Receptor
PDB id Resolution Class Description Source Keywords
3VMF 2.3 Å NON-ENZYME: OTHER ARCHAEAL PROTEIN AEROPYRUM PERNIX TRANSLATION TERMINATION TRANSLATION
Ref.: STRUCTURAL BASIS FOR TRANSLATION TERMINATION BY ARC AND GTP-BOUND EF1ALPHA COMPLEX NUCLEIC ACIDS RES. V. 40 9319 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GTP A:501;
Valid;
none;
submit data
523.18 C10 H16 N5 O14 P3 c1nc2...
MG A:502;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
SO4 A:503;
Invalid;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3VMF 2.3 Å NON-ENZYME: OTHER ARCHAEAL PROTEIN AEROPYRUM PERNIX TRANSLATION TERMINATION TRANSLATION
Ref.: STRUCTURAL BASIS FOR TRANSLATION TERMINATION BY ARC AND GTP-BOUND EF1ALPHA COMPLEX NUCLEIC ACIDS RES. V. 40 9319 2012
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 3VMF - GTP C10 H16 N5 O14 P3 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 3VMF - GTP C10 H16 N5 O14 P3 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 3VMF - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GTP; Similar ligands found: 156
No: Ligand ECFP6 Tc MDL keys Tc
1 GTP 1 1
2 GP3 0.921053 0.973684
3 GDP 0.909091 1
4 GSP 0.853659 0.948718
5 GNH 0.82716 0.986667
6 G1R 0.819277 0.986667
7 GAV 0.811765 0.961039
8 9GM 0.809524 0.973684
9 GNP 0.809524 0.973684
10 GCP 0.797619 0.973684
11 5GP 0.797468 0.986486
12 G 0.797468 0.986486
13 GMV 0.764706 0.973684
14 G2R 0.764045 0.961039
15 G5P 0.755319 0.973684
16 GTG 0.752688 0.936709
17 G2P 0.747126 0.961039
18 G3A 0.744681 0.973684
19 GDD 0.741935 0.961039
20 GDC 0.741935 0.961039
21 GKE 0.741935 0.961039
22 0O2 0.736264 0.986486
23 GP2 0.729412 0.961039
24 6CK 0.726316 0.936709
25 Y9Z 0.723404 0.902439
26 GPG 0.717391 0.961039
27 GFB 0.715789 0.961039
28 GDR 0.715789 0.961039
29 GPD 0.704082 0.925
30 GKD 0.693878 0.961039
31 JB2 0.693878 0.961039
32 GDX 0.686869 0.973684
33 ALF 5GP 0.685393 0.888889
34 GH3 0.681319 0.973333
35 YGP 0.677083 0.901235
36 G3D 0.67033 0.986486
37 GDP AF3 0.659574 0.888889
38 ALF GDP 0.659574 0.888889
39 GDP ALF 0.659574 0.888889
40 DGT 0.659341 0.923077
41 GMP 0.658228 0.88
42 G4P 0.655914 0.986486
43 JB3 0.653846 0.948718
44 NGD 0.647619 0.961039
45 CAG 0.642202 0.880952
46 2MD 0.62963 0.891566
47 MGP 0.619565 0.961039
48 U2G 0.616822 0.936709
49 6G0 0.612903 0.961039
50 MGD 0.612613 0.891566
51 TPG 0.608696 0.840909
52 CG2 0.605505 0.936709
53 GDP 7MG 0.601942 0.911392
54 FEG 0.601852 0.879518
55 G G 0.598039 0.948052
56 ZGP 0.59633 0.869048
57 PGD 0.591304 0.925
58 MD1 0.591304 0.891566
59 3GP 0.590909 0.946667
60 GPX 0.581633 0.946667
61 DGI 0.580645 0.923077
62 IDP 0.576087 0.972973
63 DBG 0.567797 0.948718
64 2GP 0.555556 0.96
65 FE9 0.555556 0.776596
66 G4M 0.547619 0.880952
67 BGO 0.544643 0.924051
68 GCP G 0.543689 0.921053
69 ATP 0.537634 0.92
70 HEJ 0.537634 0.92
71 G1G 0.533898 0.925
72 AQP 0.531915 0.92
73 5FA 0.531915 0.92
74 A G 0.525862 0.935065
75 G A A A 0.525862 0.923077
76 U A G G 0.521368 0.935065
77 HFD 0.520833 0.873418
78 R5I 0.520408 0.946667
79 R7I 0.520408 0.946667
80 01G 0.518868 0.902439
81 P2G 0.510638 0.883117
82 ITT 0.510638 0.868421
83 AKW 0.504348 0.890244
84 GGM 0.504274 0.901235
85 G1R G1R 0.504065 0.924051
86 DGP 0.5 0.910256
87 PGD O 0.5 0.850575
88 MGO 0.5 0.864198
89 DG 0.5 0.910256
90 P1G 0.5 0.871795
91 GTA 0.495495 0.936709
92 PRT 0.490741 0.959459
93 B4P 0.489362 0.894737
94 AP5 0.489362 0.894737
95 IMP 0.489362 0.959459
96 G U 0.487179 0.9
