Receptor
PDB id Resolution Class Description Source Keywords
3WY9 2.3 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF A COMPLEX OF THE ARCHAEAL RIBOSOMAL STA AP1 AND THE GDP-BOUND ARCHAEAL ELONGATION FACTOR AEF1ALPHA PYROCOCCUS HORIKOSHII OT3 MULTI-DOMAIN GTPASE AMINOACYL-TRNA DELIVERY GTP AMINOACYSTALK PROTEIN TRANSLATION-RIBOSOMAL PROTEIN COMPLEX
Ref.: MOLECULAR INSIGHTS INTO THE INTERACTION OF THE RIBO STALK PROTEIN WITH ELONGATION FACTOR 1 ALPHA NUCLEIC ACIDS RES. 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP A:500;
B:500;
Valid;
Valid;
none;
none;
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443.201 C10 H15 N5 O11 P2 c1nc2...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3WY9 2.3 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF A COMPLEX OF THE ARCHAEAL RIBOSOMAL STA AP1 AND THE GDP-BOUND ARCHAEAL ELONGATION FACTOR AEF1ALPHA PYROCOCCUS HORIKOSHII OT3 MULTI-DOMAIN GTPASE AMINOACYL-TRNA DELIVERY GTP AMINOACYSTALK PROTEIN TRANSLATION-RIBOSOMAL PROTEIN COMPLEX
Ref.: MOLECULAR INSIGHTS INTO THE INTERACTION OF THE RIBO STALK PROTEIN WITH ELONGATION FACTOR 1 ALPHA NUCLEIC ACIDS RES. 2014
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 3WY9 - GDP C10 H15 N5 O11 P2 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 3WY9 - GDP C10 H15 N5 O11 P2 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 3WY9 - 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 : 3WY9; Ligand: GDP; Similar sites found with APoc: 179
This union binding pocket(no: 1) in the query (biounit: 3wy9.bio2) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 1Z0A GDP None
2 1Y3A GDP 1.51976
3 2OM2 GDP 1.53846
4 2A5J GDP 1.57068
5 1BH2 GSP 1.5873
6 1VG1 GDP 2.16216
7 2HV8 GTP 2.32558
8 2D7C GTP 2.39521
9 2RCN GDP 2.51397
10 3TK1 GDP 2.72727
11 5Z2M GTP 2.89855
12 1G16 GDP 2.94118
13 2F9L GDP 3.01508
14 1ZJ6 G3D 3.20856
15 1YZG GDP 3.35196
16 1GWN GTP 3.41463
17 3MD0 GDP 3.66197
18 1OIX GDP 3.66492
19 1OIV GDP 3.66492
20 5KUT GDP 3.7037
21 1M7B GTP 3.80435
22 1YRB GDP 3.81679
23 4LC1 GDP 3.91705
24 3GJ4 GDP 4.0724
25 3GJ5 GDP 4.0724
26 1Z2A GDP 4.14747
27 2XTZ GSP 4.23729
28 1PUJ GNP 4.25532
29 3RWO GDP 4.32432
30 1Z0F GDP 4.46927
31 4U5X GNP 4.49438
32 5XKT GNP 4.5
33 2G77 GDP 4.54545
34 4DID GDP 4.60526
35 1Z06 GNP 4.7619
36 3MJH GTP 4.7619
37 5OCG GNP 4.7619
38 1O3Y GTP 4.81928
39 5TAR GDP 4.86486
40 5TB5 GDP 4.86486
41 1RE0 GDP 4.87805
42 1WF3 GNP 4.98339
43 5O2T GSP 5.32544
44 3T1O GDP 5.55556
45 3T12 GDP ALF 5.88235
46 1TU3 GNP 6.32911
47 1CLU DBG 6.45161
48 6D5E GNP 6.45161
49 6D5G GNP 6.45161
50 6D5J GNP 6.45161
51 6BVL GNP 6.45161
52 6D56 GNP 6.45161
53 6D5L GNP 6.45161
54 6BVJ GNP 6.45161
55 6D59 GNP 6.45161
