Receptor
PDB id Resolution Class Description Source Keywords
3cnn 2.3 Å NON-ENZYME: OTHER GTP-BOUND STRUCTURE OF TM YLQF THERMOTOGA MARITIMA YLQF CIRCULAR PERMUTATION GTP SIGNALING PROTEIN
Ref.: CRYSTAL STRUCTURE OF YLQF, A CIRCULARLY PERMUTED GTPASE: IMPLICATIONS FOR ITS GTPASE ACTIVATION IN 50 S RIBOSOMAL SUBUNIT ASSEMBLY PROTEINS V. 72 1363 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GTP A:263;
 Valid;
 none;
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523.18 C10 H16 N5 O14 P3 c1nc2...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3CNL 2 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF GNP-BOUND YLQF FROM T. MARITIMA THERMOTOGA MARITIMA YLQF CIRCULAR PERMUTATION GNP SIGNALING PROTEIN
Ref.: CRYSTAL STRUCTURE OF YLQF, A CIRCULARLY PERMUTED GTPASE: IMPLICATIONS FOR ITS GTPASE ACTIVATION IN 50 S RIBOSOMAL SUBUNIT ASSEMBLY PROTEINS V. 72 1363 2008
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 3CNN - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
2 3CNL - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
3 3CNO - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 3CNN - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
2 3CNL - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
3 3CNO - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
50% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 214 families.
1 6G12 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
2 6G14 Kd = 3.26 uM G4P C10 H17 N5 O17 P4 c1nc2c(n1[....
3 6G15 Kd = 4.31 uM C1Z C10 H18 N5 O20 P5 c1nc2c(n1[....
4 6G0Z Kd = 4.84 uM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
5 1PUJ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
6 3CNN - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
7 3CNL - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
8 3CNO - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: GTP; Similar ligands found: 155
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 GDP BEF 0.696629 0.935065
31 JB2 0.693878 0.961039
32 GKD 0.693878 0.961039
33 GTP MG 0.688889 0.96
34 GDX 0.686869 0.973684
35 ALF 5GP 0.685393 0.888889
36 GH3 0.681319 0.973333
37 YGP 0.677083 0.901235
38 G3D 0.67033 0.986486
39 GDP AF3 0.659574 0.888889
40 GDP ALF 0.659574 0.888889
41 DGT 0.659341 0.923077
42 GMP 0.658228 0.88
43 G4P 0.655914 0.986486
44 JB3 0.653846 0.948718
45 NGD 0.647619 0.961039
46 QBQ 0.644444 0.986486
47 CAG 0.642202 0.880952
48 2MD 0.62963 0.891566
49 MGP 0.619565 0.961039
50 U2G 0.616822 0.936709
51 6G0 0.612903 0.961039
52 MGD 0.612613 0.891566
53 KB7 0.608696 0.82716
54 TPG 0.608696 0.840909
55 CG2 0.605505 0.936709
56 GDP 7MG 0.601942 0.911392
57 FEG 0.601852 0.879518
58 ZGP 0.59633 0.869048
59 PGD 0.591304 0.925
60 MD1 0.591304 0.891566
61 3GP 0.590909 0.946667
