Receptor
PDB id Resolution Class Description Source Keywords
5W76 2.15 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF RECONSTRUCTED BACTERIAL ELONGATION FACT 168 SYNTHETIC CONSTRUCT ANCESTRAL GENE RECONSTRUCTION THERMOSTABILITY EF-TU ASR TRANSLATION
Ref.: STRUCTURAL AND DYNAMICS COMPARISON OF THERMOSTABILI ANCIENT, MODERN, AND CONSENSUS ELONGATION FACTOR TU STRUCTURE V. 26 118 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:402;
Invalid;
none;
submit data
96.063 O4 S [O-]S...
PEG A:405;
A:406;
Invalid;
Invalid;
none;
none;
submit data
106.12 C4 H10 O3 C(COC...
MG A:401;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
GDP A:404;
Valid;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
PGE A:403;
Invalid;
none;
submit data
150.173 C6 H14 O4 C(COC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5W76 2.15 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF RECONSTRUCTED BACTERIAL ELONGATION FACT 168 SYNTHETIC CONSTRUCT ANCESTRAL GENE RECONSTRUCTION THERMOSTABILITY EF-TU ASR TRANSLATION
Ref.: STRUCTURAL AND DYNAMICS COMPARISON OF THERMOSTABILI ANCIENT, MODERN, AND CONSENSUS ELONGATION FACTOR TU STRUCTURE V. 26 118 2018
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 5W76 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
70% Homology Family (18)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1D2E Kd = 1 uM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 5W76 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 5W7Q - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 1DG1 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
5 2BVN - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
6 1EFC - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
7 6EZE - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
8 4H9G - 14J C5 H3 Br O3 c1cc(oc1C(....
9 4LBZ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
10 4LC0 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
11 1EXM - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
12 2C78 - PUL C47 H66 O13 C[C@@H]1[C....
13 1EFT - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
14 4LBV - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
15 4LBW - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
16 1HA3 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
17 4J0Q - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
18 5W75 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
50% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 209 families.
1 5W76 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 5W7Q - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 4LC0 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
4 1EXM - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
5 2C78 - PUL C47 H66 O13 C[C@@H]1[C....
6 1EFT - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
7 4LBV - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
8 4LBW - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
9 1HA3 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
10 1SKQ - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
11 1JNY - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
12 3WYA - 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 : 5W76; Ligand: GDP; Similar sites found with APoc: 168
This union binding pocket(no: 1) in the query (biounit: 5w76.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 1VG1 GDP 1.62162
2 1OIX GDP 2.09424
