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(n1C....
2 1DEK - DGP C10 H14 N5 O7 P c1nc2c(n1C....
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(n1C....
2 1DEK - DGP C10 H14 N5 O7 P c1nc2c(n1C....
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(n1C....
2 1DEK - DGP C10 H14 N5 O7 P c1nc2c(n1C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: AMP; Similar ligands found: 331
No: Ligand ECFP6 Tc MDL keys Tc
1 AMP 1 1
2 A 1 1
3 ABM 0.833333 0.943662
4 A2D 0.833333 0.943662
5 ADP 0.823529 0.971429
6 AMP MG 0.818182 0.916667
7 AP2 0.808824 0.931507
8 BA3 0.808824 0.943662
9 A12 0.808824 0.931507
10 SRA 0.80303 0.944444
11 B4P 0.797101 0.943662
12 AP5 0.797101 0.943662
13 ATP 0.788732 0.971429
14 5FA 0.777778 0.971429
15 APC 0.777778 0.931507
16 AQP 0.777778 0.971429
17 AU1 0.774648 0.944444
18 CA0 0.774648 0.917808
19 M33 0.774648 0.930556
20 ADX 0.774648 0.848101
21 ACP 0.763889 0.944444
22 50T 0.763889 0.957747
23 25A 0.75641 0.971429
24 PRX 0.753425 0.917808
25 APR 0.753425 0.943662
26 AR6 0.753425 0.943662
27 ADP MG 0.75 0.90411
28 TAT 0.746667 0.931507
29 ACQ 0.746667 0.944444
30 RBY 0.743243 0.905405
31 ADV 0.743243 0.905405
32 AD9 0.743243 0.944444
33 SAP 0.743243 0.918919
34 AGS 0.743243 0.918919
35 ADP BEF 0.739726 0.88
36 BEF ADP 0.739726 0.88
37 ANP 0.723684 0.944444
38 ADP PO3 0.72 0.942857
39 5AL 0.714286 0.930556
40 SON 0.712329 0.931507
41 ATP MG 0.710526 0.90411
42 ADN 0.709677 0.842857
43 XYA 0.709677 0.842857
44 RAB 0.709677 0.842857
45 ATF 0.705128 0.931507
46 GAP 0.701299 0.891892
47 A22 0.7 0.957747
48 SRP 0.696203 0.905405
49 A3P 0.684932 0.971014
50 A2P 0.684932 0.956522
51 ALF ADP 0.683544 0.868421
52 ADP ALF 0.683544 0.868421
53 ADQ 0.682927 0.917808
54 MAP 0.679012 0.918919
55 ADP VO4 0.675 0.930556
56 ANP MG 0.675 0.893333
57 PTJ 0.670588 0.894737
58 AOC 0.666667 0.84507
59 PAJ 0.662651 0.858974
60 4AD 0.662651 0.893333
61 A1R 0.662651 0.881579
62 AMO 0.662651 0.905405
63 5N5 0.661538 0.816901
64 DAL AMP 0.658537 0.90411
65 IMO 0.657534 0.928571
66 AHX 0.654762 0.87013
67 DLL 0.654762 0.930556
68 00A 0.654762 0.881579
69 5AS 0.653333 0.776471
70 5CD 0.651515 0.828571
71 A4D 0.651515 0.816901
72 OAD 0.647059 0.917808
73 ADP BMA 0.647059 0.891892
74 25L 0.643678 0.957747
75 LAD 0.639535 0.858974
76 PR8 0.639535 0.848101
77 DTA 0.637681 0.808219
78 V3L 0.6375 0.971429
79 3DH 0.633803 0.794521
80 NB8 0.632184 0.87013
81 1ZZ 0.632184 0.8375
82 ME8 0.632184 0.8375
83 BIS 0.632184 0.906667
84 3OD 0.632184 0.917808
85 FYA 0.632184 0.930556
86 TXA 0.632184 0.905405
87 MTA 0.628571 0.794521
88 3AM 0.625 0.956522
89 EP4 0.623188 0.773333
90 M2T 0.614286 0.753247
91 YAP 0.611111 0.893333
92 FA5 0.611111 0.905405
93 MYR AMP 0.606742 0.814815
94 G5A 0.604938 0.776471
95 XAH 0.604396 0.8375
96 ATP A A A 0.593407 0.929577
97 PAP 0.592593 0.957143
98 G3A 0.591398 0.894737
99 2AM 0.589041 0.942857
100 6C6 0.585366 0.905405
101 G5P 0.585106 0.894737
102 AFH 0.585106 0.858974
103 A5A 0.583333 0.804878
104 TSB 0.581395 0.795181
105 AMP DBH 0.580645 0.891892
106 2A5 0.580247 0.891892
107 DSH 0.578947 0.74359
108 TAD 0.578947 0.858974
109 GTA 0.578947 0.860759
110 6IA 0.578313 0.858974
111 SSA 0.576471 0.776471
112 AMZ 0.575342 0.888889
113 C2R 0.575342 0.876712
114 PGS 0.575 0.857143
115 ZAS 0.573333 0.786667
116 ATR 0.573171 0.942857
117 LAQ 0.572917 0.8375
118 AIR 0.571429 0.927536
