Receptor
PDB id Resolution Class Description Source Keywords
1MKY 1.9 Å NON-ENZYME: BINDING STRUCTURAL ANALYSIS OF THE DOMAIN INTERACTIONS IN DER, A SWI PROTEIN CONTAINING TWO GTPASE DOMAINS THERMOTOGA MARITIMA GTPASE ENGA DER KH-DOMAIN TANDEM G-DOMAINS LIGAND BINDIPROTEIN
Ref.: DOMAIN ARRANGEMENT OF DER, A SWITCH PROTEIN CONTAIN GTPASE DOMAINS STRUCTURE V. 10 1649 2002
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP A:500;
Valid;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
PO4 A:601;
A:602;
A:603;
A:604;
A:605;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
94.971 O4 P [O-]P...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1MKY 1.9 Å NON-ENZYME: BINDING STRUCTURAL ANALYSIS OF THE DOMAIN INTERACTIONS IN DER, A SWI PROTEIN CONTAINING TWO GTPASE DOMAINS THERMOTOGA MARITIMA GTPASE ENGA DER KH-DOMAIN TANDEM G-DOMAINS LIGAND BINDIPROTEIN
Ref.: DOMAIN ARRANGEMENT OF DER, A SWITCH PROTEIN CONTAIN GTPASE DOMAINS STRUCTURE V. 10 1649 2002
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 544 families.
1 1MKY - 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 420 families.
1 1MKY - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 319 families.
1 2HJG - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 4DCT Kd = 8 uM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 4DCS Kd = 8 uM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 4DCU Kd = 8 uM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
5 1MKY - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GDP; Similar ligands found: 168
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 GNP 0.839506 0.973684
6 9GM 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 GKE 0.747253 0.961039
18 GDD 0.747253 0.961039
19 GDC 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 GDR 0.72043 0.961039
26 GFB 0.72043 0.961039
27 GTG 0.72043 0.936709
28 G4P 0.715909 0.986486
29 6CK 0.712766 0.936709
30 G3A 0.712766 0.973684
31 GDP AF3 0.7 0.888889
32 GDP ALF 0.7 0.888889
33 ALF GDP 0.7 0.888889
34 YGP 0.698925 0.901235
35 JB2 0.697917 0.961039
36 GKD 0.697917 0.961039
37 GPD 0.690722 0.925
38 GDX 0.690722 0.973684
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 GDP 7MG 0.636364 0.911392
44 DGI 0.636364 0.923077
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 KB7 0.629214 0.82716
52 CG2 0.622642 0.936709
53 FEG 0.619048 0.879518
54 MGD 0.614679 0.891566
55 ZGP 0.613208 0.869048
56 GH3 0.612903 0.973333
57 3GP 0.611765 0.946667
58 MD1 0.607143 0.891566
59 PGD 0.59292 0.925
60 DGT 0.591398 0.923077
61 BGO 0.588785 0.924051
62 TPG 0.582609 0.840909
63 DBG 0.582609 0.948718
64 KBD 0.581633 0.82716
65 2GP 0.574713 0.96
66 FE9 0.570175 0.776596
67 GCP G 0.56 0.921053
68 KBJ 0.558824 0.797619
69 G A A A 0.553571 0.923077
70 A G 0.553571 0.935065
71 MGP 0.553191 0.961039
72 U A G G 0.548673 0.935065
