Receptor
PDB id Resolution Class Description Source Keywords
5W75 2.3 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF RECONSTRUCTED BACTERIAL ELONGATION FACT 168 THERMOTOGA NEAPOLITANA (STRAIN ATCC 494359 / NS-E) 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 B:407;
C:408;
B:406;
C:407;
C:405;
D:409;
A:403;
C:403;
D:408;
D:404;
D:405;
C:406;
B:408;
B:403;
B:404;
A:404;
D:407;
B:405;
D:403;
C:404;
D:406;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
GDP B:401;
A:401;
D:401;
C:401;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
SUC B:409;
D:410;
C:410;
C:409;
Valid;
Valid;
Invalid;
Valid;
none;
none;
none;
none;
submit data
342.296 C12 H22 O11 C([C@...
MG D:402;
A:402;
B:402;
C:402;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5W75 2.3 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF RECONSTRUCTED BACTERIAL ELONGATION FACT 168 THERMOTOGA NEAPOLITANA (STRAIN ATCC 494359 / NS-E) 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 5W75 - 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 (9)
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 1DG1 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 2BVN - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
4 1EFC - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
5 6EZE - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
6 4H9G - 14J C5 H3 Br O3 c1cc(oc1C(....
7 4LBZ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
8 4J0Q - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
9 5W75 - 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
Ligand no: 2; Ligand: SUC; Similar ligands found: 16
No: Ligand ECFP6 Tc MDL keys Tc
1 SUC 1 1
2 SWE 1 1
3 RAF 0.736842 0.972973
4 STW 0.724138 0.972973
5 SUP 0.701754 0.8
6 DQR 0.666667 0.972973
7 NYT 0.612903 0.972973
8 FNY 0.612903 0.972973
9 20S 0.534247 0.8
10 SUC GLA 0.5 0.921053
11 AGR 0.467532 0.782609
12 TRE 0.42 0.864865
13 AMG 0.411765 0.789474
14 MMA 0.411765 0.789474
15 GYP 0.411765 0.789474
16 MBG 0.411765 0.789474
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5W75; Ligand: SUC; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5w75.bio4) has 12 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5W75; Ligand: GDP; Similar sites found with APoc: 169
This union binding pocket(no: 2) in the query (biounit: 5w75.bio4) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 1YZG GDP 1.67598
2 1TAD ALF 1.85185
3 1TAD GDP 1.85185
4 2XTZ GSP 1.9774
5 2G77 GDP 2.04082
6 1TQ4 GDP 2.29592
7 1EK0 GNP 2.35294
8 1SVK ALF GDP 3.11615
9 3GJ0 GDP 3.16742
10 1IBR GNP 3.24074
11 2BCG GDP 3.39806
12 5XC5 GTP 3.40909
13 2FFQ GSP 3.50877
14 4M9Q GNP 3.52423
15 1F6B GDP 3.53535
16 1YVD GNP 3.5503
17 5M04 GDP 3.61111
18 1FZQ GDP 3.8674
19 1X1R GDP 3.93258
20 2GJ8 ALF GDP 4.06977
21 3GJ4 GDP 4.0724
22 1WF3 GNP 4.31894
23 3GJ8 GDP 4.34783
24 1KY3 GDP 4.3956
25 1Z0F GDP 4.46927
26 4NON GDP 4.61538
27 2ZEJ GDP 4.8913
28 3QBT GNP 5
29 3MD0 GDP 5.07042
30 3GJ7 GDP 5.10204
31 2WIC GNP 5.24345
32 1YZQ GNP 5.29412
33 3TK1 GDP 5.45455
34 4HAT GNP 5.61225
35 3M1I GTP 5.61225
36 2A5F GTP 5.71429
37 5UQW GDP 5.82011
38 3GJ3 GDP 6.06061
39 6BSX GDP 6.17978
40 6BSX E7S 6.17978
41 3AB3 GDP 6.35359
42 1YRB GDP 6.48855
43 4V0K GDP 6.50888
44 3T1O GDP 6.56566
45 1KAO GDP 6.58683
46 2CJW GDP 6.77083
47 3CX8 GSP 6.80473
48 2C5L GTP 6.93642
49 5UWP GNP 6.99301
50 5UWQ GNP 6.99301
51 5UWU GNP 6.99301
52 5DIF GNP 6.99301
