Receptor
PDB id Resolution Class Description Source Keywords
4TMZ 2.28 Å NON-ENZYME: OTHER TRANSLATION INITIATION FACTOR EIF5B (517-858) FROM C. THERMO BOUND TO GTPGAMMAS AND POTASSIUM CHAETOMIUM THERMOPHILUM TRANSLATION TRANSLATION FACTOR GTPASE
Ref.: A MONOVALENT CATION ACTS AS STRUCTURAL AND CATALYTI COFACTOR IN TRANSLATIONAL GTPASES. EMBO J. V. 33 2547 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
K A:903;
B:903;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
39.098 K [K+]
CL B:906;
B:905;
 Invalid;
Invalid;
 none;
none;
 submit data
35.453 Cl [Cl-]
MG A:902;
B:902;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
24.305 Mg [Mg+2...
GOL B:904;
 Invalid;
 none;
 submit data
92.094 C3 H8 O3 C(C(C...
GSP B:901;
A:901;
 Valid;
Valid;
 none;
none;
 Kd = 0.92 uM
539.246 C10 H16 N5 O13 P3 S c1nc2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4TMZ 2.28 Å NON-ENZYME: OTHER TRANSLATION INITIATION FACTOR EIF5B (517-858) FROM C. THERMO BOUND TO GTPGAMMAS AND POTASSIUM CHAETOMIUM THERMOPHILUM TRANSLATION TRANSLATION FACTOR GTPASE
Ref.: A MONOVALENT CATION ACTS AS STRUCTURAL AND CATALYTI COFACTOR IN TRANSLATIONAL GTPASES. EMBO J. V. 33 2547 2014
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 4TMX - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
2 4TMZ Kd = 0.92 uM GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
3 4TMV - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
4 4TMT - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
5 4TMW Kd = 4.1 uM GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 4NCN - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
2 4NCL - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 4TMX - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
4 4TMZ Kd = 0.92 uM GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
5 4TMV - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
6 4TMT - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
7 4TMW Kd = 4.1 uM GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 4NCN - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
2 4NCL - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 4TMX - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
4 4TMZ Kd = 0.92 uM GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
5 4TMV - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
6 4TMT - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
7 4TMW Kd = 4.1 uM GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GSP; Similar ligands found: 139
No: Ligand ECFP6 Tc MDL keys Tc
1 GSP 1 1
2 GP3 0.897436 0.925
3 GTP 0.853659 0.948718
4 GNH 0.829268 0.936709
5 GDP 0.817073 0.948718
6 G1R 0.8 0.936709
7 GCP 0.77907 0.925
8 GNP 0.770115 0.925
9 9GM 0.770115 0.925
10 GMV 0.767442 0.925
11 G 0.756098 0.935897
