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Receptor
PDB id Resolution Class Description Source Keywords
3FD5 1.9 Å EC: 2.7.9.3 CRYSTAL STRUCTURE OF HUMAN SELENOPHOSPHATE SYNTHETASE 1 COMPLEX WITH AMPCP HOMO SAPIENS SELENOPHOSPHATE SYNTHETASE SELD ATP-BINDING KINASE NUCLEOTIDE-BINDING SELENIUM TRANSFERASE
Ref.: CRYSTAL STRUCTURES OF CATALYTIC INTERMEDIATES OF HUMAN SELENOPHOSPHATE SYNTHETASE 1. J.MOL.BIOL. V. 390 747 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
AP2 A:393;
B:393;
Valid;
Valid;
none;
none;
submit data
425.228 C11 H17 N5 O9 P2 c1nc(...
K A:398;
B:398;
Part of Protein;
Part of Protein;
none;
none;
submit data
39.098 K [K+]
MG A:395;
A:396;
A:397;
B:395;
B:396;
B:397;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
PO4 A:394;
B:394;
Invalid;
Invalid;
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
3FD5 1.9 Å EC: 2.7.9.3 CRYSTAL STRUCTURE OF HUMAN SELENOPHOSPHATE SYNTHETASE 1 COMPLEX WITH AMPCP HOMO SAPIENS SELENOPHOSPHATE SYNTHETASE SELD ATP-BINDING KINASE NUCLEOTIDE-BINDING SELENIUM TRANSFERASE
Ref.: CRYSTAL STRUCTURES OF CATALYTIC INTERMEDIATES OF HUMAN SELENOPHOSPHATE SYNTHETASE 1. J.MOL.BIOL. V. 390 747 2009
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3FD5 - AP2 C11 H17 N5 O9 P2 c1nc(c2c(n....
2 3FD6 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3FD5 - AP2 C11 H17 N5 O9 P2 c1nc(c2c(n....
2 3FD6 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3FD5 - AP2 C11 H17 N5 O9 P2 c1nc(c2c(n....
2 3FD6 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: AP2; Similar ligands found: 345
No: Ligand ECFP6 Tc MDL keys Tc
1 A12 1 1
2 AP2 1 1
3 APC 0.821918 1
4 ADV 0.810811 0.972973
5 RBY 0.810811 0.972973
6 AMP 0.808824 0.931507
7 A 0.808824 0.931507
8 ACP 0.808219 0.986301
9 ABM 0.774648 0.881579
10 A2D 0.774648 0.932432
11 BA3 0.753425 0.932432
12 SRA 0.746479 0.883117
13 B4P 0.743243 0.932432
14 ADP 0.743243 0.958904
15 AP5 0.743243 0.932432
16 AN2 0.733333 0.945946
17 AT4 0.733333 0.921053
18 M33 0.723684 0.92
19 CA0 0.723684 0.907895
20 ADX 0.723684 0.841463
21 AU1 0.723684 0.933333
22 ACQ 0.721519 0.986301
23 50T 0.714286 0.92
24 HEJ 0.714286 0.958904
25 ATP 0.714286 0.958904
26 5FA 0.705128 0.958904
27 PRX 0.705128 0.858974
28 AQP 0.705128 0.958904
29 AR6 0.705128 0.932432
30 APR 0.705128 0.932432
31 ADP PO3 0.696203 0.905405
32 AGS 0.696203 0.909091
33 SAP 0.696203 0.909091
34 AD9 0.696203 0.933333
35 6YZ 0.695122 0.986301
36 SON 0.688312 0.946667
37 T99 0.679012 0.921053
38 ANP 0.679012 0.933333
39 TAT 0.679012 0.921053
40 GAP 0.679012 0.858974
41 5AL 0.670732 0.894737
42 ATF 0.662651 0.921053
43 LMS 0.662162 0.797619
44 SRP 0.654762 0.896104
45 9ZD 0.651163 0.873418
46 9ZA 0.651163 0.873418
47 4AD 0.643678 0.909091
48 AMO 0.643678 0.921053
49 ALF ADP 0.642857 0.8375
50 ADP ALF 0.642857 0.8375
51 A22 0.639535 0.945946
52 MAP 0.639535 0.909091
53 DAL AMP 0.639535 0.87013
