 0.542553 0.922078
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 AKW 0.522523 0.914634
76 BGO 0.522523 0.949367
77 G1R G1R 0.521008 0.949367
78 BA3 0.516854 0.921053
79 PGD O 0.516667 0.852273
80 P2G 0.516484 0.860759
81 AP5 0.511111 0.921053
82 B4P 0.511111 0.921053
83 GGM 0.508772 0.925926
84 DGP 0.505495 0.8875
85 DG 0.505495 0.8875
86 P1G 0.505376 0.85
87 IMP 0.494505 0.934211
88 G U 0.491228 0.901235
89 G2Q 0.490196 0.936709
90 AQP 0.489362 0.921053
91 5FA 0.489362 0.921053
92 GPC 0.483051 0.880952
93 G C 0.482759 0.901235
94 ATP 0.478723 0.921053
95 HEJ 0.478723 0.921053
96 A2D 0.477778 0.921053
97 G7M 0.473118 0.924051
98 SAP 0.46875 0.875
99 AGS 0.46875 0.875
100 01G 0.46729 0.903614
101 HFD 0.463918 0.875
102 A4P 0.46087 0.892857
103 G G G RPC 0.457627 0.9
104 AT4 0.457447 0.886076
105 APC G U 0.454545 0.911392
106 ITT 0.452632 0.87013
107 SGP 0.452632 0.807229
108 C2E 0.44898 0.947368
109 PCG 0.44898 0.934211
110 35G 0.44898 0.934211
111 UP5 0.447368 0.898734
112 G G G C 0.447154 0.9375
113 ADP 0.446809 0.921053
114 MGO 0.445545 0.843373
115 ANP 0.444444 0.897436
116 5GP 5GP 0.444444 0.909091
117 A G C C 0.443548 0.9125
118 AR6 0.443299 0.896104
119 APR 0.443299 0.896104
120 AN2 0.442105 0.909091
121 G U34 0.440678 0.890244
122 PRT 0.440367 0.934211
123 AD9 0.438776 0.897436
124 M33 0.4375 0.884615
125 ACP 0.43299 0.897436
126 6YZ 0.431373 0.897436
127 ACQ 0.43 0.897436
128 G C C C 0.429688 0.925
129 T5A 0.428571 0.825581
130 7DT 0.428571 0.907895
131 A1R 0.428571 0.841463
132 DG DG 0.425926 0.890244
133 CA0 0.42268 0.897436
134 UCG 0.421875 0.9125
135 ATF 0.421569 0.886076
136 ADQ 0.415094 0.897436
137 A3R 0.415094 0.841463
138 MGQ 0.415094 0.961538
139 C1Z 0.412844 0.960526
140 93A 0.412371 0.813953
141 6AD 0.411765 0.843373
142 A G U 0.411765 0.91358
143 A22 0.409524 0.934211
144 25L 0.409091 0.934211
145 ADX 0.408163 0.811765
146 AGO 0.406504 0.91358
147 AVV 0.40566 0.831325
148 50T 0.40404 0.884615
149 MGV 0.40367 0.914634
150 4TC 0.403361 0.876543
151 4AD 0.401869 0.875
152 RGT 0.401786 0.910256
153 CGP 0.401639 0.869048
154 PRX 0.4 0.82716
155 JBT 0.4 0.8
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5TEF; Ligand: GTG; 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: 5tef.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback