Receptor
PDB id Resolution Class Description Source Keywords
3U6B 2.12 Å NON-ENZYME: OTHER EF-TU (ESCHERICHIA COLI) IN COMPLEX WITH NVP-LDI028 ESCHERICHIA COLI TRANSLATION FACTOR-ANTIBIOTIC COMPLEX
Ref.: ANTIBACTERIAL OPTIMIZATION OF 4-AMINOTHIAZOLYL ANAL THE NATURAL PRODUCT GE2270 A: IDENTIFICATION OF THE CYCLOALKYLCARBOXYLIC ACIDS. J.MED.CHEM. V. 54 8099 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP A:402;
B:401;
Valid;
Valid;
none;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
MG A:401;
B:402;
Part of Protein;
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
3U6B 2.12 Å NON-ENZYME: OTHER EF-TU (ESCHERICHIA COLI) IN COMPLEX WITH NVP-LDI028 ESCHERICHIA COLI TRANSLATION FACTOR-ANTIBIOTIC COMPLEX
Ref.: ANTIBACTERIAL OPTIMIZATION OF 4-AMINOTHIAZOLYL ANAL THE NATURAL PRODUCT GE2270 A: IDENTIFICATION OF THE CYCLOALKYLCARBOXYLIC ACIDS. J.MED.CHEM. V. 54 8099 2011
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 3U6B - 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 1205 families.
1 3U6B - 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 1039 families.
1 3U6B - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GDP; Similar ligands found: 161
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 9GM 0.839506 0.973684
6 GNP 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 GDC 0.747253 0.961039
18 GKE 0.747253 0.961039
19 GDD 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 GFB 0.72043 0.961039
26 GTG 0.72043 0.936709
27 GDR 0.72043 0.961039
28 G4P 0.715909 0.986486
29 G3A 0.712766 0.973684
30 6CK 0.712766 0.936709
31 GDP AF3 0.7 0.888889
32 ALF GDP 0.7 0.888889
33 GDP ALF 0.7 0.888889
34 YGP 0.698925 0.901235
35 GKD 0.697917 0.961039
36 JB2 0.697917 0.961039
37 GDX 0.690722 0.973684
38 GPD 0.690722 0.925
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 DGI 0.636364 0.923077
44 GDP 7MG 0.636364 0.911392
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 CG2 0.622642 0.936709
52 FEG 0.619048 0.879518
53 MGD 0.614679 0.891566
54 ZGP 0.613208 0.869048
55 GH3 0.612903 0.973333
56 3GP 0.611765 0.946667
57 MD1 0.607143 0.891566
58 PGD 0.59292 0.925
59 DGT 0.591398 0.923077
60 BGO 0.588785 0.924051
61 TPG 0.582609 0.840909
62 DBG 0.582609 0.948718
63 2GP 0.574713 0.96
64 FE9 0.570175 0.776596
65 GCP G 0.56 0.921053
66 A G 0.553571 0.935065
67 G A A A 0.553571 0.923077
68 MGP 0.553191 0.961039
69 U A G G 0.548673 0.935065
70 G4M 0.548387 0.880952
71 6G0 0.547368 0.961039
72 G1R G1R 0.542373 0.924051
73 P2G 0.527473 0.883117
74 PGD O 0.525 0.850575
75 ADP 0.522222 0.92
76 R5I 0.520833 0.946667
77 R7I 0.520833 0.946667
78 GGM 0.517544 0.901235
79 DGP 0.516484 0.910256
80 DG 0.516484 0.910256
81 P1G 0.516129 0.871795
82 G U 0.513274 0.9
83 G1G 0.508475 0.925
84 IMP 0.505495 0.959459
85 AKW 0.504425 0.890244
86 G C 0.504348 0.9
87 GPC 0.491525 0.879518
88 G7M 0.483871 0.948052
89 6AD 0.479592 0.841463
90 ATP 0.473684 0.92
91 HEJ 0.473684 0.92
92 G2Q 0.471154 0.961039
93 5FA 0.46875 0.92
94 AQP 0.46875 0.92
95 GTA 0.468468 0.936709
96 7DD 0.468085 0.906667
97 G G G RPC 0.466102 0.875
98 SGP 0.463158 0.82716
99 01G 0.462963 0.902439