97 7DT 0.484536 0.906667
98 GPC 0.479339 0.879518
99 G C 0.478992 0.9
100 BA3 0.478723 0.894737
101 ADP 0.473684 0.92
102 G2Q 0.471698 0.961039
103 6YZ 0.470588 0.896104
104 G7M 0.46875 0.948052
105 C1Z 0.462963 0.986486
106 25L 0.458716 0.907895
107 A2D 0.457447 0.894737
108 RGT 0.45045 0.909091
109 AGS 0.45 0.873418
110 SAP 0.45 0.873418
111 SGP 0.44898 0.82716
112 A4P 0.445378 0.869048
113 G G G RPC 0.442623 0.875
114 ANP 0.441176 0.896104
115 ACQ 0.441176 0.896104
116 8GT 0.441176 0.875
117 APC G U 0.44 0.886076
118 AT4 0.438776 0.884615
119 G U34 0.438017 0.888889
120 6AD 0.436893 0.841463
121 G G G C 0.433071 0.9125
122 UP5 0.432203 0.873418
123 PCG 0.431373 0.933333
124 C2E 0.431373 0.921053
125 35G 0.431373 0.933333
126 A G C C 0.429688 0.911392
127 T99 0.427184 0.884615
128 5GP 5GP 0.427184 0.883117
129 TAT 0.427184 0.884615
130 AR6 0.425743 0.894737
131 APR 0.425743 0.894737
132 7DD 0.424242 0.906667
133 AN2 0.424242 0.907895
134 DG DG 0.423423 0.865854
135 AD9 0.421569 0.896104
136 M33 0.42 0.883117
137 7D4 0.42 0.835443
138 UCG 0.419847 0.911392
139 HDV 0.419048 0.825
140 H6Y 0.419048 0.946667
141 G C C C 0.416667 0.924051
142 ACP 0.415842 0.896104
143 T5A 0.414634 0.802326
144 A1R 0.412844 0.839506
145 ADQ 0.412844 0.871795
146 MGQ 0.412844 0.935897
147 A3R 0.412844 0.839506
148 MGT 0.411215 0.823529
149 A G U 0.410072 0.888889
150 93A 0.41 0.833333
151 A22 0.407407 0.907895
152 CA0 0.405941 0.896104
153 ATF 0.40566 0.884615
154 AGO 0.404762 0.888889
155 MGV 0.401786 0.890244
156 CGP 0.4 0.86747
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3VMF; Ligand: GTP; Similar sites found with APoc: 83
This union binding pocket(no: 1) in the query (biounit: 3vmf.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 2RCN GDP 2.51397
2 5M04 GDP 2.94906
3 3MD0 GDP 3.38028
4 2XTZ GSP 3.38983
5 3GJ3 GDP 3.61991
6 3GJ0 GDP 3.61991
7 3GJ4 GDP 4.0724
8 3GJ5 GDP 4.0724
9 1PUJ GNP 4.25532
10 6G14 G4P 4.42177
11 2A5J GDP 4.71204
12 1RYH GNP 4.92611
13 3TK1 GDP 5.15152
14 1Z0A GDP 5.17241
15 2FFQ GSP 5.26316
16 1YZQ GNP 5.29412
17 1Z0F GDP 5.58659
18 1VG8 GNP 5.7971
19 1KY3 GDP 6.04396
20 3GJ7 GDP 6.12245
21 1NRJ GTP 6.32911
22 1ZJ6 G3D 6.41711
23 1VG1 GDP 6.48649
24 1VG9 GDP 6.48649
25 1O3Y GTP 6.62651
26 1MR3 G3D 6.62983
27 1RE0 GDP 6.78733
28 3Q72 GNP 7.22892
29 1YZG GDP 7.26257
30 2GCO GNP 7.46269
31 3EC1 GDP 7.58808
32 2WIC GNP 7.86517
33 2FJU GSP 7.86517
34 1S8F GDP 7.9096
35 1YRB GDP 8.01527
36 3GJ8 GDP 8.69565
37 3RAB GNP 8.87574
38 2G77 GDP 9.09091
39 3QBT GNP 9.28571
40 5BXQ GDP 9.44882
41 1Z06 GNP 9.52381
42 4DCT GDP 9.65147
43 1SVI GDP 9.74359
44 2A5F GTP 10.3627
45 2BME GNP 10.7527
46 1M2O GNP 11.0526
47 2CJW GDP 11.4583
48 3CH5 GDP 11.5385
49 5WLB GNP 11.7647
50 3BC1 GNP 11.8644
51 2HT6 GDP 12.6437
52 4M9Q GNP 12.7753
53 1UPT GTP 15
54 2W2X GSP 15.3226
55 2FH5 GTP 15.4206
56 1CXZ GSP 16.2791
57 1EK0 GNP 17.0588
58 4BAS GNP 17.0854
59 3Q85 GNP 17.1598
60 3T12 GDP ALF 17.1717
61 1KSH GDP 17.7632
62 3T5G GDP 17.7632
63 1LFD GNP 18.3908
64 1FZQ GDP 18.7845
65 1Z0K GTP 18.8406
66 1MKY GDP 19.1344
67 2WJG GDP 19.6809
68 4LC1 GDP 19.8813
69 3MJH GTP 20.8333
70 1R4A GNP 21.5686
71 1S9D GDP 22.1675
72 2WJH GDP 22.2892
73 1F6B GDP 22.7273
74 1YVD GNP 23.6686
75 4RD0 GDP 23.8554
76 2QN6 GDP 24.1546
77 1J2J GTP 24.4444
78 4NCN GTP 26.8182
79 5FG3 GDP 30.4545
80 5O74 GDP 30.4569
81 4B47 GDP 34.7107
82 5YT0 GDP 35.989
83 1KK1 GNP 38.5366
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