53 5UWJ GNP 6.99301
54 6CIT GNP 6.99301
55 5UWW GNP 6.99301
56 5UWI GNP 6.99301
57 5UWH GNP 6.99301
58 5UWR GNP 6.99301
59 5DHF GNP 6.99301
60 1MR3 G3D 7.18232
61 1LFD GNP 7.18563
62 6D5J GNP 7.18563
63 6D5E GNP 7.18563
64 6BVJ GNP 7.18563
65 6D59 GNP 7.18563
66 6D56 GNP 7.18563
67 6BVL GNP 7.18563
68 6D5G GNP 7.18563
69 6D55 GNP 7.18563
70 6D5M GNP 7.18563
71 6D5L GNP 7.18563
72 6D5V GNP 7.18563
73 6BVI GNP 7.18563
74 6D5H GNP 7.18563
75 6BVK GNP 7.18563
76 6BVM GNP 7.18563
77 5O74 GDP 7.22222
78 1O3Y GTP 7.22892
79 1CLU DBG 7.22892
80 1J2J GTP 7.22892
81 3KUD GDP 7.22892
82 1WQ1 GDP 7.22892
83 1Z0K GTP 7.24638
84 1RE0 GDP 7.31707
85 1S9D GDP 7.31707
86 2HT6 GDP 7.47126
87 2RCN GDP 7.5419
88 4DCT GDP 7.67544
89 3T12 GDP ALF 8.08823
90 6FA4 GNP 8.09249
91 5O2T GSP 8.28402
92 1WA5 GTP 8.41837
93 5WLB GNP 8.43373
94 2F9L GDP 8.54271
95 1ZJ6 G3D 8.55615
96 2A9K GDP 8.55615
97 1UPT GTP 8.77193
98 1PUJ GNP 8.86525
99 1ZC3 GNP 9.14286
100 3RWO GDP 9.18919
101 2ODE ALF GDP 9.21986
102 6G14 G4P 9.52381
103 1U8Z GDP 9.52381
104 3CH5 GDP 9.61539
105 4LC1 GDP 9.79228
106 2HV8 GTP 9.88372
107 5OCG GNP 10.0529
108 3BC1 GNP 10.1695
109 2D7C GTP 10.1796
110 1YZN GNP 10.2703
111 1R4A GNP 10.303
112 1OIV GDP 10.4712
113 3T5G GDP 10.5263
114 1ZD9 GDP 10.6383
115 1Y3A GDP 10.6383
116 5TB5 GDP 10.6667
117 2OM2 GDP 10.7692
118 5TAR GDP 10.8108
119 5BXQ GDP 11.0236
120 3DDC GNP 11.0429
121 1BH2 GSP 11.1111
122 1OIX GDP 11.5183
123 2UZI GTP 11.5385
124 3GJ5 GDP 11.7647
125 4C4P GNP 12.1495
126 6AU6 GDP 12.2016
127 1CS4 GSP 12.2642
128 3EC1 GDP 12.7371
129 2A5J GDP 12.7551
130 2BME GNP 12.9032
131 1FQK GDP 12.9231
132 1Z08 GNP 12.9412
133 1D5C GDP 12.963
134 1S8F GDP 13.5593
135 1MKY GDP 14.0306
136 1Z06 GNP 14.2857
137 1GUA GNP 14.3713
138 1DAR GDP 14.7959
139 1Z2A GDP 14.881
140 4HDO GNP 14.9701
141 5UWO GNP 15
142 4BAS GNP 15.0754
143 1Z0J GTP 15.2542
144 1G7S GDP 15.8163
145 4NCN GTP 15.8163
146 3Q85 GNP 15.9763
147 3Q72 GNP 16.8675
148 3RAB GNP 17.1598
149 1M2O GNP 17.3684
150 1VG8 GNP 17.3913
151 1VG0 GDP 17.3913
152 5Z2M GTP 18.8406
153 5FG3 GDP 19.1327
154 1KSH GDP 19.3548
155 1VG1 GDP 19.4595
156 1VG9 GDP 19.4595
157 4B47 GDP 21.2121
158 2WJG GDP 26.0638
159 3MJH GTP 26.4706
160 5KDO GDP 27.027
161 1GOT GDP 27.3973
162 1Z0A GDP 28.7356
163 2WJH GDP 29.5181
164 4RD0 GDP 35.2041
165 6CRK GDP 35.2113
166 1GP2 GDP 35.2113
167 2QN6 GDP 35.4592
168 5UWS GNP 36.3636
169 5YT0 GDP 38.0952
Pocket No.: 3; Query (leader) PDB : 5W75; 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: 3) in the query (biounit: 5w75.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5W75; 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: 4) in the query (biounit: 5w75.bio3) has 16 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5W75; Ligand: SUC; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 5w75.bio3) has 12 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 5W75; Ligand: SUC; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 5w75.bio3) has 5 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 5W75; 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: 7) in the query (biounit: 5w75.bio2) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 5W75; Ligand: SUC; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 5w75.bio2) has 13 residues
No: Leader PDB Ligand Sequence Similarity
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