Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
UNX A:814;
A:810;
A:822;
A:808;
A:811;
A:821;
A:815;
A:817;
A:818;
A:812;
A:823;
A:805;
A:813;
A:807;
A:809;
A:816;
A:819;
A:806;
A:820;
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;
submit data n/a n/a X n/a
GTG A:801;
Valid;
Atoms found LESS than expected: % Diff = 0.365;
Kd = 4 uM
803.44 C21 H30 N10 O18 P3 C[n+]...
GOL A:802;
A:803;
A:804;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
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: GTG; Similar ligands found: 104
No: Ligand ECFP6 Tc MDL keys Tc
1 GTG 1 1
2 GP3 0.806818 0.962025
3 GDP 7MG 0.79798 0.974684
4 6G0 0.752688 0.974684
5 GTP 0.752688 0.936709
6 MGP 0.741935 0.974684
7 GSP 0.736842 0.891566
8 GDP 0.72043 0.936709
9 GNH 0.712766 0.925
10 G1R 0.708333 0.925
11 GCP 0.690722 0.91358
12 GTA 0.688679 1
13 GNP 0.683673 0.91358
14 G3A 0.669811 0.962025
15 G2R 0.666667 0.902439
16 G 0.666667 0.924051
17 5GP 0.666667 0.924051
18 G5P 0.663551 0.962025
19 GMV 0.663265 0.91358
20 G7M 0.655914 0.962025
21 Y9Z 0.650943 0.872093
22 GFB 0.64486 0.95
23 GDR 0.64486 0.95
24 GAV 0.637255 0.902439
25 GDC 0.635514 0.925926
26 GKE 0.635514 0.925926
27 GDD 0.635514 0.925926
28 GP2 0.632653 0.902439
29 GKD 0.627273 0.925926
30 JB2 0.627273 0.95
31 6CK 0.623853 0.903614
32 GPD 0.621622 0.915663
33 GDP MG 0.62 0.890244
34 G2P 0.617647 0.902439
35 NGD 0.617391 0.974684
36 GDP BEF 0.613861 0.869048
37 GPG 0.613208 0.95
38 YGP 0.611111 0.892857
39 GDX 0.607143 0.9375
40 GCP G 0.605769 0.901235
41 CAG 0.6 0.917647
42 ALF 5GP 0.598039 0.858824
43 GTP MG 0.596154 0.890244
44 BEF GDP 0.596154 0.858824
45 JB3 0.594828 0.938272
46 GDP AF3 0.579439 0.858824
47 GDP ALF 0.579439 0.858824
48 TPG 0.571429 0.855556
49 0O2 0.568807 0.924051
50 2MD 0.561983 0.862069
51 FEG 0.55 0.894118
52 G G 0.54955 0.949367
53 MGD 0.548387 0.862069
54 GMP 0.548387 0.825
55 ZGP 0.545455 0.883721
56 MD1 0.543307 0.862069
57 G3D 0.542056 0.924051
58 CG2 0.540984 0.903614
59 MG7 0.537634 0.8625
60 U2G 0.53719 0.903614
61 G4P 0.53211 0.924051
62 PGD 0.53125 0.892857
63 G1G 0.527559 0.9875
64 DBG 0.523077 0.938272
65 GH3 0.522936 0.9125
66 FE9 0.511628 0.791667
67 DGT 0.504587 0.86747
68 3GP 0.5 0.8875
69 G4M 0.496403 0.895349
70 I2C FE2 CMO CMO 0.496124 0.824176
71 GPX 0.486726 0.8875
72 BGO 0.47619 0.9625
73 2GP 0.471154 0.9
74 U A G G 0.469231 0.949367
75 MGO 0.468468 0.879518
76 DGI 0.46789 0.86747
77 G1R G1R 0.466667 0.938272
78 GGM 0.465116 0.939024
79 IDP 0.462963 0.911392
80 G A A A 0.461538 0.9375
81 PGD O 0.452555 0.844444
82 G G U 0.443548 0.949367
83 MGQ 0.439655 0.95
84 P2G 0.435185 0.829268
85 BA3 0.433962 0.886076
86 GPC 0.432836 0.850575
87 B4P 0.429907 0.886076
88 AP5 0.429907 0.886076
89 MGV 0.428571 0.904762
90 P1G 0.427273 0.819277
91 DGP 0.425926 0.855422
92 DG 0.425926 0.855422
93 G C 0.421053 0.891566
94 G2Q 0.420168 0.902439
95 IMP 0.416667 0.898734
96 01G 0.414634 0.872093
97 5FA 0.414414 0.886076
98 AQP 0.414414 0.886076
99 A4P 0.412214 0.862069
100 ATP 0.405405 0.886076
101 G G G C 0.402878 0.926829
102 A2D 0.401869 0.886076
103 G G G RPC 0.4 0.890244
104 U G A 0.4 0.903614
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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