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 = 0.529;
 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 1610 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 1331 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 1144 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 (2D)
Ligand no: 1; Ligand: GP3; Similar ligands found: 154
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 5GP 0.815789 0.960526
11 G 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 Y9Z 0.755556 0.880952
20 GKE 0.755556 0.961538
21 GDC 0.755556 0.961538
22 GDD 0.755556 0.961538
23 GDR 0.747253 0.961538
24 GFB 0.747253 0.961538
25 G2P 0.741176 0.936709
26 6CK 0.73913 0.9375
27 GPG 0.730337 0.987013
28 GDP BEF 0.729412 0.911392
29 GKD 0.723404 0.961538
30 JB2 0.723404 0.961538
31 GTP MG 0.72093 0.935065
32 ALF 5GP 0.717647 0.86747
33 GPD 0.715789 0.925926
34 GDX 0.715789 0.974026
35 YGP 0.706522 0.902439
36 GDP AF3 0.688889 0.86747
37 GDP ALF 0.688889 0.86747
38 CAG 0.682692 0.904762
39 JB3 0.68 0.949367
40 0O2 0.673913 0.960526
41 NGD 0.673267 0.987013
42 GMP 0.671053 0.857143
43 2MD 0.653846 0.892857
44 TPG 0.645455 0.842697
45 G3D 0.644444 0.960526
46 KB7 0.636364 0.807229
47 MGD 0.635514 0.892857
48 G4P 0.630435 0.960526
49 GDP 7MG 0.626263 0.936709
50 FEG 0.625 0.903614
51 U2G 0.625 0.9375
52 GH3 0.619565 0.948052
53 ZGP 0.619048 0.892857
54 CG2 0.613208 0.9375
55 MD1 0.612613 0.892857
56 PGD 0.612613 0.925926
57 3GP 0.6 0.922078
58 DGT 0.597826 0.9
59 DBG 0.587719 0.974359
60 KBD 0.587629 0.851852
61 QBQ 0.582418 0.960526
62 FE9 0.575221 0.778947
63 6G0 0.569892 0.936709
64 G1G 0.566372 0.95
65 KBJ 0.564356 0.821429
66 2GP 0.563218 0.935065
67 MGP 0.55914 0.936709
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 I2C FE2 CMO CMO 0.547826 0.811111
73 R5I 0.542553 0.922078
74 R7I 0.542553 0.922078
75 GTA 0.528302 0.962025
76 AKW 0.522523 0.914634
77 BGO 0.522523 0.949367
78 CZF 0.521277 0.909091
79 G1R G1R 0.521008 0.949367
80 BA3 0.516854 0.921053
81 PGD O 0.516667 0.852273
82 P2G 0.516484 0.860759
83 B4P 0.511111 0.921053
84 AP5 0.511111 0.921053
85 GGM 0.508772 0.925926
86 DG 0.505495 0.8875
87 DGP 0.505495 0.8875
88 P1G 0.505376 0.85
89 IMP 0.494505 0.934211
90 G2Q 0.490196 0.936709
91 AQP 0.489362 0.921053
92 5FA 0.489362 0.921053
93 GPC 0.483051 0.880952
94 G C 0.482759 0.901235
95 ATP 0.478723 0.921053
96 HEJ 0.478723 0.921053
97 A2D 0.477778 0.921053
98 G7M 0.473118 0.924051
99 AGS 0.46875 0.875
100 01G 0.46729 0.903614
101 HFD 0.463918 0.875
102 JSQ 0.463918 0.875
103 A4P 0.46087 0.892857
104 AT4 0.457447 0.886076
105 APC G U 0.455285 0.911392
106 SGP 0.452632 0.807229
107 ITT 0.452632 0.87013
108 35G 0.44898 0.934211
109 C2E 0.44898 0.947368
110 PCG 0.44898 0.934211
111 UP5 0.447368 0.898734
112 ADP 0.446809 0.921053
113 MGO 0.445545 0.843373
114 5GP 5GP 0.444444 0.909091
115 ANP 0.444444 0.897436
116 AR6 0.443299 0.896104
117 APR 0.443299 0.896104
118 AN2 0.442105 0.909091
119 PRT 0.440367 0.934211
120 AD9 0.438776 0.897436
121 M33 0.4375 0.884615
122 ACP 0.43299 0.897436
123 6YZ 0.431373 0.897436
124 GZ0 0.431034 0.949367
125 ACQ 0.43 0.897436
126 A1R 0.428571 0.841463
127 7DT 0.428571 0.907895
128 T5A 0.428571 0.825581
129 M7G A2M G 0.425676 0.831461
130 CA0 0.42268 0.897436
131 UCG 0.421875 0.9125
132 ATF 0.421569 0.886076
133 NYZ 0.42 0.9125
134 KG4 0.418367 0.897436
135 ADQ 0.415094 0.897436
136 A3R 0.415094 0.841463
137 MGQ 0.415094 0.961538
138 HQG 0.413462 0.909091
139 C1Z 0.412844 0.960526
140 93A 0.412371 0.813953
141 6AD 0.411765 0.843373
142 A22 0.409524 0.934211
143 25L 0.409091 0.934211
144 ADX 0.408163 0.811765
145 AGO 0.406504 0.91358
146 AVV 0.40566 0.831325
147 50T 0.40404 0.884615
148 MGV 0.40367 0.914634
149 4TC 0.403361 0.876543
150 4AD 0.401869 0.875
151 RGT 0.401786 0.910256
152 CGP 0.401639 0.869048
153 PRX 0.4 0.82716
154 JBT 0.4 0.8
Similar Ligands (3D)
Ligand no: 1; Ligand: GP3; 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 : 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
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