3 2XTZ GSP 2.25989
4 2HV8 GTP 2.32558
5 2D7C GTP 2.39521
6 2G77 GDP 2.52525
7 1TQ4 GDP 2.5974
8 1MR3 G3D 2.76243
9 4LC1 GDP 2.96736
10 5XKT GNP 3
11 4M9Q GNP 3.0837
12 5M04 GDP 3.11688
13 1TAD GDP 3.11688
14 1TAD ALF 3.11688
15 4HDO GNP 3.59281
16 6AU6 GDP 3.63636
17 1Z0F GDP 3.91061
18 3QBT GNP 4.02299
19 3Q85 GNP 4.14201
20 1Z06 GNP 4.15584
21 1O3Y GTP 4.21687
22 1J2J GTP 4.21687
23 1CS4 GSP 4.24528
24 2ODE ALF GDP 4.28571
25 1WF3 GNP 4.31894
26 1YZN GNP 4.32432
27 5Z2M GTP 4.34783
28 1VG9 GDP 4.41558
29 1VG0 GDP 4.41558
30 1FZQ GDP 4.41989
31 1RE0 GDP 4.52489
32 1Y3A GDP 4.55927
33 4NON GDP 4.61538
34 1YZQ GNP 4.70588
35 1EK0 GNP 4.70588
36 1BH2 GSP 4.7619
37 3RWO GDP 4.86486
38 1D5C GDP 4.93827
39 5XC5 GTP 5.11364
40 1GUA GNP 5.38922
41 1S9D GDP 5.41872
42 3T12 GDP ALF 5.55556
43 3T1O GDP 5.55556
44 3MD0 GDP 5.6338
45 1OIV GDP 5.75916
46 6CRK GDP 5.7971
47 2GJ8 ALF GDP 5.81395
48 1GP2 GDP 5.88235
49 2F9L GDP 6.03015
50 3TK1 GDP 6.06061
51 1PUJ GNP 6.49351
52 2HT6 GDP 6.49351
53 2CJW GDP 6.49351
54 4DCT GDP 6.49351
55 4V0K GDP 6.50888
56 3Q72 GNP 6.75325
57 1RYH GNP 6.89655
58 1Z0J GTP 7.05882
59 1LFD GNP 7.18563
60 6D5J GNP 7.18563
61 6D5E GNP 7.18563
62 6BVJ GNP 7.18563
63 6D59 GNP 7.18563
64 6BVL GNP 7.18563
65 6D56 GNP 7.18563
66 6D55 GNP 7.18563
67 6D5L GNP 7.18563
68 6D5H GNP 7.18563
69 6BVI GNP 7.18563
70 6BVK GNP 7.18563
71 6D5V GNP 7.18563
72 6D5G GNP 7.18563
73 6BVM GNP 7.18563
74 4P4T GDP 7.22222
75 1CLU DBG 7.22892
76 2UZI GTP 7.22892
77 3KUD GDP 7.22892
78 1WQ1 GDP 7.22892
79 1F6B GDP 7.53247
80 1YRB GDP 8.01527
81 1ZJ6 G3D 8.02139
82 2RCN GDP 8.05195
83 4C4P GNP 8.41121
84 1KY3 GDP 8.57143
85 3RAB GNP 8.87574
86 2A5J GDP 8.90052
87 1X1R GDP 8.98876
88 5UQW GDP 8.99471
89 5OCG GNP 8.99471
90 3T5G GDP 9.21053
91 1SVI GDP 9.23077
92 5TAR GDP 9.45946
93 1M2O GNP 9.61039
94 2QTV GNP 9.61039
95 1ZC3 GNP 9.71429
96 1M7B GTP 9.78261
97 3DDC GNP 9.81595
98 5O2T GSP 10.0592
99 1U8Z GDP 10.119
100 4BAS GNP 10.5528
101 2C5L GTP 11.1111
102 2A5F GTP 11.399
103 2ZEJ GDP 11.413
104 5O74 GDP 11.6751
105 3AB3 GDP 12.4675
106 1NRJ GTP 12.6582
107 2BME GNP 12.7273
108 1KSH GDP 12.9032
109 1Z08 GNP 12.9412
110 3EC1 GDP 12.987
111 1Z2A GDP 13.0952
112 3CX8 GSP 13.3136
113 4HI0 GDP 13.3858
114 2A9K GDP 14.3498
115 2FFQ GSP 14.6199
116 1G7S GDP 15.0649
117 3BC1 GNP 15.2542
118 1G16 GDP 15.2941
119 5FG3 GDP 15.8442
120 1Z0K GTP 15.942
121 5YT0 GDP 16.4835
122 2OM2 GDP 16.6667
123 1UPT GTP 16.6667
124 3M1I GTP 16.895
125 4HAT GNP 17.1296
126 5BXQ GDP 17.1296
127 5WLB GNP 17.6471
128 1DAR GDP 18.1818
129 1YZG GDP 18.9944
130 1MKY GDP 19.2208
131 1A4R GDP 19.3717
132 1R4A GNP 19.6078
133 1ZD9 GDP 19.6809
134 2WIC GNP 19.8502
135 4R98 GNH 20
136 1YVD GNP 20.1183
137 1WA5 GTP 20.4545
138 5UWP GNP 21.097
139 5UWU GNP 21.097
140 5DIF GNP 21.097
141 5UWH GNP 21.097
142 5UWQ GNP 21.097
143 6CIT GNP 21.097
144 5UWO GNP 21.097
145 5UWI GNP 21.097
146 5UWJ GNP 21.097
147 5UWT GNP 21.097
148 5UWS GNP 21.097
149 5UWW GNP 21.097
150 5UWR GNP 21.097
151 5DHF GNP 21.097
152 3GJ8 GDP 22.6244
153 3GJ3 GDP 22.6244
154 3GJ0 GDP 22.6244
155 3GJ7 GDP 22.6244
156 3GJ4 GDP 22.6244
157 3GJ5 GDP 22.6244
158 5KDO GDP 22.973
159 1GOT GDP 23.2877
160 3CH5 GDP 25
161 2WJG GDP 27.6596
162 4B47 GDP 27.8237
163 1FQK GDP 29.2517
164 2WJH GDP 31.3253
165 3MJH GTP 32.3529
166 4RD0 GDP 36.3636
167 2QN6 GDP 36.6234
168 6G14 G4P 39.4558
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