100 HFD 0.459184 0.873418
101 B4P 0.457447 0.894737
102 AP5 0.457447 0.894737
103 A2D 0.456522 0.894737
104 6YZ 0.455446 0.896104
105 G G G C 0.455285 0.9125
106 5GP 5GP 0.454545 0.883117
107 ANP 0.454545 0.896104
108 ACQ 0.454545 0.896104
109 AT4 0.452632 0.884615
110 A G C C 0.451613 0.911392
111 APC G U 0.45082 0.886076
112 PRT 0.449541 0.959459
113 G U34 0.449153 0.888889
114 DG DG 0.448598 0.865854
115 ITT 0.447917 0.868421
116 BA3 0.446809 0.894737
117 C2E 0.444444 0.921053
118 PCG 0.444444 0.933333
119 35G 0.444444 0.933333
120 MGO 0.441176 0.864198
121 AN2 0.4375 0.907895
122 G C C C 0.4375 0.924051
123 M33 0.43299 0.883117
124 UCG 0.429688 0.911392
125 A G U 0.42963 0.888889
126 ACP 0.428571 0.896104
127 MGQ 0.424528 0.935897
128 AR6 0.424242 0.894737
129 7DT 0.424242 0.906667
130 APR 0.424242 0.894737
131 93A 0.42268 0.833333
132 A4P 0.420168 0.869048
133 G8D 0.42 0.875
134 AD9 0.42 0.896104
135 SAP 0.42 0.873418
136 AGS 0.42 0.873418
137 CA0 0.418367 0.896104
138 ATF 0.417476 0.884615
139 AGO 0.414634 0.888889
140 A G U U 0.414286 0.888889
141 NIA 0.413043 0.82716
142 MGV 0.412844 0.890244
143 TAT 0.411765 0.884615
144 T99 0.411765 0.884615
145 ADQ 0.411215 0.871795
146 A1R 0.411215 0.839506
147 RGT 0.410714 0.909091
148 CGP 0.409836 0.86747
149 C1Z 0.409091 0.986486
150 A 0.408602 0.893333
151 AMP 0.408602 0.893333
152 UP5 0.40678 0.873418
153 AMZ 0.406593 0.918919
154 C2R 0.406593 0.906667
155 JBT 0.405882 0.778947
156 A22 0.40566 0.907895
157 25L 0.405405 0.907895
158 ADX 0.40404 0.809524
159 8OD 0.401961 0.946667
160 50T 0.4 0.883117
161 4TC 0.4 0.851852
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3U6B; Ligand: GDP; Similar sites found with APoc: 206
This union binding pocket(no: 1) in the query (biounit: 3u6b.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 1EK0 GNP None
2 1D5C GDP 1.23457
3 2WKQ GTP 1.50602
4 1Z0F GDP 1.67598
5 2G77 GDP 1.77665
6 1TAD GDP 1.85185
7 1TAD ALF 1.85185
8 2F9L GDP 2.01005
9 1OIX GDP 2.09424
10 1OIV GDP 2.09424
11 1MH1 GNP 2.15054
12 1G4U GDP 2.17391
13 5HCN GCP 2.29885
14 2D7C GTP 2.39521
15 4LPS GDP 2.47934
16 2QTV GNP 2.79188
17 2FFQ GSP 2.92398
18 1YZQ GNP 2.94118
19 3MJH GTP 2.97619
20 3Q72 GNP 3.01205
21 1GOT GDP 3.04569
22 2XTZ GSP 3.10734
23 5XC5 GTP 3.40909
24 1KAO GDP 3.59281
25 5UQW GDP 3.7037
26 1TU3 GNP 3.79747
27 1Z06 GNP 3.80711
28 1MR3 G3D 3.8674
29 5M04 GDP 3.88889
30 3Q85 GNP 4.14201
31 4HDO GNP 4.19162
32 1O3Y GTP 4.21687
33 1J2J GTP 4.21687
34 2J0V GDP 4.24528
35 3QBT GNP 4.28571
36 3RWO GDP 4.32432
37 1RYH GNP 4.4335
38 2GCN GDP 4.47761
39 4NON GDP 4.61538
40 1Z08 GNP 4.70588
41 2A5F GTP 4.82234
42 1VG8 GNP 4.83092
43 1VG0 GDP 4.83092
44 1KY3 GDP 4.94506
45 1RE0 GDP 4.97738
46 5XKT GNP 5
47 4M9Q GNP 5.07614
48 2ZEJ GDP 5.07614
49 5KUT GDP 5.29101
50 1VG9 GDP 5.40541
51 1VG1 GDP 5.40541
52 3T1O GDP 5.55556
53 1WF3 GNP 5.58376
54 1SVK ALF GDP 5.58376
55 6CRK GDP 5.58376
56 1GP2 GDP 5.58376
57 5KDO GDP 5.58376
58 6BSX GDP 5.61798
59 6BSX E7S 5.61798
60 3REF GDP 5.6701
61 5Z2M GTP 5.68182
62 1YRB GDP 5.72519
63 2BME GNP 5.91398
64 1YZN GNP 5.94595
65 1BH2 GSP 6.03175
66 1TQ4 GDP 6.05327
67 4U5X GNP 6.17978
