Receptor
PDB id Resolution Class Description Source Keywords
1DEL 2.2 Å EC: 2.7.4.13 DEOXYNUCLEOSIDE MONOPHOSPHATE KINASE COMPLEXED WITH DEOXY-GM ENTEROBACTERIA PHAGE T4 TRANSFERASE PHOSPHOTRANSFERASE
Ref.: CRYSTAL STRUCTURE OF BACTERIOPHAGE T4 DEOXYNUCLEOTI WITH ITS SUBSTRATES DGMP AND ATP. EMBO J. V. 15 3487 1996
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
AMP B:302;
Valid;
none;
submit data
347.221 C10 H14 N5 O7 P c1nc(...
DGP A:301;
B:301;
Valid;
Valid;
none;
none;
submit data
347.221 C10 H14 N5 O7 P c1nc2...
MG A:300;
B:300;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1DEK 2 Å EC: 2.7.4.13 DEOXYNUCLEOSIDE MONOPHOSPHATE KINASE COMPLEXED WITH DEOXY-GM ENTEROBACTERIA PHAGE T4 TRANSFERASE PHOSPHOTRANSFERASE
Ref.: CRYSTAL STRUCTURE OF BACTERIOPHAGE T4 DEOXYNUCLEOTI WITH ITS SUBSTRATES DGMP AND ATP. EMBO J. V. 15 3487 1996
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1DEL - DGP C10 H14 N5 O7 P c1nc2c(n1[....
2 1DEK - DGP C10 H14 N5 O7 P c1nc2c(n1[....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1DEL - DGP C10 H14 N5 O7 P c1nc2c(n1[....
2 1DEK - DGP C10 H14 N5 O7 P c1nc2c(n1[....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1DEL - DGP C10 H14 N5 O7 P c1nc2c(n1[....
2 1DEK - DGP C10 H14 N5 O7 P c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: AMP; Similar ligands found: 382
No: Ligand ECFP6 Tc MDL keys Tc
1 AMP 1 1
2 A 1 1
3 A2D 0.833333 0.943662
4 ABM 0.833333 0.943662
5 ADP 0.823529 0.971429
6 AMP MG 0.818182 0.916667
7 A12 0.808824 0.931507
8 AP2 0.808824 0.931507
9 BA3 0.808824 0.943662
10 SRA 0.80303 0.944444
11 AP5 0.797101 0.943662
12 B4P 0.797101 0.943662
13 ATP 0.788732 0.971429
14 AN2 0.785714 0.957747
15 APC 0.777778 0.931507
16 AQP 0.777778 0.971429
17 5FA 0.777778 0.971429
18 ADX 0.774648 0.848101
19 CA0 0.774648 0.917808
20 M33 0.774648 0.930556
21 AU1 0.774648 0.944444
22 ACP 0.763889 0.944444
23 50T 0.763889 0.957747
24 25A 0.75641 0.971429
25 AR6 0.753425 0.943662
26 APR 0.753425 0.943662
27 PRX 0.753425 0.917808
28 ADP MG 0.75 0.90411
29 TAT 0.746667 0.931507
30 ACQ 0.746667 0.944444
31 RBY 0.743243 0.905405
32 SAP 0.743243 0.918919
33 AGS 0.743243 0.918919
34 ADV 0.743243 0.905405
35 AD9 0.743243 0.944444
36 BEF ADP 0.739726 0.88
37 ADP BEF 0.739726 0.88
38 ANP 0.723684 0.944444
39 ADP PO3 0.72 0.942857
40 5AL 0.714286 0.930556
41 SON 0.712329 0.931507
42 ATP MG 0.710526 0.90411
43 ADN 0.709677 0.842857
44 XYA 0.709677 0.842857
45 RAB 0.709677 0.842857
46 ATF 0.705128 0.931507
