Receptor
PDB id Resolution Class Description Source Keywords
5JBQ 2.01 Å NON-ENZYME: OTHER EF-TU (ESCHERICHIA COLI) IN COMPLEX WITH THIOMURACIN ANALOG ESCHERICHIA COLI (STRAIN K12) NATURAL PRODUCT INHIBITOR ELONGATION FACTOR RNA BINDING PRANTIMICROBIAL COMPLEX
Ref.: ANTIBACTERIAL AND SOLUBILITY OPTIMIZATION OF THIOMU J.MED.CHEM. V. 59 6920 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:404;
Invalid;
none;
submit data
96.063 O4 S [O-]S...
GDP A:401;
Valid;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
MG A:402;
A:403;
Invalid;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5JBQ 2.01 Å NON-ENZYME: OTHER EF-TU (ESCHERICHIA COLI) IN COMPLEX WITH THIOMURACIN ANALOG ESCHERICHIA COLI (STRAIN K12) NATURAL PRODUCT INHIBITOR ELONGATION FACTOR RNA BINDING PRANTIMICROBIAL COMPLEX
Ref.: ANTIBACTERIAL AND SOLUBILITY OPTIMIZATION OF THIOMU J.MED.CHEM. V. 59 6920 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1579 families.
1 5JBQ - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1312 families.
1 5JBQ - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1130 families.
1 5JBQ - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GDP; Similar ligands found: 168
No: Ligand ECFP6 Tc MDL keys Tc
1 GDP 1 1
2 GTP 0.909091 1
3 GP3 0.881579 0.973684
4 GNH 0.858974 0.986667
5 GNP 0.839506 0.973684
6 9GM 0.839506 0.973684
7 G 0.828947 0.986486
8 5GP 0.828947 0.986486
9 G1R 0.82716 0.986667
10 GCP 0.82716 0.973684
11 GSP 0.817073 0.948718
12 GAV 0.797619 0.961039
13 GMV 0.792683 0.973684
14 G2P 0.77381 0.961039
15 G2R 0.770115 0.961039
16 GP2 0.756098 0.961039
17 GKE 0.747253 0.961039
18 GDD 0.747253 0.961039
19 GDC 0.747253 0.961039
20 GPG 0.741573 0.961039
21 G3D 0.732558 0.986486
22 ALF 5GP 0.729412 0.888889
23 Y9Z 0.728261 0.902439
24 G5P 0.723404 0.973684
25 GDR 0.72043 0.961039
26 GFB 0.72043 0.961039
27 GTG 0.72043 0.936709
28 G4P 0.715909 0.986486
29 6CK 0.712766 0.936709
30 G3A 0.712766 0.973684
31 GDP AF3 0.7 0.888889
32 GDP ALF 0.7 0.888889
33 ALF GDP 0.7 0.888889
34 YGP 0.698925 0.901235
35 JB2 0.697917 0.961039
36 GKD 0.697917 0.961039
37 GPD 0.690722 0.925
38 GDX 0.690722 0.973684
39 GMP 0.684211 0.88
40 0O2 0.666667 0.986486
41 JB3 0.656863 0.948718
42 NGD 0.650485 0.961039
43 GDP 7MG 0.636364 0.911392
44 DGI 0.636364 0.923077
45 U2G 0.634615 0.936709
46 GPX 0.634409 0.946667
47 G G 0.632653 0.948052
48 IDP 0.632184 0.972973
49 2MD 0.632075 0.891566
50 CAG 0.62963 0.880952
51 KB7 0.629214 0.82716
52 CG2 0.622642 0.936709
53 FEG 0.619048 0.879518
54 MGD 0.614679 0.891566
55 ZGP 0.613208 0.869048
56 GH3 0.612903 0.973333
57 3GP 0.611765 0.946667
58 MD1 0.607143 0.891566