73 G4M 0.548387 0.880952
74 6G0 0.547368 0.961039
75 G1R G1R 0.542373 0.924051
76 P2G 0.527473 0.883117
77 PGD O 0.525 0.850575
78 ADP 0.522222 0.92
79 R5I 0.520833 0.946667
80 R7I 0.520833 0.946667
81 GGM 0.517544 0.901235
82 DGP 0.516484 0.910256
83 DG 0.516484 0.910256
84 P1G 0.516129 0.871795
85 G U 0.513274 0.9
86 G1G 0.508475 0.925
87 IMP 0.505495 0.959459
88 AKW 0.504425 0.890244
89 G C 0.504348 0.9
90 GPC 0.491525 0.879518
91 G7M 0.483871 0.948052
92 6AD 0.479592 0.841463
93 ATP 0.473684 0.92
94 HEJ 0.473684 0.92
95 G2Q 0.471154 0.961039
96 AQP 0.46875 0.92
97 5FA 0.46875 0.92
98 GTA 0.468468 0.936709
99 7DD 0.468085 0.906667
100 G G G RPC 0.466102 0.875
101 SGP 0.463158 0.82716
102 01G 0.462963 0.902439
103 JSQ 0.459184 0.873418
104 HFD 0.459184 0.873418
105 AP5 0.457447 0.894737
106 B4P 0.457447 0.894737
107 A2D 0.456522 0.894737
108 6YZ 0.455446 0.896104
109 G G G C 0.455285 0.9125
110 ANP 0.454545 0.896104
111 5GP 5GP 0.454545 0.883117
112 ACQ 0.454545 0.896104
113 AT4 0.452632 0.884615
114 A G C C 0.451613 0.911392
115 APC G U 0.45082 0.886076
116 PRT 0.449541 0.959459
117 G U34 0.449153 0.888889
118 DG DG 0.448598 0.865854
119 ITT 0.447917 0.868421
120 BA3 0.446809 0.894737
121 35G 0.444444 0.933333
122 PCG 0.444444 0.933333
123 C2E 0.444444 0.921053
124 MGO 0.441176 0.864198
125 AN2 0.4375 0.907895
126 G C C C 0.4375 0.924051
127 NO7 0.436893 0.860759
128 M33 0.43299 0.883117
129 UCG 0.429688 0.911392
130 A G U 0.42963 0.888889
131 ACP 0.428571 0.896104
132 MGQ 0.424528 0.935897
133 7DT 0.424242 0.906667
134 APR 0.424242 0.894737
135 AR6 0.424242 0.894737
136 93A 0.42268 0.833333
137 A4P 0.420168 0.869048
138 AGS 0.42 0.873418
139 AD9 0.42 0.896104
140 G8D 0.42 0.875
141 SAP 0.42 0.873418
142 CA0 0.418367 0.896104
143 ATF 0.417476 0.884615
144 AGO 0.414634 0.888889
145 A G U U 0.414286 0.888889
146 KG4 0.414141 0.896104
147 NIA 0.413043 0.82716
148 MGV 0.412844 0.890244
149 T99 0.411765 0.884615
150 TAT 0.411765 0.884615
151 A1R 0.411215 0.839506
152 ADQ 0.411215 0.871795
153 RGT 0.410714 0.909091
154 CGP 0.409836 0.86747
155 HQG 0.409524 0.907895
156 C1Z 0.409091 0.986486
157 AMP 0.408602 0.893333
158 A 0.408602 0.893333
159 UP5 0.40678 0.873418
160 C2R 0.406593 0.906667
161 AMZ 0.406593 0.918919
162 JBT 0.405882 0.778947
163 A22 0.40566 0.907895
164 25L 0.405405 0.907895
165 ADX 0.40404 0.809524
166 8OD 0.401961 0.946667
167 4TC 0.4 0.851852
168 50T 0.4 0.883117
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1MKY; Ligand: GDP; Similar sites found with APoc: 284
This union binding pocket(no: 1) in the query (biounit: 1mky.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 5CK5 GDP 2.8481
2 5CK5 GDP 2.8481
3 5CK5 GDP 2.8481
4 5CK5 GDP 2.8481
5 6AU6 GDP 2.91777
6 1KK1 GNP 2.92683
7 4BAS GNP 3.51759
8 1GOT GDP 3.52941
9 2XTZ GSP 3.67232
10 1TQ4 GDP 3.87409