54 ADP VO4 0.635294 0.894737
55 VO4 ADP 0.635294 0.894737
56 RAB 0.632353 0.810811
57 XYA 0.632353 0.810811
58 ADN 0.632353 0.810811
59 OOB 0.632184 0.894737
60 5SV 0.632184 0.839506
61 8QN 0.632184 0.894737
62 25A 0.632184 0.932432
63 TAD 0.631579 0.923077
64 PAJ 0.625 0.851852
65 A3R 0.625 0.922078
66 ADQ 0.625 0.907895
67 A1R 0.625 0.922078
68 AOC 0.623377 0.789474
69 B5V 0.622222 0.871795
70 DLL 0.617977 0.894737
71 AHX 0.617977 0.886076
72 00A 0.617977 0.85
73 5N5 0.614286 0.786667
74 5AS 0.6125 0.752809
75 9X8 0.611111 0.884615
76 3UK 0.611111 0.883117
77 OAD 0.611111 0.907895
78 A4D 0.605634 0.786667
79 5CD 0.605634 0.773333
80 WAQ 0.604396 0.897436
81 LAD 0.604396 0.875
82 PR8 0.604396 0.864198
83 NB8 0.597826 0.886076
84 3OD 0.597826 0.907895
85 FYA 0.597826 0.894737
86 ME8 0.597826 0.831325
87 TXA 0.597826 0.896104
88 BIS 0.597826 0.897436
89 1ZZ 0.597826 0.831325
90 PTJ 0.597826 0.8625
91 M2T 0.594595 0.707317
92 ADP BMA 0.593407 0.883117
93 25L 0.591398 0.945946
94 MYR AMP 0.591398 0.809524
95 A A 0.586957 0.906667
96 9SN 0.585106 0.839506
97 EP4 0.581081 0.725
98 JB6 0.580645 0.873418
99 A3P 0.580247 0.931507
100 7D5 0.578947 0.868421
101 FA5 0.578947 0.896104
102 B5M 0.578947 0.860759
103 ATP A A A 0.578947 0.893333
104 YAP 0.578947 0.884615
105 B5Y 0.578947 0.860759
106 DTA 0.573333 0.779221
107 XAH 0.572917 0.853659
108 3DH 0.571429 0.74359
109 GA7 0.571429 0.896104
110 AFH 0.571429 0.875
111 G5A 0.569767 0.772727
112 4TC 0.568627 0.910256
113 4UV 0.56701 0.860759
114 TYR AMP 0.56701 0.860759
115 MTA 0.565789 0.74359
116 UP5 0.564356 0.884615
117 3AM 0.564103 0.891892
118 G3A 0.561224 0.886076
119 A2P 0.560976 0.917808
120 DZD 0.560748 0.923077
121 LAQ 0.56 0.831325
122 G5P 0.555556 0.886076
123 ARG AMP 0.555556 0.821429
124 4UU 0.555556 0.860759
125 LPA AMP 0.554455 0.809524
126 AMP DBH 0.55102 0.858974
127 A5A 0.550562 0.77907
128 6RE 0.55 0.753086
129 GTA 0.55 0.853659
130 DQV 0.55 0.92
131 TSB 0.549451 0.790698
132 4UW 0.54902 0.829268
133 NAX 0.54902 0.864198
134 S4M 0.548781 0.681818
135 AHZ 0.544554 0.788235
136 SSA 0.544444 0.793103
137 PAP 0.54023 0.945205
138 7MD 0.54 0.853659
139 AR6 AR6 0.54 0.881579
140 YLP 0.539216 0.833333
141 48N 0.539216 0.886076
142 54H 0.538462 0.761364
143 52H 0.538462 0.752809
144 VMS 0.538462 0.761364
145 ZAS 0.5375 0.7375
146 A3N 0.536585 0.75641
147 IMO 0.536585 0.891892
148 J7C 0.536585 0.7625
149 NAI 0.533981 0.873418
150 NXX 0.533981 0.896104
151 6V0 0.533981 0.8625
152 TXD 0.533981 0.873418
153 DND 0.533981 0.896104
154 8X1 0.532609 0.747253
155 53H 0.532609 0.752809
156 5CA 0.532609 0.793103
157 2AM 0.531646 0.905405
158 7D3 0.53012 0.894737
159 TYM 0.528846 0.896104
160 AF3 ADP 3PG 0.528846 0.829268
161 OMR 0.528846 0.843373
162 TXE 0.528846 0.873418
163 2A5 0.528736 0.907895
164 GP2 0.52809 0.923077
165 V3L 0.52809 0.932432
166 DSH 0.52439 0.740741