59 PGD 0.59292 0.925
60 DGT 0.591398 0.923077
61 BGO 0.588785 0.924051
62 TPG 0.582609 0.840909
63 DBG 0.582609 0.948718
64 KBD 0.581633 0.82716
65 2GP 0.574713 0.96
66 FE9 0.570175 0.776596
67 GCP G 0.56 0.921053
68 KBJ 0.558824 0.797619
69 G A A A 0.553571 0.923077
70 A G 0.553571 0.935065
71 MGP 0.553191 0.961039
72 U A G G 0.548673 0.935065
73 G4M 0.548387 0.880952
74 6G0 0.547368 0.961039
75 G1R G1R 0.542373 0.924051
76 P2G 0.527473 0.883117
77 PGD O 0.525 0.850575
78 ADP 0.522222 0.92
79 R5I 0.520833 0.946667
80 R7I 0.520833 0.946667
81 GGM 0.517544 0.901235
82 DGP 0.516484 0.910256
83 DG 0.516484 0.910256
84 P1G 0.516129 0.871795
85 G U 0.513274 0.9
86 G1G 0.508475 0.925
87 IMP 0.505495 0.959459
88 AKW 0.504425 0.890244
89 G C 0.504348 0.9
90 GPC 0.491525 0.879518
91 G7M 0.483871 0.948052
92 6AD 0.479592 0.841463
93 ATP 0.473684 0.92
94 HEJ 0.473684 0.92
95 G2Q 0.471154 0.961039
96 AQP 0.46875 0.92
97 5FA 0.46875 0.92
98 GTA 0.468468 0.936709
99 7DD 0.468085 0.906667
100 G G G RPC 0.466102 0.875
101 SGP 0.463158 0.82716
102 01G 0.462963 0.902439
103 JSQ 0.459184 0.873418
104 HFD 0.459184 0.873418
105 AP5 0.457447 0.894737
106 B4P 0.457447 0.894737
107 A2D 0.456522 0.894737
108 6YZ 0.455446 0.896104
109 G G G C 0.455285 0.9125
110 ANP 0.454545 0.896104
111 5GP 5GP 0.454545 0.883117
112 ACQ 0.454545 0.896104
113 AT4 0.452632 0.884615
114 A G C C 0.451613 0.911392
115 APC G U 0.45082 0.886076
116 PRT 0.449541 0.959459
117 G U34 0.449153 0.888889
118 DG DG 0.448598 0.865854
119 ITT 0.447917 0.868421
120 BA3 0.446809 0.894737
121 35G 0.444444 0.933333
122 PCG 0.444444 0.933333
123 C2E 0.444444 0.921053
124 MGO 0.441176 0.864198
125 AN2 0.4375 0.907895
126 G C C C 0.4375 0.924051
127 NO7 0.436893 0.860759
128 M33 0.43299 0.883117
129 UCG 0.429688 0.911392
130 A G U 0.42963 0.888889
131 ACP 0.428571 0.896104
132 MGQ 0.424528 0.935897
133 7DT 0.424242 0.906667
134 APR 0.424242 0.894737
135 AR6 0.424242 0.894737
136 93A 0.42268 0.833333
137 A4P 0.420168 0.869048
138 AGS 0.42 0.873418
139 AD9 0.42 0.896104
140 G8D 0.42 0.875
141 SAP 0.42 0.873418
142 CA0 0.418367 0.896104
143 ATF 0.417476 0.884615
144 AGO 0.414634 0.888889
145 A G U U 0.414286 0.888889
146 KG4 0.414141 0.896104
147 NIA 0.413043 0.82716
148 MGV 0.412844 0.890244
149 T99 0.411765 0.884615
150 TAT 0.411765 0.884615
151 A1R 0.411215 0.839506
152 ADQ 0.411215 0.871795
153 RGT 0.410714 0.909091
154 CGP 0.409836 0.86747
155 HQG 0.409524 0.907895
156 C1Z 0.409091 0.986486
157 AMP 0.408602 0.893333
158 A 0.408602 0.893333
159 UP5 0.40678 0.873418
160 C2R 0.406593 0.906667
161 AMZ 0.406593 0.918919
162 JBT 0.405882 0.778947
163 A22 0.40566 0.907895
