Receptor
PDB id Resolution Class Description Source Keywords
5W7Q 2.5 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
GDP A:402;
Valid;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
MG A:401;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5W7Q 2.5 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 5W7Q - 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 : 5W7Q; Ligand: GDP; Similar sites found with APoc: 144
This union binding pocket(no: 1) in the query (biounit: 5w7q.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 1VG1 GDP 1.62162
2 2XTZ GSP 1.69492
3 1Y3A GDP 1.82371
4 2OM2 GDP 1.84615
5 1BH2 GSP 1.90476
6 5M04 GDP 1.94444
7 5CK5 GDP 2.21519
8 1TQ4 GDP 2.68097
9 2FFQ GSP 2.92398
10 3MJH GTP 2.97619
11 1WF3 GNP 2.99003
12 3GJ3 GDP 3.16742
13 3GJ0 GDP 3.16742
14 1TAD GDP 3.21716
15 1TAD ALF 3.21716
16 1GOT GDP 3.23529
17 5KDO GDP 3.23529
18 1Z0A GDP 3.44828
19 3M1I GTP 3.48525
20 1OIX GDP 3.66492
21 1OIV GDP 3.66492
22 3RWO GDP 3.78378
23 1Z0F GDP 3.91061
24 1S8F GDP 3.9548
25 1Z06 GNP 4.02145
26 3GJ8 GDP 4.0724
27 3GJ4 GDP 4.0724
28 3GJ5 GDP 4.0724
29 1Z08 GNP 4.11765
30 3Q85 GNP 4.14201
31 3RAB GNP 4.14201
32 4LC1 GDP 4.1543
33 6AU6 GDP 4.28954
34 1FZQ GDP 4.41989
35 1MR3 G3D 4.41989
36 4NON GDP 4.61538
37 2A5J GDP 4.71204
38 3MD0 GDP 4.78873
39 1O3Y GTP 4.81928
40 1J2J GTP 4.81928
41 1RE0 GDP 4.87805
42 1S9D GDP 4.87805
43 1RYH GNP 4.92611
44 5XC5 GTP 5.11364
45 1I4D GDP 5.20833
46 1MH1 GNP 5.37634
47 6G14 G4P 5.44218
48 2ZEJ GDP 5.63003
49 1WA5 GTP 5.63003
50 4HAT GNP 5.71429
51 3TK1 GDP 5.75758
52 2A9K GDP 5.88235
53 3T1O GDP 6.06061
54 5UWQ GNP 6.32911
55 5UWP GNP 6.32911
56 5DIF GNP 6.32911
57 5UWU GNP 6.32911
58 5UWI GNP 6.32911
59 6CIT GNP 6.32911
60 5UWW GNP 6.32911
61 5UWH GNP 6.32911
62 5UWR GNP 6.32911
63 5UWS GNP 6.32911
64 5UWT GNP 6.32911
65 5DHF GNP 6.32911
66 1U8Z GDP 6.54762
67 4DCT GDP 6.70241
68 4D0N GDP 6.70241
69 2C5L GTP 6.93642
70 6CRK GDP 7.04225
71 1GP2 GDP 7.04225
72 6D5J GNP 7.18563
73 6D5E GNP 7.18563
74 6BVJ GNP 7.18563
75 6BVL GNP 7.18563
76 6D59 GNP 7.18563
77 6D56 GNP 7.18563
78 6D5G GNP 7.18563
79 6BVI GNP 7.18563
80 6BVK GNP 7.18563
81 6D5H GNP 7.18563
82 6D5V GNP 7.18563
83 1CLU DBG 7.22892
84 3KUD GDP 7.22892
85 1WQ1 GDP 7.22892
86 1F6B GDP 7.5067
87 4HI0 GDP 7.53769
88 1YVD GNP 7.69231
89 2CJW GDP 7.7748
90 1VG9 GDP 7.7748
91 2HV8 GTP 7.8125
92 1ZC3 GNP 7.9646
93 1CS4 GSP 8.01887
94 2W2X GSP 8.06452
95 1PUJ GNP 8.51064
96 1ZJ6 G3D 8.55615
97 1Z0K GTP 8.69565
98 1GWN GTP 8.78049
99 3T5G GDP 9.21053
100 1SVI GDP 9.23077
101 5TB5 GDP 9.33333
102 1DS6 GDP 9.44444
103 1YRB GDP 9.54198
104 1ZD9 GDP 9.57447
105 2QTV GNP 9.58084
106 1M7B GTP 9.78261
107 4BAS GNP 10.0503
108 5O2T GSP 10.0592
109 1Z0J GTP 10.1695
110 3T12 GDP ALF 10.2941
111 5O74 GDP 11.6751
112 3BC1 GNP 11.8644
113 2HT6 GDP 12.6437
114 2RCN GDP 12.8686
115 4V0K GDP 13.0178
116 3EC1 GDP 13.1367
117 3GJ7 GDP 13.2653
118 3CX8 GSP 13.6729
119 1MKY GDP 14.2091
120 5WLB GNP 14.7059
121 4B47 GDP 15.7025
122 5FG3 GDP 15.8177
123 1G7S GDP 16.0858
124 4HDO GNP 16.1677
125 1UPT GTP 16.6667
126 5BXQ GDP 17.3228
127 1DAR GDP 17.4263
128 1GUA GNP 17.9641
129 3W5J GDP 18.2306
130 5YT0 GDP 18.7668
131 1YZG GDP 18.9944
132 1R4A GNP 19.6078
133 2WIC GNP 19.8502
134 4R98 GNH 19.9262
135 1G16 GDP 20
136 1Z2A GDP 20.2381
137 1KSH GDP 25.8065
138 3Q72 GNP 26.506
139 2WJG GDP 26.5957
140 2WJH GDP 30.1205
141 3CH5 GDP 32.6923
142 5UWO GNP 35
143 2QN6 GDP 35.6568
144 1KK1 GNP 43.4316
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