68 1M2O GNP 6.31579
69 4V0K GDP 6.50888
70 6D5J GNP 6.58683
71 6D5E GNP 6.58683
72 6D59 GNP 6.58683
73 6BVL GNP 6.58683
74 6D56 GNP 6.58683
75 6BVJ GNP 6.58683
76 6D5L GNP 6.58683
77 6D55 GNP 6.58683
78 6BVI GNP 6.58683
79 6D5G GNP 6.58683
80 6BVK GNP 6.58683
81 6D5H GNP 6.58683
82 6D5V GNP 6.58683
83 6BVM GNP 6.58683
84 1CLU DBG 6.62651
85 3KUD GDP 6.62651
86 3DDC GNP 6.62651
87 1WQ1 GDP 6.62651
88 2C5L GTP 6.83761
89 3AB3 GDP 6.85279
90 3CX8 GSP 6.85279
91 1S9D GDP 6.89655
92 5O2T GSP 6.95187
93 2GJ8 ALF GDP 6.97674
94 2RCN GDP 7.1066
95 1FZQ GDP 7.18232
96 4LC1 GDP 7.4184
97 1ZJ6 G3D 7.48663
98 2W2X GSP 7.56757
99 3MD0 GDP 7.60563
100 1KMQ GNP 7.6087
101 1YVD GNP 7.69231
102 2HV8 GTP 7.8125
103 3TK1 GDP 7.87879
104 1TX4 ALF GDP 7.9096
105 5OCG GNP 7.93651
106 1FQK GDP 8.16327
107 1GWN GTP 8.29268
108 5O74 GDP 8.33333
109 1DS6 GDP 8.33333
110 1I4D GDP 8.33333
111 1E96 GTP 8.37438
112 3M1I GTP 8.37696
113 4C4P GNP 8.41121
114 1PUJ GNP 8.51064
115 4HI0 GDP 8.54271
116 3SBD GNP 8.55615
117 1Z0K GTP 8.72093
118 4DCT GDP 8.88325
119 1S8F GDP 8.88325
120 1YZG GDP 8.93855
121 2FJU GSP 8.98876
122 1R4A GNP 9.09091
123 1M7B GTP 9.23913
124 4DID GDP 9.84456
125 4BAS GNP 10.0503
126 5CK5 GDP 10.1266
127 1NF3 GNP 10.2564
128 5UPK GNP 10.2703
129 5HPY GDP 10.3448
130 3GJ8 GDP 10.4072
131 3GJ5 GDP 10.4072
132 3GJ3 GDP 10.4072
133 3GJ0 GDP 10.4072
134 3GJ4 GDP 10.4072
135 2CJW GDP 10.4167
136 1A4R GDP 10.4712
137 1A4R GNH 10.4712
138 2NGR GDP 10.4712
139 2UZI GTP 10.5769
140 5BXQ GDP 10.6481
141 2A9K GDP 10.6952
142 6AU6 GDP 11.1675
143 3GJ7 GDP 11.2245
144 1ZC3 GNP 11.4286
145 5WLB GNP 11.7647
146 3T12 GDP ALF 11.7647
147 1U8Z GDP 11.9048
148 1OW3 GDP 11.9171
149 2A5J GDP 12.0419
150 2WIC GNP 12.3596
151 4D0N GDP 12.4324
152 1CS4 GSP 12.6904
153 4HAT GNP 12.8571
154 1WA5 GTP 13.0682
155 1Z2A GDP 13.0952
156 1Z0A GDP 13.2184
157 1SVI GDP 13.3333
158 2HT6 GDP 13.4518
159 4NCN GTP 13.4518
160 3T5G GDP 13.8158
161 5TB5 GDP 14
162 5TAR GDP 14.1892
163 3RAB GNP 14.7929
164 1G16 GDP 15.2941
165 5UWQ GNP 15.3846
166 5UWP GNP 15.3846
167 5UWU GNP 15.3846
168 5UWR GNP 15.3846
169 5UWJ GNP 15.3846
170 5UWI GNP 15.3846
171 6CIT GNP 15.3846
172 5UWT GNP 15.3846
173 5UWH GNP 15.3846
174 5UWW GNP 15.3846
175 5UWO GNP 15.3846
176 5UWS GNP 15.3846
177 1G7S GDP 15.4822
178 1DAR GDP 15.4822
179 3EC1 GDP 15.4822
180 2ODE ALF GDP 15.6028
181 4B47 GDP 15.978
182 1F6B GDP 16.1616
183 1UPT GTP 16.6667
184 2OM2 GDP 16.6667
185 1CXZ GSP 17.4419
186 1KSH GDP 18.2796
187 1NRJ GTP 18.3486
188 3BC1 GNP 18.4615
189 1MKY GDP 19.5431
190 1ZD9 GDP 19.6809
191 4R98 GNH 19.9262
192 1GUA GNP 21.5569
193 1LFD GNP 21.8391
194 1Z0J GTP 22.0339
195 1X1R GDP 23.5955
196 6G14 G4P 24.3655
197 2WJG GDP 26.0638
198 3PQC GDP 26.1538
199 3CH5 GDP 28.8462
200 2WJH GDP 29.5181
201 5FG3 GDP 29.6954
202 5DIF GNP 31.5789
203 5YT0 GDP 31.5934
204 4RD0 GDP 35.7868
205 2QN6 GDP 36.0406
206 1KK1 GNP 42.3858
207 1Y3A GDP 50
Pocket No.: 2; Query (leader) PDB : 3U6B; Ligand: GDP; 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: 3u6b.bio2) has 15 residues
No: Leader PDB Ligand Sequence Similarity
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