164 25L 0.405405 0.907895
165 ADX 0.40404 0.809524
166 8OD 0.401961 0.946667
167 4TC 0.4 0.851852
168 50T 0.4 0.883117
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5JBQ; Ligand: GDP; Similar sites found with APoc: 236
This union binding pocket(no: 1) in the query (biounit: 5jbq.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 1Z0F GDP 1.67598
2 1TAD GDP 1.85185
3 1TAD ALF 1.85185
4 1OIV GDP 2.09424
5 1OIV GDP 2.09424
6 1MH1 GNP 2.15054
7 5HCN GCP 2.29885
8 2D7C GTP 2.39521
9 2QTV GNP 2.79188
10 2FFQ GSP 2.92398
11 3MJH GTP 2.97619
12 3Q72 GNP 3.01205
13 3Q72 GNP 3.01205
14 1GOT GDP 3.04569
15 2XTZ GSP 3.10734
16 2FH5 GTP 3.24324
17 2FH5 GTP 3.24324
18 5UQW GDP 3.7037
19 4D0N GDP 3.78378
20 1TU3 GNP 3.79747
21 1TU3 GNP 3.79747
22 1TU3 GNP 3.79747
23 1MR3 G3D 3.8674
24 5M04 GDP 3.88889
25 2AWN ADP 4.06091
26 3Q85 GNP 4.14201
27 3Q85 GNP 4.14201
28 4HDO GNP 4.19162
29 1O3Y GTP 4.21687
30 1J2J GTP 4.21687
31 3QBT GNP 4.28571
32 3QBT GNP 4.28571
33 3RWO GDP 4.32432
34 3RWO GDP 4.32432
35 3RWO GDP 4.32432
36 3RWO GDP 4.32432
37 1RYH GNP 4.4335
38 4NON GDP 4.61538
39 1Z08 GNP 4.70588
40 1Z08 GNP 4.70588
41 1Z08 GNP 4.70588
42 1Z08 GNP 4.70588
43 1Z08 GNP 4.70588
44 1VG8 GNP 4.83092
45 1VG8 GNP 4.83092
46 1VG8 GNP 4.83092
47 1RE0 GDP 4.97738
48 4M9Q GNP 5.07614
49 5KUT GDP 5.29101
50 1VG9 GDP 5.40541
51 1VG9 GDP 5.40541
52 1VG9 GDP 5.40541
53 1VG1 GDP 5.40541
54 1VG9 GDP 5.40541
55 3T1O GDP 5.55556
56 3T1O GDP 5.55556
57 6CRK GDP 5.58376
58 1GP2 GDP 5.58376
59 5KDO GDP 5.58376
60 6BSX GDP 5.61798
61 6BSX E7S 5.61798
62 6BSX GDP 5.61798
63 5Z2M GTP 5.68182
64 1YRB GDP 5.72519
65 1YRB GDP 5.72519
66 6FA3 GNP 5.81395
67 6FA3 GNP 5.81395
68 6FA3 GNP 5.81395
69 2BME GNP 5.91398
70 2BME GNP 5.91398
71 1BH2 GSP 6.03175
72 1TQ4 GDP 6.05327
73 1M2O GNP 6.31579
74 1M2O GNP 6.31579
75 1M2O GNP 6.31579
76 4K81 GTP 6.43275
77 4K81 GTP 6.43275
78 4V0K GDP 6.50888
79 6D5J GNP 6.58683
80 6D5E GNP 6.58683
81 6BVJ GNP 6.58683
82 6BVL GNP 6.58683
83 6D5H GNP 6.58683
84 6BVK GNP 6.58683
85 6D5G GNP 6.58683
86 6D5W GNP 6.58683
87 2J0V GDP 6.60377
88 2J0V GDP 6.60377
89 1CLU DBG 6.62651
90 1WQ1 GDP 6.62651
91 1NVV GNP 6.62651
92 1NVV GNP 6.62651
93 3DDC GNP 6.62651
94 2C5L GTP 6.83761
95 2C5L GTP 6.83761
96 3CX8 GSP 6.85279
97 1S9D GDP 6.89655
98 2RCN GDP 7.1066
99 2RCN GDP 7.1066
100 1FZQ GDP 7.18232
101 4LC1 GDP 7.4184
102 4LC1 GDP 7.4184
103 1ZJ6 G3D 7.48663
104 1ZJ6 G3D 7.48663
105 1ZJ6 G3D 7.48663
106 2W2X GSP 7.56757
107 3MD0 GDP 7.60563
108 1YVD GNP 7.69231
109 2HV8 GTP 7.8125
110 3TK1 GDP 7.87879
111 3TK1 GDP 7.87879
112 1FQK GDP 8.16327
113 1GWN GTP 8.29268
114 5O74 GDP 8.33333
115 5O74 GDP 8.33333