47 GAP 0.701299 0.891892
48 A22 0.7 0.957747
49 SRP 0.696203 0.905405
50 7D5 0.691176 0.902778
51 A3P 0.684932 0.971014
52 A2P 0.684932 0.956522
53 ALF ADP 0.683544 0.868421
54 ADP ALF 0.683544 0.868421
55 ADQ 0.682927 0.917808
56 MAP 0.679012 0.918919
57 ANP MG 0.675 0.893333
58 ADP VO4 0.675 0.930556
59 VO4 ADP 0.675 0.930556
60 5SV 0.670732 0.87013
61 OOB 0.670732 0.930556
62 8QN 0.670732 0.930556
63 PTJ 0.670588 0.894737
64 AOC 0.666667 0.84507
65 4AD 0.662651 0.893333
66 A1R 0.662651 0.881579
67 AMO 0.662651 0.905405
68 PAJ 0.662651 0.858974
69 5N5 0.661538 0.816901
70 DAL AMP 0.658537 0.90411
71 IMO 0.657534 0.928571
72 DLL 0.654762 0.930556
73 AHX 0.654762 0.87013
74 00A 0.654762 0.881579
75 5AS 0.653333 0.776471
76 5CD 0.651515 0.828571
77 A4D 0.651515 0.816901
78 3UK 0.647059 0.917808
79 ADP BMA 0.647059 0.891892
80 OAD 0.647059 0.917808
81 25L 0.643678 0.957747
82 PR8 0.639535 0.848101
83 WAQ 0.639535 0.881579
84 LAD 0.639535 0.858974
85 DTA 0.637681 0.808219
86 V3L 0.6375 0.971429
87 3DH 0.633803 0.794521
88 BIS 0.632184 0.906667
89 TXA 0.632184 0.905405
90 FYA 0.632184 0.930556
91 ME8 0.632184 0.8375
92 1ZZ 0.632184 0.8375
93 3OD 0.632184 0.917808
94 NB8 0.632184 0.87013
95 MTA 0.628571 0.794521
96 3AM 0.625 0.956522
97 EP4 0.623188 0.773333
98 A A 0.62069 0.971429
99 9SN 0.617977 0.87013
100 M2T 0.614286 0.753247
101 JB6 0.613636 0.881579
102 YAP 0.611111 0.893333
103 FA5 0.611111 0.905405
104 MYR AMP 0.606742 0.814815
105 G5A 0.604938 0.776471
106 XAH 0.604396 0.8375
107 4UV 0.597826 0.893333
108 71V 0.597403 0.906667
109 ATP A A A 0.593407 0.929577
110 PAP 0.592593 0.957143
111 G3A 0.591398 0.894737
112 2AM 0.589041 0.942857
113 5X8 0.5875 0.783784
114 TYR AMP 0.586957 0.88
115 6RE 0.586667 0.779221
116 6C6 0.585366 0.905405
117 4UU 0.585106 0.893333
118 G5P 0.585106 0.894737
119 AFH 0.585106 0.858974
120 7D3 0.584416 0.878378
121 A5A 0.583333 0.804878
122 TSB 0.581395 0.795181
123 AMP DBH 0.580645 0.891892
124 2A5 0.580247 0.891892
125 DSH 0.578947 0.74359
126 TAD 0.578947 0.858974
127 GTA 0.578947 0.860759
128 6IA 0.578313 0.858974
129 SSA 0.576471 0.776471
130 C2R 0.575342 0.876712
131 AMZ 0.575342 0.888889
132 7D4 0.575 0.878378
133 PGS 0.575 0.857143
134 ZAS 0.573333 0.786667
135 ATR 0.573171 0.942857
136 LAQ 0.572917 0.8375
137 PPS 0.571429 0.848101
138 AAM 0.571429 1
139 AIR 0.571429 0.927536
140 J7C 0.571429 0.789474
141 A3N 0.571429 0.783784
142 54H 0.569767 0.785714
143 VMS 0.569767 0.785714
144 52H 0.569767 0.776471