11 1TAD GDP 4.01235
12 1TAD ALF 4.01235
13 1Z08 GNP 4.11765
14 1Z08 GNP 4.11765
15 1Z08 GNP 4.11765
16 1Z08 GNP 4.11765
17 2RCN GDP 4.46927
18 2RCN GDP 4.46927
19 3MD0 GDP 4.50704
20 1S8F GDP 4.51977
21 1S8F GDP 4.51977
22 1S8F GDP 4.51977
23 1S8F GDP 4.51977
24 1GP2 GDP 4.81586
25 1GWN GTP 4.87805
26 4HDO GNP 4.96894
27 4LC1 GDP 5.04451
28 4LC1 GDP 5.04451
29 1Y3A GDP 5.16717
30 6JFK GDP 5.25114
31 5KUT GDP 5.29101
32 5KUT GDP 5.29101
33 5KUT GDP 5.29101
34 5HCN GCP 5.36398
35 1BH2 GSP 5.39683
36 3TK1 GDP 5.45455
37 3TK1 GDP 5.45455
38 6IF2 GTP 5.91398
39 2AWN ADP 6.03675
40 4LPS GDP 6.19835
41 4LPS GDP 6.19835
42 4M9Q GNP 6.60793
43 3Q72 GNP 6.62651
44 3Q72 GNP 6.62651
45 1MR3 G3D 6.62983
46 3SFV GDP 6.62983
47 6HH2 GDP 6.66667
48 3NKV GNP 6.85714
49 4KVG GTP 6.92308
50 4YLG GDP 6.93642
51 4YLG GDP 6.93642
52 2J59 GTP 7.22892
53 2J59 GTP 7.22892
54 1O3Y GTP 7.22892
55 1S9D GDP 7.31707
56 1RE0 GDP 7.31707
57 2A5J GDP 7.32984
58 4J0Q GDP 7.3903
59 4J0Q GDP 7.3903
60 4J0Q GDP 7.3903
61 4J0Q GDP 7.3903
62 4J0Q GDP 7.3903
63 2BME GNP 7.52688
64 2BME GNP 7.52688
65 5O74 GDP 7.61421
66 5O74 GDP 7.61421
67 5O74 GDP 7.61421
68 5O74 GDP 7.61421
69 5O74 GDP 7.61421
70 1DAR GDP 7.97267
71 4NON GDP 8.07692
72 2WKQ GTP 8.13253
73 1Z0K GTP 8.13953
74 2C78 GNP 8.14815
75 1G16 GDP 8.23529
76 1G16 GDP 8.23529
77 1G16 GDP 8.23529
78 1G16 GDP 8.23529
79 3BC1 GNP 8.47458
80 3BC1 GNP 8.47458
81 1D2E GDP 8.81612
82 1D2E GDP 8.81612
83 1D2E GDP 8.81612
84 1D2E GDP 8.81612
85 2X77 GDP 9.52381
86 2X77 GDP 9.52381
87 3AQ4 GDP 9.78261
88 3AQ4 GDP 9.78261
89 1SKQ GDP 9.88506
90 1SKQ GDP 9.88506
91 3T12 GDP ALF 10.101
92 3T1O GDP 10.101
93 3T1O GDP 10.101
94 3WYA GDP 10.5991
95 5GOE GDP 10.9005
96 1GUA GNP 11.3772
97 5XKT GNP 11.5
98 5XKT GNP 11.5
99 5M04 GDP 11.6667
100 1G7S GDP 11.8451
101 1PUJ GNP 12.0567
102 5FG3 GDP 12.0729
103 5H7J GCP 12.0729
104 3N5C GDP 12.3457
105 3N5C GDP 12.3457
106 3CNL GNP 13.7405
107 5H7K GDP 13.8539
108 5W75 GDP 14.0306
109 5W75 GDP 14.0306
110 5W75 GDP 14.0306
111 5W75 GDP 14.0306
112 5W7Q GDP 14.2091
113 5TB5 GDP 14.5946
114 5TB5 GDP 14.5946
115 5TAR GDP 14.5946
116 1FQJ GDP 14.966
117 2C5L GTP 15.0289
118 2C5L GTP 15.0289
119 2QN6 GDP 15.0538
120 1F6B GDP 15.1515
121 1F6B GDP 15.1515
122 4K81 GTP 15.2047
123 1M2O GNP 15.2632
124 1M2O GNP 15.2632
125 1M2O GNP 15.2632
126 5WHA GDP 15.2941
127 5WHA GDP 15.2941
128 5WHA GDP 15.2941
129 5WHA GDP 15.2941
130 5E95 GDP 15.4762
131 6BVJ GNP 15.5689
132 5WLB GNP 15.6627
133 3DDC GNP 15.6627
134 1WQ1 GDP 15.6627
135 6D5J GNP 16.1677
136 6D5E GNP 16.1677
137 6D5G GNP 16.1677
138 6D5H GNP 16.1677
139 6BVK GNP 16.1677
140 6D5W GNP 16.1677
141 1NVV GNP 16.2651
142 6FA3 GNP 16.2791
143 6FA3 GNP 16.2791
144 6FA3 GNP 16.2791
145 2HCJ GDP 16.4179
146 3A1S GDP 16.6667
147 4D0N GDP 17.2973
148 5HPY GDP 17.2973
149 6BC0 GSP 17.2973