56 6D5H GNP 6.45161
57 6D55 GNP 6.45161
58 6BVI GNP 6.45161
59 6BVK GNP 6.45161
60 6D5V GNP 6.45161
61 1U8Z GDP 6.54762
62 3T5G GDP 6.62983
63 2CJW GDP 6.77083
64 3GJ3 GDP 6.78733
65 3GJ0 GDP 6.78733
66 3CH5 GDP 6.94444
67 5BXQ GDP 6.94444
68 2A9K GDP 7.17489
69 3Q72 GNP 7.22892
70 5XC5 GTP 7.38636
71 3KUD GDP 7.40741
72 2HT6 GDP 7.47126
73 1KSH GDP 7.52688
74 3GJ8 GDP 7.6087
75 3RAB GNP 7.69231
76 1ZD9 GDP 7.97872
77 1LFD GNP 8.04598
78 3Q85 GNP 8.28402
79 4V0K GDP 8.28402
80 1X1R GDP 8.29493
81 5UPK GNP 8.33333
82 1FZQ GDP 8.75576
83 2FFQ GSP 8.77193
84 1ZC3 GNP 8.84956
85 2ODE ALF GDP 8.98618
86 3QBT GNP 9.1954
87 3EC1 GDP 9.21409
88 4HAT GNP 9.21659
89 5DIF GNP 9.21659
90 5UWP GNP 9.21659
91 5UWW GNP 9.21659
92 5UWQ GNP 9.21659
93 5UWU GNP 9.21659
94 5UWI GNP 9.21659
95 6CIT GNP 9.21659
96 5UWJ GNP 9.21659
97 5UWR GNP 9.21659
98 5UWH GNP 9.21659
99 5DHF GNP 9.21659
100 5UWO GNP 9.21659
101 1GUA GNP 9.58084
102 3GJ7 GDP 10.2041
103 2GCN GDP 10.4478
104 1D5C GDP 10.4938
105 5KDO GDP 10.8108
106 5HCN GCP 10.8295
107 4BAS GNP 11.0553
108 5HPY GDP 11.3514
109 1KMQ GNP 11.413
110 1MR3 G3D 11.6022
111 1S9D GDP 11.8227
112 3CX8 GSP 11.9816
113 6G14 G4P 12.5
114 1CXZ GSP 12.7907
115 1SVI GDP 13.1336
116 1KY3 GDP 13.1868
117 4HI0 GDP 13.5678
118 1Z0K GTP 14.4928
119 1TAD GDP 15.625
120 1TAD ALF 15.625
121 1R4A GNP 15.6863
122 4C4P GNP 15.8879
123 4DCT GDP 16.3594
124 3PQC GDP 16.5899
125 5WLB GNP 17.6471
126 6CRK GDP 18.3099
127 1GP2 GDP 18.3099
128 1UPT GTP 18.3333
129 4NON GDP 18.75
130 4HDO GNP 18.75
131 2NGR GDP 18.75
132 1NF3 GNP 18.75
133 1OW3 GDP 18.75
134 1G7S GDP 19.1244
135 2C5L GTP 21.875
136 2QTV GNP 21.875
137 2ZEJ GDP 21.875
138 3BC1 GNP 22.0339
139 1DAR GDP 22.5806
140 4R98 GNH 23.2472
141 1YVD GNP 24.8521
142 1MKY GDP 25
143 1VG9 GDP 25
144 1VG0 GDP 25
145 1F6B GDP 25
146 1S8F GDP 25
147 1Z0J GTP 25.4237
148 2WJG GDP 26.0638
149 5UWT GNP 26.087
150 5FG3 GDP 26.4977
151 5UWS GNP 27.2727
152 1GOT GDP 28.125
153 1WA5 GTP 28.125
154 2WIC GNP 28.125
155 2WJH GDP 29.5181
156 3AB3 GDP 31.25
157 6AU6 GDP 31.25
158 1CS4 GSP 31.25
159 1TQ4 GDP 31.25
160 1Z08 GNP 31.25
161 1WQ1 GDP 31.25
162 4RD0 GDP 34.6988
163 2QN6 GDP 35.5072
164 5M04 GDP 37.5
165 1FQK GDP 37.5
166 1DS6 GDP 37.5
167 1MH1 GNP 37.5
168 2W2X GSP 37.5
169 1I4D GDP 37.5
170 2FJU GSP 37.5
171 1E96 GTP 37.5
172 2WKQ GTP 37.5
173 1G4U GDP 37.5
174 5YT0 GDP 38.0952
175 4B47 GDP 40.625
176 3M1I GTP 40.625
177 1KK1 GNP 41.2195
178 1J2J GTP 44.4444
179 5O74 GDP 46.875
Pocket No.: 2; Query (leader) PDB : 3WY9; 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: 3wy9.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
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