Receptor
PDB id Resolution Class Description Source Keywords
1D2E 1.94 Å NON-ENZYME: TRANSCRIPT_TRANSLATE CRYSTAL STRUCTURE OF MITOCHONDRIAL EF-TU IN COMPLEX WITH GDP BOS TAURUS G-PROTEIN BETA-BARREL RNA BINDING PROTEIN
Ref.: HIGH RESOLUTION CRYSTAL STRUCTURE OF BOVINE MITOCHO EF-TU IN COMPLEX WITH GDP. J.MOL.BIOL. V. 297 421 2000
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP A:1301;
B:1302;
C:1303;
D:1304;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Kd = 1 uM
443.201 C10 H15 N5 O11 P2 c1nc2...
MG A:501;
B:502;
C:503;
D:504;
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
1D2E 1.94 Å NON-ENZYME: TRANSCRIPT_TRANSLATE CRYSTAL STRUCTURE OF MITOCHONDRIAL EF-TU IN COMPLEX WITH GDP BOS TAURUS G-PROTEIN BETA-BARREL RNA BINDING PROTEIN
Ref.: HIGH RESOLUTION CRYSTAL STRUCTURE OF BOVINE MITOCHO EF-TU IN COMPLEX WITH GDP. J.MOL.BIOL. V. 297 421 2000
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 291 families.
1 1D2E Kd = 1 uM 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
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1D2E; Ligand: GDP; Similar sites found with APoc: 57
This union binding pocket(no: 1) in the query (biounit: 1d2e.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 3N5C GDP 1.23457
2 3AQ4 GDP 1.63043
3 5GOE GDP 2.01511
4 3TK1 GDP 2.42424
5 4DKX GDP 2.77778
6 3T5G GDP 3.28947
7 4YC7 GNP 3.31492
8 3MD0 GDP 3.38028
9 5M04 GDP 3.61111
10 4D0N GDP 3.75335
11 4LC1 GDP 4.1543
12 2A5J GDP 4.18848
13 1BG2 ADP 4.30769
14 1FZQ GDP 4.41989
15 1Z0F GDP 4.46927
16 1Z0A GDP 4.5977
17 1YRB GDP 5.34351
18 3CNL GNP 5.34351
19 1VG1 GDP 5.40541
20 1VG9 GDP 5.40541
21 1RE0 GDP 5.42986
22 1F6B GDP 6.56566
23 1YZG GDP 7.82123
24 1S8F GDP 7.9096
25 3T1O GDP 8.08081
26 5O74 GDP 8.12183
27 1TAD ALF 8.33333
28 1TAD GDP 8.33333
29 4HDO GNP 8.38323
30 1ZJ6 G3D 8.55615
31 1MKY GDP 8.81612
32 1PUJ GNP 8.86525
33 5E95 GDP 8.92857
34 6D5E GNP 8.98204
35 4DCT GDP 9.06801
36 6G14 G4P 9.18367
37 2RCN GDP 10.0559
38 3Q72 GNP 10.241
39 1SVI GDP 10.2564
40 2CJW GDP 10.9375
41 4R98 GNH 12.1771
42 2WIC GNP 13.1086
43 1S9D GDP 13.3005
44 2HT6 GDP 13.7931
45 1DS6 GDP 13.8889
46 1OIV GDP 14.1361
47 3EC1 GDP 17.0732
48 5H7J GCP 18.3879
49 5H7K GDP 18.3879
50 3GJ0 GDP 21.267
51 1MR3 G3D 21.547
52 5BXQ GDP 21.7593
53 3CH5 GDP 21.7593
54 2WJG GDP 25.5319
55 2WJH GDP 28.9157
56 3Q85 GNP 30.7692
57 1I4D GDP 31.6964
Pocket No.: 2; Query (leader) PDB : 1D2E; 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: 1d2e.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1D2E; 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: 1d2e.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 1D2E; 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: 1d2e.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
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