150 2QTV GNP 17.3653
151 4DID GDP 17.6166
152 4R98 GNH 17.7122
153 1G7C 5GP 17.7677
154 2NGR GDP 17.801
155 1KMQ GNP 17.9348
156 1NF3 GNP 17.9487
157 2WIC GNP 17.9775
158 2WIC GNP 17.9775
159 4B47 GDP 17.9954
160 3REF GDP 18.0412
161 3WYF GTP 18.2648
162 3M1I GTP 18.2648
163 3WYF GTP 18.2648
164 4XOI GTP 18.3333
165 4YC7 GNP 18.7845
166 5UPK GNP 18.9189
167 1YVD GNP 18.9349
168 3EC1 GDP 18.9702
169 3EC1 GDP 18.9702
170 1D8T GDP 19.084
171 1D8T GDP 19.084
172 3VMF GTP 19.1344
173 3WXM GTP 19.1344
174 3WXM GTP 19.1344
175 5W76 GDP 19.2208
176 3U6B GDP 19.5431
177 3U6B GDP 19.5431
178 4P3Y GDP 19.5431
179 3U6K GDP 19.5431
180 5JBQ GDP 19.5431
181 4G5G GDP 19.5431
182 3U6K GDP 19.5431
183 4PC3 GDP 19.5431
184 4PC3 GDP 19.5431
185 2BVN GNP 19.5929
186 2BVN GNP 19.5929
187 1VG8 GNP 20.2899
188 1VG0 GDP 20.2899
189 5UWQ GNP 20.6751
190 5UWO GNP 20.6751
191 5UWS GNP 20.6751
192 2G77 GDP 20.7071
193 3GJ8 GDP 21.7195
194 3GJ5 GDP 21.7195
195 3GJ8 GDP 21.7195
196 3GJ3 GDP 21.7195
197 3GJ0 GDP 21.7195
198 3GJ0 GDP 21.7195
199 3GJ7 GDP 21.7195
200 3GJ7 GDP 21.7195
201 3GJ5 GDP 21.7195
202 3WYG GTP 21.978
203 5BXQ GDP 22.2222
204 5BXQ GDP 22.2222
205 3CH5 GDP 22.2222
206 4HAT GNP 22.2222
207 5BXQ GDP 22.2222
208 1IBR GNP 22.2222
209 3CH5 GDP 22.2222
210 1U8Z GDP 22.619
211 1VG9 GDP 22.7027
212 1VG9 GDP 22.7027
213 1VG1 GDP 22.7027
214 1VG9 GDP 22.7027
215 1VG9 GDP 22.7027
216 3GJ4 GDP 24.2424
217 3GJ4 GDP 24.2424
218 3W5J GDP 24.5098
219 2EFE GNH 24.8619
220 2EFE GNH 24.8619
221 3WY9 GDP 25
222 3WY9 GDP 25
223 5UWU GNP 25
224 1ZJ6 G3D 26.2032
225 1ZJ6 G3D 26.2032
226 1ZJ6 G3D 26.2032
227 1FZQ GDP 26.5193
228 6G14 G4P 26.5306
229 6G14 G4P 26.5306
230 1WA5 GTP 27.8409
231 5YT0 GDP 28.5714
232 1I4D GDP 29.1667
233 1E96 GTP 29.6875
234 3SBD GNP 29.9465
235 4V0K GDP 30.7692
236 2WJG GDP 31.383
237 2WJG GDP 31.383
238 2FJU GSP 31.4607
239 1HE1 GDP 31.8182
240 1YZG GDP 31.8436
241 4DKX GDP 32.8704
242 4DKX GDP 32.8704
243 1Z0F GDP 32.9609
244 3DOE GTP 33.3333
245 1Z0A GDP 33.3333
246 1Z0A GDP 33.3333
247 1Z0A GDP 33.3333
248 1Z0A GDP 33.3333
249 1Z0A GDP 33.3333
250 1Z0A GDP 33.3333
251 1Z0A GDP 33.3333
252 1Z0A GDP 33.3333
253 2OM2 GDP 33.3333
254 1Z0A GDP 33.3333
255 1Z0A GDP 33.3333
256 1Z0A GDP 33.3333
257 1Z0A GDP 33.3333
258 1KSH GDP 34.4086
259 2WJH GDP 35.5422
260 3CPJ GDP 36.3229
261 2FH5 GTP 36.9159
262 6HDU GTP 36.9565
263 6HDU GTP 36.9565
264 1UAD GNP 37.1429
265 1UAD GNP 37.1429
266 1ZC3 GNP 37.7143
267 1TU3 GNP 38.0117
268 1TU3 GNP 38.0117
269 1TU3 GNP 38.0117
270 1DS6 GDP 38.5417
271 1SVI GDP 39.4872
272 2Y8E GNP 39.6648
273 2Y8E GNP 39.6648
274 5WDR GNP 39.7661
275 3MJH GTP 39.881
276 1OIV GDP 40.3141
277 1OIV GDP 40.3141
278 2FFQ GSP 41.5205
279 5JCZ GDP 43.0168
280 2D7C GTP 46.1078
281 3QBT GNP 47.7011
282 3QBT GNP 47.7011
283 4LHW GNP 47.7011
284 4LHW GNP 47.7011
APoc FAQ
Feedback