12 5GP 0.756098 0.935897
13 G2R 0.747253 0.91358
14 GDD 0.744681 0.91358
15 GDC 0.744681 0.91358
16 GKE 0.744681 0.91358
17 GPG 0.73913 0.91358
18 GTG 0.736842 0.891566
19 G3A 0.729167 0.925
20 G5P 0.721649 0.925
21 GDR 0.71875 0.91358
22 GFB 0.71875 0.91358
23 GAV 0.714286 0.987179
24 GP2 0.712644 0.91358
25 6CK 0.71134 0.891566
26 Y9Z 0.708333 0.860465
27 JB2 0.69697 0.91358
28 GKD 0.69697 0.91358
29 G2P 0.692308 0.91358
30 GDX 0.69 0.925
31 GPD 0.69 0.880952
32 ALF 5GP 0.67033 0.847059
33 0O2 0.666667 0.935897
34 YGP 0.663265 0.858824
35 JB3 0.657143 0.902439
36 GDP ALF 0.645833 0.847059
37 GDP AF3 0.645833 0.847059
38 ALF GDP 0.645833 0.847059
39 GMP 0.641975 0.835443
40 G3D 0.638298 0.935897
41 NGD 0.635514 0.91358
42 2MD 0.633027 0.894118
43 CAG 0.630631 0.840909
44 G4P 0.625 0.935897
45 FEG 0.62037 0.83908
46 U2G 0.62037 0.891566
47 G G 0.617647 0.901235
48 MGD 0.616071 0.894118
49 ZGP 0.614679 0.872093
50 CG2 0.609091 0.891566
51 TPG 0.598291 0.804348
52 3GP 0.595506 0.898734
53 GDP 7MG 0.590476 0.86747
54 GH3 0.581633 0.924051
55 PGD 0.581197 0.926829
56 MD1 0.581197 0.894118
57 2GP 0.577778 0.911392
58 GCP G 0.563107 0.875
59 DGT 0.561224 0.878049
60 DBG 0.558333 0.902439
61 G1G 0.550847 0.880952
62 AGS 0.547368 0.924051
63 SAP 0.547368 0.924051
64 FE9 0.546219 0.8
65 A G 0.543103 0.888889
66 G4M 0.539062 0.840909
67 U A G G 0.538462 0.888889
68 G A A A 0.529915 0.878049
69 MGP 0.525253 0.91358
70 GPX 0.524272 0.898734
71 BGO 0.521739 0.879518
72 DGI 0.520408 0.878049
73 6G0 0.52 0.91358
74 IDP 0.515464 0.923077
75 R7I 0.51 0.898734
76 R5I 0.51 0.898734
77 GGM 0.508475 0.858824
78 G1R G1R 0.508065 0.879518
79 PGD O 0.504 0.875
80 AKW 0.495726 0.915663
81 G U 0.491525 0.857143
82 GTA 0.486726 0.891566
83 P2G 0.484536 0.839506
84 GPC 0.483607 0.83908
85 G C 0.483333 0.857143
86 P1G 0.474747 0.829268
87 DG 0.474227 0.865854
88 DGP 0.474227 0.865854
89 BA3 0.46875 0.85
90 IMP 0.463918 0.910256
91 B4P 0.463918 0.85
92 AP5 0.463918 0.85
93 G2Q 0.462963 0.91358
94 G G G RPC 0.459016 0.833333
95 APC G U 0.456 0.843373
96 ATP 0.45 0.873418
97 HEJ 0.45 0.873418
98 G G G C 0.448819 0.869048
99 A2D 0.447917 0.85
100 5FA 0.445545 0.873418
101 AQP 0.445545 0.873418
102 A G C C 0.445312 0.86747
103 G7M 0.444444 0.901235
104 G U34 0.442623 0.847059
105 01G 0.442478 0.860465
106 ITT 0.44 0.825
107 SGP 0.44 0.876543
108 HFD 0.436893 0.831325
109 G C C C 0.431818 0.879518
110 AT4 0.43 0.911392
111 AN2 0.43 0.8625
112 DG DG 0.428571 0.825581
113 A4P 0.42623 0.829545
114 UCG 0.424242 0.86747
115 PCG 0.423077 0.886076
116 C2E 0.423077 0.875
117 35G 0.423077 0.886076
118 MGO 0.420561 0.823529
119 ADP 0.42 0.873418
120 ANP 0.419048 0.851852
121 5GP 5GP 0.419048 0.839506
122 ADQ 0.418182 0.829268
123 7DT 0.417476 0.860759
