Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GNP A:501;
Valid;
none;
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522.196 C10 H17 N6 O13 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: GNP; Similar ligands found: 129
No: Ligand ECFP6 Tc MDL keys Tc
1 9GM 1 1
2 GNP 1 1
3 GDP 0.839506 0.973684
4 GP3 0.82716 0.948718
5 GTP 0.809524 0.973684
6 GNH 0.807229 0.986842
7 GCP 0.77907 0.948718
8 G1R 0.77907 0.961039
9 GSP 0.770115 0.925
10 5GP 0.756098 0.960526
11 G 0.756098 0.960526
12 G2R 0.747253 0.936709
13 GMV 0.747126 0.948718
14 GAV 0.714286 0.936709
15 GP2 0.712644 0.936709
16 G2P 0.711111 0.936709
17 Y9Z 0.708333 0.880952
18 GDD 0.690722 0.936709
19 GKE 0.690722 0.936709
20 GDC 0.690722 0.936709
21 G5P 0.686869 0.948718
22 GPG 0.684211 0.936709
23 GFB 0.683673 0.936709
24 GDR 0.683673 0.936709
25 GTG 0.683673 0.91358
26 GDP BEF 0.681319 0.911392
27 GKD 0.68 0.936709
28 JB2 0.68 0.936709
29 6CK 0.676768 0.91358
30 G3A 0.676768 0.948718
31 GTP MG 0.673913 0.935065
32 GDX 0.673267 0.948718
33 ALF 5GP 0.67033 0.86747
34 YGP 0.663265 0.879518
35 GPD 0.656863 0.902439
36 GDP AF3 0.645833 0.86747
37 GDP ALF 0.645833 0.86747
38 JB3 0.641509 0.925
39 DBG 0.640351 0.974359
40 G3D 0.638298 0.960526
41 G4P 0.625 0.960526
42 GMP 0.621951 0.857143
43 NGD 0.62037 0.936709
44 GGM 0.618182 0.925926
45 0O2 0.616162 0.960526
46 KB7 0.612903 0.807229
47 2MD 0.603604 0.870588
48 CAG 0.60177 0.904762
49 FEG 0.590909 0.858824
50 U2G 0.590909 0.91358
51 GDP 7MG 0.590476 0.888889
52 MGD 0.587719 0.870588
53 ZGP 0.585586 0.848837
54 CG2 0.580357 0.91358
55 KBD 0.568627 0.807229
56 ANP 0.568421 0.922078
57 PGD 0.567797 0.902439
58 MD1 0.567797 0.870588
59 3GP 0.56044 0.922078
60 TPG 0.558333 0.822222
61 GH3 0.55 0.948052
62 KBJ 0.54717 0.77907
63 FE9 0.546219 0.778947
64 GPX 0.539216 0.922078
65 G4M 0.539062 0.860465
66 DGI 0.536082 0.9
67 BGO 0.535088 0.901235
68 IDP 0.53125 0.947368
69 DGT 0.53 0.9
70 2GP 0.526882 0.935065
71 G1R G1R 0.520325 0.901235
72 QBQ 0.515152 0.960526
73 I2C FE2 CMO CMO 0.508197 0.811111
74 AGO 0.504202 0.91358
75 P2G 0.5 0.860759
76 G1G 0.5 0.902439
77 MGP 0.49505 0.936709
78 R5I 0.49505 0.922078
79 R7I 0.49505 0.922078
80 PGD O 0.492063 0.831461
81 6G0 0.490196 0.936709
82 P1G 0.489796 0.85
83 AKW 0.483051 0.869048
84 DG 0.474227 0.8875
85 DGP 0.474227 0.8875
86 IMP 0.463918 0.934211
87 G2Q 0.462963 0.936709
88 CZF 0.460784 0.909091
89 GPC 0.459677 0.858824
90 G C 0.459016 0.878049
91 GTA 0.448276 0.91358
92 G7M 0.444444 0.924051
93 MAP 0.439252 0.898734
94 B4P 0.434343 0.871795
95 ADP 0.434343 0.896104
96 AP5 0.434343 0.871795
97 A2D 0.43299 0.871795
98 AT4 0.43 0.8625
99 SGP 0.425743 0.807229
100 AU1 0.425743 0.922078
101 BA3 0.424242 0.871795
102 APC G U 0.423077 0.864198
103 C2E 0.423077 0.897436
104 35G 0.423077 0.909091
105 PCG 0.423077 0.909091
106 HEJ 0.421569 0.896104
107 ATP 0.421569 0.896104
108 ACQ 0.419048 0.873418
109 5GP 5GP 0.419048 0.860759
110 AQP 0.417476 0.896104
111 5FA 0.417476 0.896104
112 01G 0.417391 0.880952
113 UNP 0.415842 0.810127
114 AN2 0.415842 0.909091
115 6AD 0.415094 0.821429
116 M33 0.411765 0.860759
117 ITT 0.411765 0.846154
118 JSQ 0.409524 0.851852
119 HFD 0.409524 0.851852
120 ACP 0.407767 0.873418
121 KG4 0.407767 0.873418
122 6YZ 0.407407 0.873418
123 AR6 0.403846 0.871795
124 APR 0.403846 0.871795
125 A4P 0.403226 0.848837
126 UCG 0.402985 0.888889
127 M7G A2M G 0.4 0.791209
128 AD9 0.4 0.873418
129 AGS 0.4 0.851852
Similar Ligands (3D)
Ligand no: 1; Ligand: GNP; Similar ligands found: 41
No: Ligand Similarity coefficient
1 BEF GDP 0.9966
2 ALF GDP 0.9853
3 BEF ADP 0.9788
4 DTP 0.9719
5 ADP BEF 0.9564
6 ADP ALF 0.9518
7 GDP MG 0.9489
8 ADP AF3 0.9407
9 UTP 0.9203
10 ADP MG 0.9170
11 CTP 0.9164
12 ATF 0.9160
13 MGT 0.9145
14 P5A 0.9069
15 APC 0.8983
16 AMO 0.8940
17 DSZ 0.8934
18 SSA 0.8828
19 TSB 0.8826
20 A12 0.8814
21 ATP MG 0.8808
22 8X1 0.8806
23 PR8 0.8796
24 DAT 0.8750
25 5AL 0.8746
26 MGO 0.8726
27 NSS 0.8721
28 G5A 0.8710
29 3AT 0.8675
30 SRP 0.8665
31 SAM 0.8658
32 TAT 0.8655
33 A5A 0.8651
34 4AD 0.8639
35 KAA 0.8631
36 8DG 0.8607
37 VO4 ADP 0.8602
38 GCP G 0.8590
39 ADX 0.8588
40 ANP MG 0.8566
41 TTP 0.8526
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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