62 GPX 0.581633 0.946667
63 CZF 0.580645 0.933333
64 DGI 0.580645 0.923077
65 IDP 0.576087 0.972973
66 DBG 0.567797 0.948718
67 KBD 0.564356 0.82716
68 2GP 0.555556 0.96
69 FE9 0.555556 0.776596
70 G4M 0.547619 0.880952
71 BGO 0.544643 0.924051
72 KBJ 0.542857 0.797619
73 HEJ 0.537634 0.92
74 ATP 0.537634 0.92
75 G1G 0.533898 0.925
76 AQP 0.531915 0.92
77 5FA 0.531915 0.92
78 JSQ 0.520833 0.873418
79 HFD 0.520833 0.873418
80 R7I 0.520408 0.946667
81 R5I 0.520408 0.946667
82 01G 0.518868 0.902439
83 I2C FE2 CMO CMO 0.516667 0.808989
84 ITT 0.510638 0.868421
85 P2G 0.510638 0.883117
86 AKW 0.504348 0.890244
87 GGM 0.504274 0.901235
88 G1R G1R 0.504065 0.924051
89 DG 0.5 0.910256
90 DGP 0.5 0.910256
91 PGD O 0.5 0.850575
92 MGO 0.5 0.864198
93 P1G 0.5 0.871795
94 GTA 0.495495 0.936709
95 PRT 0.490741 0.959459
96 AP5 0.489362 0.894737
97 IMP 0.489362 0.959459
98 B4P 0.489362 0.894737
99 7DT 0.484536 0.906667
100 GPC 0.479339 0.879518
101 G C 0.478992 0.9
102 BA3 0.478723 0.894737
103 ADP 0.473684 0.92
104 G2Q 0.471698 0.961039
105 6YZ 0.470588 0.896104
106 G7M 0.46875 0.948052
107 C1Z 0.462963 0.986486
108 25L 0.458716 0.907895
109 A2D 0.457447 0.894737
110 RGT 0.45045 0.909091
111 AGS 0.45 0.873418
112 SGP 0.44898 0.82716
113 A4P 0.445378 0.869048
114 ANP 0.441176 0.896104
115 8GT 0.441176 0.875
116 ACQ 0.441176 0.896104
117 APC G U 0.440945 0.886076
118 AT4 0.438776 0.884615
119 6AD 0.436893 0.841463
120 UP5 0.432203 0.873418
121 35G 0.431373 0.933333
122 C2E 0.431373 0.921053
123 PCG 0.431373 0.933333
124 5GP 5GP 0.427184 0.883117
125 TAT 0.427184 0.884615
126 T99 0.427184 0.884615
127 APR 0.425743 0.894737
128 AR6 0.425743 0.894737
129 AN2 0.424242 0.907895
130 7DD 0.424242 0.906667
131 AD9 0.421569 0.896104
132 7D4 0.42 0.835443
133 M33 0.42 0.883117
134 UCG 0.419847 0.911392
135 HDV 0.419048 0.825
136 H6Y 0.419048 0.946667
137 GZ0 0.416667 0.948718
138 ACP 0.415842 0.896104
139 T5A 0.414634 0.802326
140 A3R 0.412844 0.839506
141 MGQ 0.412844 0.935897
142 A1R 0.412844 0.839506
143 ADQ 0.412844 0.871795
144 HQG 0.411215 0.907895
145 MGT 0.411215 0.823529
146 93A 0.41 0.833333
147 A22 0.407407 0.907895
148 CA0 0.405941 0.896104
149 ATF 0.40566 0.884615
150 M7G A2M G 0.405229 0.808989
151 AGO 0.404762 0.888889
152 NYZ 0.403846 0.935897
153 KG4 0.401961 0.896104
154 MGV 0.401786 0.890244
155 CGP 0.4 0.86747
Similar Ligands (3D)
Ligand no: 1; Ligand: GTP; Similar ligands found: 41
No: Ligand Similarity coefficient
1 BEF GDP 0.9967
2 ALF GDP 0.9831
3 BEF ADP 0.9768
4 DTP 0.9699
5 8DG 0.9681
6 3AT 0.9677
7 APC 0.9540
8 GDP MG 0.9519
9 ADP BEF 0.9514
10 ADP ALF 0.9503
11 ADP AF3 0.9408
12 ALF ADP 0.9332
13 HF7 0.9242
14 UTP 0.9210
15 DZ4 0.9149
16 CTP 0.9139
17 AMO 0.9072
18 ADP MG 0.9070
19 DSZ 0.8952
20 2KH 0.8870
21 TTP 0.8866
22 6U4 0.8793