145 7MD 0.568421 0.8375
146 AR6 AR6 0.568421 0.916667
147 48N 0.56701 0.87013
148 YLP 0.56701 0.817073
149 OVE 0.565789 0.90411
150 UPA 0.565657 0.881579
151 2SA 0.564706 0.905405
152 S4M 0.564103 0.682353
153 53H 0.563218 0.776471
154 5CA 0.563218 0.776471
155 4UW 0.561224 0.858974
156 NAI 0.561224 0.881579
157 TXD 0.561224 0.881579
158 6V0 0.561224 0.87013
159 UP5 0.561224 0.893333
160 DND 0.561224 0.905405
161 NXX 0.561224 0.905405
162 NAX 0.561224 0.848101
163 NIA 0.56 0.820513
164 D5M 0.558442 0.902778
165 DA 0.558442 0.902778
166 MAO 0.556962 0.777778
167 AHZ 0.556701 0.814815
168 ARG AMP 0.556701 0.82716
169 ITT 0.555556 0.915493
170 TXE 0.555556 0.881579
171 TYM 0.555556 0.905405
172 OMR 0.555556 0.82716
173 5AD 0.552239 0.768116
174 A2R 0.551724 0.957747
175 LPA AMP 0.55102 0.814815
176 DSZ 0.550562 0.776471
177 LSS 0.550562 0.758621
178 NSS 0.550562 0.776471
179 YLB 0.55 0.817073
180 YLC 0.55 0.8375
181 4TC 0.55 0.87013
182 AP0 0.55 0.87013
183 P5A 0.549451 0.741573
184 139 0.54902 0.848101
185 A4P 0.544554 0.819277
186 NVA LMS 0.544444 0.758621
187 GJV 0.544304 0.769231
188 7D7 0.544118 0.763889
189 A7D 0.54321 0.797297
190 ALF ADP 3PG 0.54 0.835443
191 LA8 ALF 3PG 0.54 0.835443
192 AF3 ADP 3PG 0.54 0.835443
193 6K6 0.539326 0.957143
194 IOT 0.539216 0.829268
195 LEU LMS 0.538462 0.758621
196 A3G 0.538462 0.797297
197 A5D 0.535714 0.808219
198 7MC 0.534653 0.817073
199 T5A 0.533981 0.817073
200 YLA 0.533981 0.817073
201 ADJ 0.533981 0.82716
202 KAA 0.532609 0.75
203 GSU 0.532609 0.776471
204 7RA 0.531646 0.985507
205 SFG 0.53012 0.77027
206 SAH 0.529412 0.763158
207 AYB 0.528846 0.807229
208 CNA 0.528846 0.905405
209 N6P 0.527473 0.942029
210 8BR 0.525 0.931507
211 Y3J 0.521127 0.746479
212 YSA 0.520833 0.776471
213 7RP 0.518987 0.955882
214 G A A A 0.518868 0.87013
215 COD 0.518868 0.788235
216 BTX 0.518868 0.839506
217 NAD 0.518868 0.930556
218 MHZ 0.518072 0.714286
219 SA8 0.517647 0.725
220 6AD 0.517241 0.883117
221 DZD 0.514019 0.858974
222 BT5 0.514019 0.829268
223 RMB 0.5125 0.898551
224 SAI 0.511628 0.753247
225 AV2 0.511364 0.890411
226 NAD IBO 0.509434 0.868421
227 A3D 0.509259 0.917808
228 A3S 0.506024 0.808219
229 SAM 0.505747 0.707317
230 3AT 0.505747 0.943662
231 SMM 0.505618 0.702381
232 NA7 0.505376 0.931507
233 4TA 0.504673 0.804878
234 5GP 0.5 0.905405
235 EEM 0.5 0.707317
236 NEC 0.5 0.743243
237 AAT 0.5 0.725
238 G 0.5 0.905405
239 YLY 0.495495 0.807229
240 M24 0.495495 0.848101
241 7C5 0.494949 0.815789