116 5O74 GDP 8.33333
117 5O74 GDP 8.33333
118 5O74 GDP 8.33333
119 1I4D GDP 8.33333
120 1DS6 GDP 8.33333
121 3M1I GTP 8.37696
122 1PUJ GNP 8.51064
123 3SBD GNP 8.55615
124 1Z0K GTP 8.72093
125 1S8F GDP 8.88325
126 1S8F GDP 8.88325
127 4DCT GDP 8.88325
128 1S8F GDP 8.88325
129 1S8F GDP 8.88325
130 1YZG GDP 8.93855
131 1R4A GNP 9.09091
132 1R4A GNP 9.09091
133 1R4A GNP 9.09091
134 1R4A GNP 9.09091
135 4BAS GNP 10.0503
136 5CK5 GDP 10.1266
137 5CK5 GDP 10.1266
138 5CK5 GDP 10.1266
139 5HPY GDP 10.3448
140 3GJ8 GDP 10.4072
141 3GJ5 GDP 10.4072
142 3GJ8 GDP 10.4072
143 3GJ3 GDP 10.4072
144 3GJ0 GDP 10.4072
145 3GJ4 GDP 10.4072
146 3GJ0 GDP 10.4072
147 3GJ4 GDP 10.4072
148 3GJ5 GDP 10.4072
149 2CJW GDP 10.4167
150 2CJW GDP 10.4167
151 5BXQ GDP 10.6481
152 5BXQ GDP 10.6481
153 5BXQ GDP 10.6481
154 1IBR GNP 10.6481
155 6AU6 GDP 11.1675
156 3GJ7 GDP 11.2245
157 3GJ7 GDP 11.2245
158 1ZC3 GNP 11.4286
159 5WLB GNP 11.7647
160 3T12 GDP ALF 11.7647
161 1U8Z GDP 11.9048
162 1U8Z GDP 11.9048
163 2A5J GDP 12.0419
164 2WIC GNP 12.3596
165 2WIC GNP 12.3596
166 1CS4 GSP 12.6904
167 4HAT GNP 12.8571
168 1WA5 GTP 13.0682
169 1Z2A GDP 13.0952
170 1Z0A GDP 13.2184
171 1Z0A GDP 13.2184
172 1Z0A GDP 13.2184
173 1Z0A GDP 13.2184
174 1Z0A GDP 13.2184
175 1Z0A GDP 13.2184
176 1Z0A GDP 13.2184
177 1Z0A GDP 13.2184
178 1Z0A GDP 13.2184
179 1Z0A GDP 13.2184
180 1Z0A GDP 13.2184
181 1Z0A GDP 13.2184
182 1SVI GDP 13.3333
183 2HT6 GDP 13.4518
184 2HT6 GDP 13.4518
185 3T5G GDP 13.8158
186 5TB5 GDP 14
187 5TB5 GDP 14
188 5WHA GDP 14.2857
189 5WHA GDP 14.2857
190 5WHA GDP 14.2857
191 5WHA GDP 14.2857
192 1G16 GDP 15.2941
193 1G16 GDP 15.2941
194 1G16 GDP 15.2941
195 1G16 GDP 15.2941
196 5UWQ GNP 15.3846
197 5UWP GNP 15.3846
198 5UWU GNP 15.3846
199 6CIT GNP 15.3846
200 5UWO GNP 15.3846
201 5UWH GNP 15.3846
202 5UWT GNP 15.3846
203 5UWW GNP 15.3846
204 5UWS GNP 15.3846
205 1G7S GDP 15.4822
206 1DAR GDP 15.4822
207 3EC1 GDP 15.4822
208 3EC1 GDP 15.4822
209 4B47 GDP 15.978
210 1F6B GDP 16.1616
211 1F6B GDP 16.1616
212 2OM2 GDP 16.6667
213 2OM2 GDP 16.6667
214 3W5J GDP 17.5127
215 6JFK GDP 18.0203
216 1KSH GDP 18.2796
217 3BC1 GNP 18.4615
218 3BC1 GNP 18.4615
219 6A8D GDP 18.75
220 1MKY GDP 19.5431
221 4R98 GNH 19.9262
222 1GUA GNP 21.5569
223 1Z0J GTP 22.0339
224 6G14 G4P 24.3655
225 6G14 G4P 24.3655
226 2WJG GDP 26.0638
227 2WJG GDP 26.0638
228 3PQC GDP 26.1538
229 3CH5 GDP 28.8462
230 3CH5 GDP 28.8462
231 2WJH GDP 29.5181
232 5FG3 GDP 29.6954
233 1FQJ GDP 30.9524
234 5YT0 GDP 31.5934
235 2QN6 GDP 36.0406
236 1KK1 GNP 42.3858
237 1Y3A GDP 50
238 1Y3A GDP 50
239 6MHE GDP 50
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