167 MAO 0.52381 0.77381
168 YLC 0.52381 0.853659
169 UPA 0.52381 0.873418
170 AP0 0.52381 0.8625
171 YLB 0.52381 0.833333
172 7D4 0.523256 0.894737
173 ATR 0.522727 0.931507
174 PPS 0.522222 0.841463
175 LSS 0.521277 0.755556
176 DSZ 0.521277 0.793103
177 NSS 0.521277 0.793103
178 P5A 0.520833 0.758242
179 A4P 0.518868 0.813953
180 5X8 0.517241 0.75641
181 NVA LMS 0.515789 0.747253
182 9K8 0.515464 0.691489
183 IOT 0.514019 0.845238
184 5AD 0.513889 0.716216
185 OVE 0.512195 0.87013
186 GJV 0.511905 0.743902
187 LEU LMS 0.510417 0.747253
188 7MC 0.509434 0.833333
189 YLA 0.509259 0.833333
190 139 0.509259 0.864198
191 ADJ 0.509259 0.843373
192 T5A 0.509259 0.855422
193 ITT 0.505747 0.905405
194 A2R 0.505376 0.945946
195 GSU 0.505155 0.772727
196 KAA 0.505155 0.766667
197 CNA 0.504587 0.896104
198 AYB 0.504587 0.823529
199 6C6 0.5 0.896104
200 F2R 0.5 0.855422
201 SFG 0.5 0.766234
202 BTX 0.495495 0.855422
203 NAD 0.495495 0.894737
204 AMP NAD 0.495495 0.87013
205 4TA 0.495495 0.821429
206 COD 0.495495 0.825581
207 YSA 0.49505 0.772727
208 SMM 0.494624 0.701149
209 SAM 0.494505 0.705882
210 A7D 0.494253 0.792208
211 BT5 0.491071 0.845238
212 SA8 0.488889 0.722892
213 A5D 0.488889 0.779221
214 MHZ 0.488636 0.712644
215 71V 0.488372 0.873418
216 A3G 0.488095 0.792208
217 M24 0.486957 0.819277
218 Y3J 0.486842 0.697368
219 A3D 0.486726 0.883117
220 80F 0.486726 0.833333
221 7D7 0.486486 0.736842
222 8PZ 0.485149 0.793103
223 HFD 0.483516 0.909091
224 SAH 0.483516 0.759494
225 SAI 0.483516 0.75
226 G A A A 0.482143 0.839506
227 PO4 PO4 A A A A PO4 0.479592 0.866667
228 S7M 0.478723 0.705882
229 3AT 0.478261 0.958904
230 6IA 0.478261 0.829268
231 YLY 0.474138 0.823529
232 EEM 0.473118 0.705882
233 6AD 0.473118 0.875
234 PGS 0.47191 0.85
235 7C5 0.471154 0.7875
236 DA 0.470588 0.893333
237 D5M 0.470588 0.893333
238 NEC 0.470588 0.717949
239 NAE 0.470085 0.860759
240 NIA 0.46988 0.792683
241 U A 0.469565 0.873418
242 NAJ PZO 0.469565 0.817073
243 A G 0.469027 0.85
244 2SA 0.468085 0.921053
245 AV2 0.468085 0.881579
246 NAQ 0.466102 0.839506
247 AAM 0.465116 0.931507
248 U A G G 0.464912 0.85
249 NA7 0.464646 0.972973
250 A A A 0.464646 0.92
251 GEK 0.463918 0.753086
252 A U 0.463636 0.8375
253 AMZ 0.463415 0.88
254 C2R 0.463415 0.868421
255 4YB 0.462264 0.755556
256 N0B 0.462185 0.833333
257 ZID 0.462185 0.883117
258 3AD 0.461538 0.797297
259 A3S 0.460674 0.802632
260 101 0.458824 0.868421
261 WSA 0.458716 0.781609
262 Z5A 0.458333 0.772727
263 AAT 0.457447 0.722892
264 AIR 0.455696 0.864865
265 EAD 0.454545 0.841463
266 ARU 0.454545 0.829268
267 NAJ PYZ 0.453782 0.77907
268 GGZ 0.453608 0.795181
269 DAT 0.450549 0.92
270 A3T 0.450549 0.789474
271 A6D 0.45 0.717647
272 6K6 0.44898 0.893333
273 AVV 0.44898 0.910256
274 DTP 0.446809 0.92
275 649 0.445455 0.758242
276 0UM 0.444444 0.714286
277 8BR 0.443182 0.871795
278 8Q2 0.441441 0.766667