124 AR6 0.417476 0.85
125 APR 0.417476 0.85
126 PRT 0.417391 0.910256
127 C1Z 0.415929 0.935897
128 A G U 0.414286 0.847059
129 AD9 0.413462 0.851852
130 UP5 0.413223 0.831325
131 A22 0.412844 0.8625
132 25L 0.412281 0.8625
133 M33 0.411765 0.839506
134 JBT 0.410405 0.783505
135 ACP 0.407767 0.851852
136 6YZ 0.407407 0.851852
137 ACQ 0.40566 0.851852
138 A1R 0.405405 0.8
139 A G U U 0.4 0.847059
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4TMZ; Ligand: GSP; Similar sites found with APoc: 97
This union binding pocket(no: 1) in the query (biounit: 4tmz.bio2) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 3CX8 GSP 3.5503
2 1O3Y GTP 3.61446
3 1YZN GNP 4.32432
4 3RAB GNP 4.73373
5 2XTZ GSP 5.7971
6 1Z06 GNP 5.82011
7 1OIX GDP 6.28272
8 1KSH GDP 6.45161
9 2HV8 GTP 6.97674
10 4BAS GNP 7.03518
11 2D7C GTP 7.18563
12 2FH5 GTP 7.47664
13 2GJ8 ALF GDP 8.13953
14 3BC1 GNP 8.71795
15 1R4A GNP 9.69697
16 2A5F GTP 10.8808
17 5DIF GNP 11.8143
18 5DHF GNP 11.8143
19 6CIT GNP 11.8143
20 5UWP GNP 11.8143
21 5UWQ GNP 11.8143
22 5UWJ GNP 11.8143
23 5UWU GNP 11.8143
24 5UWI GNP 11.8143
25 5UWR GNP 11.8143
26 5UWW GNP 11.8143
27 5UWH GNP 11.8143
28 5UWS GNP 11.8143
29 3M1I GTP 12.7854
30 1YZQ GNP 12.9412
31 5BXQ GDP 12.963
32 4HAT GNP 12.963
33 1IBR GNP 12.963
34 2FFQ GSP 13.4503
35 5OCG GNP 13.7566
36 4M9Q GNP 14.5374
37 5UWO GNP 15
38 2C5L GTP 15.0289
39 4K81 GTP 15.2047
40 2BVN GNP 15.3623
41 5O2T GSP 15.3846
42 6D5E GNP 15.5689
43 6D5J GNP 15.5689
44 6D59 GNP 15.5689
45 6BVI GNP 15.5689
46 1LFD GNP 15.5689
47 6BVL GNP 15.5689
48 6D55 GNP 15.5689
49 6D56 GNP 15.5689
50 6BVJ GNP 15.5689
51 6D5G GNP 15.5689
52 6D5H GNP 15.5689
53 6BVK GNP 15.5689
54 6D5L GNP 15.5689
55 6BVM GNP 15.5689
56 6D5V GNP 15.5689
57 6D5M GNP 15.5689
58 6FA4 GNP 15.6069
59 4RD0 GDP 15.6522
60 3DDC GNP 15.6627
61 2UZI GTP 15.6627
62 1NVV GNP 15.6627
63 5WLB GNP 15.6627
64 3QBT GNP 15.7143
65 1WA5 GTP 15.9091
66 1ZC3 GNP 16.5714
67 2C78 GNP 16.8116
68 2C77 GNP 16.8116
69 1UPT GTP 16.9591
70 1M2O GNP 17.8947
71 1WF3 GNP 17.9402
72 4HDO GNP 17.9641
73 1GUA GNP 17.9641
74 1J2J GTP 20
75 1CS4 GSP 20.4444
76 2GCO GNP 20.8955
77 3MJH GTP 21.4286
78 5UWT GNP 21.7391
79 1E96 GTP 21.875
80 3SBD GNP 22.9947
81 1MH1 GNP 23.1183
82 2W2X GSP 23.2432
83 2FJU GSP 24.1573
84 1CXZ GSP 24.7253
85 1KMQ GNP 25
86 5XC5 GTP 25.5682
87 1TX4 ALF GDP 25.9887
88 3WXM GTP 26.3982
89 1NF3 GNP 27.1795
90 5UPK GNP 27.5676
91 1Z0K GTP 29.0698
92 2BME GNP 29.5699
93 1TU3 GNP 31.6456
94 1EK0 GNP 31.7647
95 1VG8 GNP 33.8164
96 1Z0J GTP 36.4706
97 1YVD GNP 37.2781
Pocket No.: 2; Query (leader) PDB : 4TMZ; Ligand: GSP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4tmz.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
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