242 DAT 0.494118 0.878378
243 A3T 0.494118 0.819444
244 FAI 0.493827 0.888889
245 P2P 0.493827 0.928571
246 1RB 0.493671 0.911765
247 NAE 0.491071 0.893333
248 NAJ PZO 0.490909 0.846154
249 TM1 0.489583 0.771084
250 A6D 0.489362 0.740741
251 PO4 PO4 A A A A PO4 0.489362 0.901408
252 A A A 0.489362 0.90411
253 S7M 0.488889 0.707317
254 DTP 0.488636 0.878378
255 101 0.4875 0.902778
256 RBZ 0.4875 0.873239
257 EAD 0.486957 0.848101
258 NAQ 0.486726 0.87013
259 U A G G 0.486239 0.881579
260 4YB 0.485149 0.758621
261 NDE 0.483051 0.931507
262 N0B 0.482456 0.817073
263 ZID 0.482456 0.917808
264 WSA 0.480769 0.785714
265 RGT 0.479592 0.931507
266 ARU 0.478723 0.835443
267 GGZ 0.478261 0.8
268 JLN 0.47561 0.863014
269 ANZ 0.475248 0.820513
270 ACK 0.475 0.885714
271 QQY 0.475 0.837838
272 NAJ PYZ 0.473684 0.848101
273 S8M 0.473118 0.779221
274 GEK 0.473118 0.734177
275 AVV 0.473118 0.87013
276 3AD 0.472973 0.828571
277 A U 0.471698 0.868421
278 P1H 0.470588 0.82716
279 AMP NAD 0.469565 0.88
280 0UM 0.468085 0.716049
281 RVP 0.467532 0.847222
282 649 0.466667 0.741573
283 Z5A 0.465517 0.776471
284 PMO 0.464286 0.873239
285 SXZ 0.463918 0.707317
286 62X 0.463158 0.682353
287 QQX 0.4625 0.826667
288 2VA 0.45977 0.797297
289 IMP 0.458824 0.90411
290 K15 0.458333 0.698795
291 CC5 0.458333 0.84058
292 AS 0.457831 0.855263
293 DDS 0.455556 0.851351
294 V1N 0.455446 0.943662
295 NJP 0.454545 0.918919
296 93A 0.453488 0.804878
297 G7M 0.453488 0.87013
298 7DD 0.453488 0.957143
299 3D1 0.453333 0.77027
300 3L1 0.453333 0.77027
301 NDC 0.45082 0.87013
302 FB0 0.45082 0.781609
303 0WD 0.45045 0.894737
304 26A 0.447368 0.76
305 2FA 0.447368 0.810811
306 CMP 0.447059 0.927536
307 2BA 0.447059 0.914286
308 D3Y 0.446809 0.786667
309 SO8 0.444444 0.786667
310 APU 0.444444 0.893333
311 VRT 0.444444 0.766234
312 KB1 0.444444 0.716049
313 FDA 0.443548 0.809524
314 PUA 0.443478 0.858974
315 ODP 0.441441 0.883117
316 6FA 0.44 0.817073
317 RP1 0.439024 0.864865
318 SP1 0.439024 0.864865
319 103 0.439024 0.861111
320 3NZ 0.438776 0.779221
321 7DT 0.438202 0.957143
322 U G A 0.436508 0.8375
323 NDP 0.436364 0.894737
324 NPW 0.436364 0.860759
325 MTP 0.434211 0.727273
326 NVA 2AD 0.433333 0.74026
327 FAD 0.433071 0.82716
328 SFD 0.433071 0.712766
329 FAS 0.433071 0.82716
330 TXP 0.432432 0.894737
331 IRN 0.432432 0.867647
332 NZQ 0.432432 0.883117
333 ZZB 0.432432 0.792683
334 FNK 0.430769 0.781609
335 62F 0.430769 0.8375
336 128 0.429907 0.752941
337 PLP AAD 0.429825 0.758621