23 54H 0.8791
24 VO4 ADP 0.8791
25 EEM 0.8762
26 ATP MG 0.8751
27 SSA 0.8728
28 5AL 0.8707
29 SAM 0.8703
30 KAA 0.8702
31 2TM 0.8697
32 DCP 0.8670
33 DAT 0.8669
34 ADX 0.8660
35 GSU 0.8654
36 SFG 0.8645
37 8X1 0.8616
38 A5A 0.8614
39 D3T 0.8609
40 G5A 0.8580
41 RSN 0.8567
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3CNL; Ligand: GNP; Similar sites found with APoc: 245
This union binding pocket(no: 1) in the query (biounit: 3cnl.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 4LPS GDP 1.65289
2 1KK1 GNP 4.19847
3 2QN6 GDP 4.58015
4 2HF9 GSP 4.86726
5 2HF9 GSP 4.86726
6 3CX8 GSP 5.34351
7 1SKQ GDP 5.34351
8 1D2E GDP 5.34351
9 1D2E GDP 5.34351
10 1D2E GDP 5.34351
11 1D2E GDP 5.34351
12 1SKQ GDP 5.34351
13 5GOE GDP 5.34351
14 1TQ4 GDP 5.72519
15 4P4T GDP 5.72519
16 1ZD9 GDP 5.85106
17 2A9K GDP 5.88235
18 2XTZ GSP 6.10687
19 2XTZ GSP 6.10687
20 6AU6 GDP 6.10687
21 6MHE GDP 6.10687
22 1YRB GDP 6.10687
23 1ZC3 GNP 6.28571
24 1ZC3 GNP 6.28571
25 5UQW GDP 6.34921
26 5M04 GDP 6.38889
27 1BH2 GSP 6.48855
28 6CRK GDP 6.48855
29 1Y3A GDP 6.48855
30 1Y3A GDP 6.48855
31 1GP2 GDP 6.48855
32 1U8Z GDP 6.54762
33 1U8Z GDP 6.54762
34 3GJ8 GDP 6.78733
35 3GJ8 GDP 6.78733
36 3GJ0 GDP 6.78733
37 3GJ7 GDP 6.78733
38 3GJ4 GDP 6.78733
39 3GJ5 GDP 6.78733
40 3GJ3 GDP 6.78733
41 3GJ7 GDP 6.78733
42 3GJ0 GDP 6.78733
43 5CK5 GDP 6.87023
44 5CK5 GDP 6.87023
45 5CK5 GDP 6.87023
46 5CK5 GDP 6.87023
47 2C5L GTP 6.93642
48 2C5L GTP 6.93642
49 6ZIO GDP 6.93642
50 6ZIO GDP 6.93642
51 1IBR GNP 6.94444
52 3CH5 GDP 6.94444
53 5BXQ GDP 6.94444
54 5BXQ GDP 6.94444
55 4K81 GTP 7.01754
56 4K81 GTP 7.01754
57 5WDR GNP 7.01754
58 5WDR GNP 7.01754
59 3Q85 GNP 7.10059
60 3Q85 GNP 7.10059
61 5O2T GSP 7.10059
62 1YVD GNP 7.10059
63 6BVJ GNP 7.18563
64 6BVL GNP 7.18563
65 6BVI GNP 7.18563
66 6D5E GNP 7.18563
67 6BVK GNP 7.18563
68 6D5H GNP 7.18563
69 6D56 GNP 7.18563
70 6D5J GNP 7.18563
71 6V9F GNP 7.18563
72 6V9L GNP 7.18563
73 6D5G GNP 7.18563
74 6V9J GNP 7.18563
75 6V9N GNP 7.18563
76 6D5W GNP 7.18563
77 3Q72 GNP 7.22892
78 3Q72 GNP 7.22892
79 5WLB GNP 7.22892
80 1NVV GNP 7.22892
81 1NVV GNP 7.22892
82 1NVV GNP 7.22892
83 3DDC GNP 7.22892
84 5FG3 GDP 7.25191
85 5YT0 GDP 7.25191
86 2CJW GDP 7.29167
87 2CJW GDP 7.29167
88 1S8F GDP 7.34463
89 1S8F GDP 7.34463
90 5KUT GDP 7.40741
91 3QBT GNP 7.47126
92 3QBT GNP 7.47126
93 4M9Q GNP 7.48899
94 5XKT GNP 7.5
95 5XKT GNP 7.5
96 5UWP GNP 7.63359
97 5DIF GNP 7.63359
98 5UWU GNP 7.63359
99 5UWW GNP 7.63359
100 4HAT GNP 7.63359
101 5UWH GNP 7.63359
102 6CIT GNP 7.63359
103 5UWS GNP 7.63359
104 5UWO GNP 7.63359
105 5UWQ GNP 7.63359
106 5DHF GNP 7.63359
107 5UWT GNP 7.63359
108 6X2Y GNP 7.63359
109 6X2P GNP 7.63359
110 6X2U GNP 7.63359
111 6X2S GNP 7.63359
112 1G16 GDP 7.64706
113 1G16 GDP 7.64706
114 1G16 GDP 7.64706