279 N6P 0.44 0.878378
280 62X 0.44 0.681818
281 NDE 0.44 0.896104
282 P1H 0.44 0.821429
283 G2P 0.438776 0.923077
284 K15 0.435644 0.697674
285 S8M 0.434343 0.775
286 V1N 0.433962 0.881579
287 FB0 0.433071 0.83908
288 NDC 0.433071 0.8625
289 7RA 0.431818 0.918919
290 AS 0.431818 0.848101
291 QQY 0.430233 0.78481
292 ACK 0.430233 0.826667
293 CC5 0.428571 0.808219
294 GCP 0.428571 0.910256
295 SXZ 0.427184 0.72619
296 EO7 0.426966 0.761364
297 FDA 0.426357 0.825581
298 KB1 0.423077 0.714286
299 TM1 0.423077 0.747126
300 6FA 0.423077 0.833333
301 NJP 0.422414 0.909091
302 2BA 0.422222 0.878378
303 CMP 0.422222 0.864865
304 7RP 0.420455 0.890411
305 A C A C 0.420168 0.817073
306 2VA 0.419355 0.769231
307 0WD 0.418803 0.886076
308 QQX 0.418605 0.775
309 NPW 0.417391 0.876543
310 DDS 0.416667 0.868421
311 FAS 0.416667 0.843373
312 FAD 0.416667 0.843373
313 SFD 0.416667 0.729167
314 RMB 0.41573 0.837838
315 1RB 0.413793 0.849315
316 RP1 0.413793 0.810127
317 SP1 0.413793 0.810127
318 7DD 0.413043 0.945205
319 ANZ 0.412844 0.771084
320 APU 0.412281 0.860759
321 FAY 0.411765 0.853659
322 NVA 2AD 0.410526 0.753086
323 ODP 0.410256 0.875
324 D3Y 0.41 0.782051
325 5GP 0.408602 0.871795
326 G 0.408602 0.871795
327 SLU 0.408333 0.744444
328 U A C C 0.408333 0.82716
329 U A A U 0.408 0.873418
330 3L1 0.407407 0.789474
331 3D1 0.407407 0.789474
332 VRT 0.40625 0.7625
333 SO8 0.40625 0.759494
334 NDP 0.405172 0.886076
335 FNK 0.404412 0.797753
336 62F 0.404412 0.853659
337 3NZ 0.403846 0.775
338 26A 0.402439 0.734177
339 2FA 0.402439 0.782051
340 RGT 0.401869 0.921053
341 NZQ 0.401709 0.898734
342 TXP 0.401709 0.886076
343 P2P 0.4 0.866667
344 FAI 0.4 0.88
345 7DT 0.4 0.945205
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3FD5; Ligand: AP2; Similar sites found with APoc: 26
This union binding pocket(no: 1) in the query (biounit: 3fd5.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 1UYY BGC BGC None
2 5LY1 PPI 2.09974
3 3C5E ATP 2.79188
4 4XDY HIO 2.95858
5 2POC UD1 3.26975
6 1QMG DMV 3.29949
7 5FPE 3TR 3.61757
8 3VIU ADP 4.56853
9 2WHP HI6 4.56853
10 5EQ8 HSO 4.69314
11 1LSH PLD 5.07614
12 5A1S FLC 5.58376
13 5T63 ALA ALA ALA ALA 5.99455
14 4EWH T77 6.54545
15 3NOJ PYR 6.72269
16 4BWL MN9 7.23684
17 2PKA BEN 7.5
18 1Q11 TYE 7.7957
19 4LGY ADP 8.12183
20 6GNO XDI 8.88889
21 1NE7 16G 12.1107
22 3WJP ANP 12.426
23 3PD2 A3S 15.6463
24 2Z1U ATP 23.3236
25 3C9U ADP 33.6257
26 3C9U TPP 33.6257
Pocket No.: 2; Query (leader) PDB : 3FD5; Ligand: AP2; Similar sites found with APoc: 10
This union binding pocket(no: 2) in the query (biounit: 3fd5.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 1LDN OXM 2.21519
2 5LA1 XYP 2.53807
3 5JDI 6JO 3.125
4 1OFZ FUC 4.16667
5 4ZUL UN1 4.31472
6 5AIP 4HP 4.79452
7 2J5B TYE 6.32184
8 3HRD MCN 6.85279
9 5BSR AMP 8.12183
10 3IWD M2T 24.1935
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