338 PAX 0.428571 0.82716
339 6MD 0.428571 0.805556
340 1DA 0.428571 0.842857
341 SLU 0.426087 0.767442
342 XNP 0.424779 0.848101
343 12D 0.424528 0.761905
344 5F1 0.423077 0.72973
345 ETB 0.422414 0.809524
346 DCA 0.422414 0.8
347 WMP 0.421053 0.864865
348 GUO 0.421053 0.864865
349 FAY 0.416667 0.8375
350 38Y 0.415929 0.804878
351 5J9 0.415842 0.728395
352 NAD BBN 0.415385 0.817073
353 0T1 0.415254 0.8
354 COA 0.415254 0.8
355 KH3 0.415094 0.690476
356 FMP 0.413793 0.871429
357 U A C C 0.413793 0.857143
358 N01 0.413793 0.90411
359 RFL 0.413534 0.797619
360 NMN AMP PO4 0.412281 0.868421
361 NAD CJ3 0.409091 0.788235
362 GDP 0.408602 0.893333
363 GP2 0.408602 0.858974
364 NAP 0.408333 0.944444
365 NOC 0.407895 0.760563
366 CNV FAD 0.407407 0.770115
367 2ER 0.405941 0.831169
368 1PR 0.405941 0.820513
369 P5F 0.405797 0.8
370 TAP 0.404959 0.906667
371 CAO 0.404959 0.772727
372 AMX 0.404959 0.809524
373 COS 0.404959 0.781609
374 30N 0.404959 0.731183
375 XMP 0.402299 0.891892
376 G2P 0.402062 0.858974
377 APC G U 0.401709 0.833333
378 U A A U 0.401639 0.906667
379 CMX 0.401639 0.8
380 SCO 0.401639 0.8
381 NA0 0.401639 0.931507
382 F2N 0.4 0.790698
Ligand no: 2; Ligand: DGP; Similar ligands found: 88
No: Ligand ECFP6 Tc MDL keys Tc
1 DGP 1 1
2 DG 1 1
3 DGI 0.815789 0.986842
4 DGT 0.775 0.986842
5 DG DG 0.693182 0.925
6 DI 0.62963 0.973333
7 G 0.60241 0.922078
8 5GP 0.60241 0.922078
9 CGP 0.596154 0.925926
10 DC DG 0.575472 0.902439
11 GDP 0.516484 0.910256
12 GH3 0.515789 0.935065
13 D5M 0.511905 0.894737
14 DA 0.511905 0.894737
15 3GP 0.505747 0.909091
16 2GP 0.505747 0.922078
17 GP3 0.505495 0.8875
18 G3D 0.505263 0.922078
19 GP2 0.5 0.924051
20 GTP 0.5 0.910256
21 DU DU DU DU BRU DG DU 0.495935 0.850575
22 G4P 0.494845 0.922078
23 GNH 0.494624 0.898734
24 P2G 0.494382 0.871795
25 G2P 0.489583 0.924051
26 GMP 0.487805 0.797468
27 GMV 0.484211 0.8875
28 ALF 5GP 0.484211 0.833333
29 P1G 0.483516 0.884615
30 G2R 0.48 0.948718
31 GAV 0.479592 0.876543
32 GCP 0.479167 0.911392
33 G1R 0.479167 0.898734
34 0O2 0.475248 0.922078
35 GNP 0.474227 0.8875
36 GSP 0.474227 0.865854
37 GDP MG 0.473684 0.864198
38 3PD UM3 0.473214 0.878049
39 DOI 0.47191 0.87013
40 DG DA DC DG 0.469697 0.891566
41 GDP BEF 0.46875 0.843373
42 DG DC 0.466667 0.9375
43 DA DC DG DA 0.466165 0.891566
44 GPG 0.460784 0.876543
45 GPX 0.46 0.909091
46 GDP ALF 0.455446 0.833333
47 GTP MG 0.454545 0.864198
48 BEF GDP 0.454545 0.833333
49 3ZE 0.451613 0.897436
50 CF2 0.451613 0.811765