115 3BC1 GNP 7.69231
116 3BC1 GNP 7.69231
117 1Z2A GDP 7.7381
118 5O74 GDP 7.77778
119 5O74 GDP 7.77778
120 5O74 GDP 7.77778
121 1CLU DBG 7.83133
122 2HT6 GDP 8.04598
123 2HT6 GDP 8.04598
124 5KDO GDP 8.10811
125 3M1I GTP 8.21918
126 3MD0 GDP 8.73239
127 3T1O GDP 9.09091
128 3T12 GDP ALF 9.09091
129 3T1O GDP 9.09091
130 3WXM GTP 9.16031
131 3WXM GTP 9.16031
132 3WXM GTP 9.16031
133 3WXM GTP 9.16031
134 1VG8 GNP 9.17874
135 1VG8 GNP 9.17874
136 1VG8 GNP 9.17874
137 1Z0A GDP 9.1954
138 1Z0A GDP 9.1954
139 1Z0A GDP 9.1954
140 1Z0A GDP 9.1954
141 1Z0A GDP 9.1954
142 1Z0A GDP 9.1954
143 3RAB GNP 9.46746
144 1Z0F GDP 9.49721
145 1F6B GDP 9.59596
146 1F6B GDP 9.59596
147 1O3Y GTP 9.63855
148 1O3Y GTP 9.63855
149 1RE0 GDP 9.7561
150 1S9D GDP 9.7561
151 1YZG GDP 10.0559
152 1VG9 GDP 10.2703
153 1VG9 GDP 10.2703
154 1VG9 GDP 10.2703
155 1VG1 GDP 10.2703
156 1R4A GNP 10.303
157 1R4A GNP 10.303
158 1R4A GNP 10.303
159 1R4A GNP 10.303
160 1DAR GDP 10.3053
161 1ZJ6 G3D 10.6952
162 1ZJ6 G3D 10.6952
163 1ZJ6 G3D 10.6952
164 4HDO GNP 10.7784
165 2A5J GDP 10.9948
166 1MR3 G3D 11.0497
167 4BAS GNP 11.0553
168 2C78 GNP 11.4504
169 6A8D GDP 11.4583
170 1TU3 GNP 11.6959
171 1TU3 GNP 11.6959
172 1TU3 GNP 11.6959
173 1WF3 GNP 11.8321
174 6VJF GCP 11.8321
175 6VJF GCP 11.8321
176 1Z0J GTP 11.8644
177 3MJH GTP 11.9048
178 2ZEJ GDP 11.9565
179 2ZEJ GDP 11.9565
180 4B47 GDP 12.2137
181 2BVN GNP 12.2137
182 1D8T GDP 12.2137
183 1D8T GDP 12.2137
184 2HCJ GDP 12.2137
185 1G7S GDP 12.2137
186 1GOT GDP 12.2137
187 2FH5 GTP 13.0841
188 2FH5 GTP 13.0841
189 2FFQ GSP 13.3588
190 5TB5 GDP 13.3588
191 1MKY GDP 13.7405
192 4V0K GDP 14.2012
193 1KSH GDP 14.5161
194 4NON GDP 14.6154
195 1M2O GNP 15.2632
196 1M2O GNP 15.2632
197 1M2O GNP 15.2632
198 1SVI GDP 15.3846
199 1FZQ GDP 15.4696
200 2WJG GDP 17.0213
201 2WJG GDP 17.0213
202 1Z08 GNP 17.0588
203 1Z08 GNP 17.0588
204 1Z08 GNP 17.0588
205 1Z08 GNP 17.0588
206 1Z08 GNP 17.0588
207 5XC5 GTP 17.6136
208 2BME GNP 17.7419
209 2BME GNP 17.7419
210 3EC1 GDP 18.3206
211 2WJH GDP 19.2771
212 1OIV GDP 19.3717
213 1OIV GDP 19.3717
214 2OM2 GDP 19.4444
215 2OM2 GDP 19.4444
216 1Z0K GTP 19.7674
217 1J2J GTP 20
218 3W5J GDP 20.5882
219 2WIC GNP 21.3483
220 2WIC GNP 21.3483
221 1GUA GNP 22.2222
222 6BSX E7S 23.0337
223 6BSX GDP 23.0337
224 6BSX E7S 23.0337
225 6BSX GDP 23.0337
226 6BSX GDP 23.0337
227 5Z2M GTP 23.1884
228 3T5G GDP 23.2044
229 1TAD GDP 23.6641
230 1TAD ALF 23.6641
231 1FQJ GDP 23.6641
232 1FQK GDP 23.6641
233 2RCN GDP 24.0458
234 2RCN GDP 24.0458
235 3RWO GDP 25.4054
236 3RWO GDP 25.4054
237 3RWO GDP 25.4054
238 3RWO GDP 25.4054
239 2HV8 GTP 26.1628
240 1UPT GTP 26.3158
241 1UPT GTP 26.3158
242 2QTV GNP 26.5306
243 1OIX GDP 26.7016
244 2D7C GTP 26.9461
245 1CS4 GSP 29.771
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