51 DA DU DG DA 0.451327 0.845238
52 GCP G 0.45 0.875
53 GPD 0.449541 0.890244
54 Y9Z 0.443396 0.869048
55 GKE 0.443396 0.876543
56 GDD 0.443396 0.876543
57 GDC 0.443396 0.876543
58 G G 0.442308 0.875
59 GDP AF3 0.441176 0.833333
60 DG DT DC 0.439024 0.860465
61 G3A 0.435185 0.8875
62 YGP 0.433962 0.845238
63 DC DG DA DC 0.431818 0.91358
64 G5P 0.431193 0.8875
65 SGP 0.430108 0.817073
66 JB2 0.427273 0.876543
67 G G U 0.427273 0.898734
68 GDR 0.425926 0.876543
69 GTG 0.425926 0.855422
70 GFB 0.425926 0.876543
71 DAT 0.425532 0.896104
72 6CK 0.422018 0.855422
73 DT DA DC DG 0.42069 0.870588
74 DC DG DT DA 0.417808 0.870588
75 GKD 0.414414 0.876543
76 BGO 0.413793 0.865854
77 U2G 0.413793 0.855422
78 GDX 0.410714 0.8875
79 DTP 0.408163 0.896104
80 CG2 0.40678 0.855422
81 AS 0.406593 0.85
82 GDP 7MG 0.405405 0.853659
83 JB3 0.405172 0.865854
84 UCG 0.404762 0.876543
85 8OG 0.404255 0.855422
86 NGD 0.401709 0.876543
87 FEG 0.401709 0.869048
88 G A A A 0.4 0.864198
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1DEK; Ligand: DGP; Similar sites found: 30
This union binding pocket(no: 1) in the query (biounit: 1dek.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1SQL GUN 0.02158 0.40357 None
2 3CQL NAG 0.008207 0.426 1.65975
3 3PMA SCR 0.02939 0.40453 2.07469
4 1KDO C 0.007576 0.40568 2.20264
5 4OKD GLC GLC GLC 0.02474 0.404 2.48963
6 3BU1 HSM 0.01 0.42949 2.7027
7 3K4Z CBI 0.00846 0.42027 2.90456
8 3KO0 TFP 0.009751 0.41966 2.9703
9 5V3Y 5V8 0.0001036 0.44544 3.3195
10 4Q86 AMP 0.005576 0.41559 3.3195
11 2GMP NAG MAN 0.007049 0.43131 3.73444
12 2V95 HCY 0.02342 0.40339 3.73444
13 3PD6 PMP 0.01518 0.40308 3.73444
14 2PHU MAN MAN 0.0252 0.40056 3.73444
15 3WUR O4B 0.007906 0.43237 4.09357
16 3HP9 CF1 0.01995 0.40721 4.14938
17 1G0N PHH 0.02375 0.40288 4.56432
18 5E58 CPZ 0.02578 0.4004 4.56432
19 2JFZ 003 0.02784 0.41079 5.39419
20 1MZC SUC 0.004708 0.43246 5.80913
21 5DY5 5GR 0.03641 0.40627 5.80913
22 2Q2V NAD 0.04647 0.40599 6.22407
23 4UCC ZKW 0.01217 0.40188 6.43777
24 2Q89 6CS 0.01585 0.40629 6.639
25 4XDY HIO 0.02221 0.4035 9.12863
26 5DCH 1YO 0.002346 0.45445 9.375
27 3NUG NAD 0.01585 0.40086 9.7166
28 2Y69 CHD 0.02416 0.40361 10.4651
29 2V5E SCR 0.0214 0.41797 14.8515
30 1T0S BML 0.01086 0.4196 26.7442
Pocket No.: 2; Query (leader) PDB : 1DEK; Ligand: DGP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 1dek.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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