119 PPS 0.571429 0.848101
120 AAM 0.571429 1
121 A3N 0.571429 0.783784
122 54H 0.569767 0.785714
123 52H 0.569767 0.776471
124 VMS 0.569767 0.785714
125 AR6 AR6 0.568421 0.916667
126 7MD 0.568421 0.8375
127 YLP 0.56701 0.817073
128 OVE 0.565789 0.90411
129 UPA 0.565657 0.881579
130 2SA 0.564706 0.905405
131 S4M 0.564103 0.682353
132 5CA 0.563218 0.776471
133 53H 0.563218 0.776471
134 NXX 0.561224 0.905405
135 DND 0.561224 0.905405
136 TXD 0.561224 0.881579
137 NAI 0.561224 0.881579
138 UP5 0.561224 0.893333
139 NAX 0.561224 0.848101
140 NIA 0.56 0.820513
141 DA 0.558442 0.902778
142 D5M 0.558442 0.902778
143 MAO 0.556962 0.777778
144 AHZ 0.556701 0.814815
145 ITT 0.555556 0.915493
146 TYM 0.555556 0.905405
147 5AD 0.552239 0.768116
148 A2R 0.551724 0.957747
149 LPA AMP 0.55102 0.814815
150 LSS 0.550562 0.758621
151 DSZ 0.550562 0.776471
152 NSS 0.550562 0.776471
153 4TC 0.55 0.87013
154 YLB 0.55 0.817073
155 AP0 0.55 0.87013
156 YLC 0.55 0.8375
157 P5A 0.549451 0.741573
158 139 0.54902 0.848101
159 A4P 0.544554 0.819277
160 NVA LMS 0.544444 0.758621
161 A7D 0.54321 0.797297
162 AF3 ADP 3PG 0.54 0.835443
163 ALF ADP 3PG 0.54 0.835443
164 LA8 ALF 3PG 0.54 0.835443
165 6K6 0.539326 0.957143
166 IOT 0.539216 0.829268
167 A3G 0.538462 0.797297
168 LEU LMS 0.538462 0.758621
169 A5D 0.535714 0.808219
170 7MC 0.534653 0.817073
171 T5A 0.533981 0.817073
172 ADJ 0.533981 0.82716
173 YLA 0.533981 0.817073
174 GSU 0.532609 0.776471
175 KAA 0.532609 0.75
176 7RA 0.531646 0.985507
177 SFG 0.53012 0.77027
178 SAH 0.529412 0.763158
179 CNA 0.528846 0.905405
180 AYB 0.528846 0.807229
181 N6P 0.527473 0.942029
182 8BR 0.525 0.931507
183 YSA 0.520833 0.776471
184 7RP 0.518987 0.955882
185 COD 0.518868 0.788235
186 G A A A 0.518868 0.87013
187 NAD 0.518868 0.930556
188 BTX 0.518868 0.839506
189 MHZ 0.518072 0.714286
190 SA8 0.517647 0.725
191 6AD 0.517241 0.883117
192 BT5 0.514019 0.829268
193 DZD 0.514019 0.858974
194 RMB 0.5125 0.898551
195 SAI 0.511628 0.753247
196 AV2 0.511364 0.890411
197 NAD IBO 0.509434 0.868421
198 A3D 0.509259 0.917808
199 A3S 0.506024 0.808219
200 3AT 0.505747 0.943662
201 SAM 0.505747 0.707317
202 SMM 0.505618 0.702381
203 NA7 0.505376 0.931507
204 4TA 0.504673 0.804878
205 AAT 0.5 0.725
206 5GP 0.5 0.905405
207 NEC 0.5 0.743243
208 EEM 0.5 0.707317
209 G 0.5 0.905405
210 YLY 0.495495 0.807229
211 M24 0.495495 0.848101
212 A3T 0.494118 0.819444
213 DAT 0.494118 0.878378
214 FAI 0.493827 0.888889
215 P2P 0.493827 0.928571
216 1RB 0.493671 0.911765
217 NAE 0.491071 0.893333
218 NAJ PZO 0.490909 0.846154
219 TM1 0.489583 0.771084
220 PO4 PO4 A A A A PO4 0.489362 0.901408
221 A6D 0.489362 0.740741
222 A A A 0.489362 0.90411
223 S7M 0.488889 0.707317
224 DTP 0.488636 0.878378
225 101 0.4875 0.902778
226 RBZ 0.4875 0.873239
227 EAD 0.486957 0.848101
228 NAQ 0.486726 0.87013
229 NDE 0.483051 0.931507
230 N0B 0.482456 0.817073
231 ZID 0.482456 0.917808
232 WSA 0.480769 0.785714
233 RGT 0.479592 0.931507
234 ARU 0.478723 0.835443
235 GGZ 0.478261 0.8
236 JLN 0.47561 0.863014
237 ANZ 0.475248 0.820513
238 QQY 0.475 0.837838
239 ACK 0.475 0.885714
240 NAJ PYZ 0.473684 0.848101
241 GEK 0.473118 0.734177
242 AVV 0.473118 0.87013
243 3AD 0.472973 0.828571
244 A U 0.471698 0.868421
245 P1H 0.470588 0.82716
246 AMP NAD 0.469565 0.88
247 0UM 0.468085 0.716049
248 RVP 0.467532 0.847222
249 Z5A 0.465517 0.776471
250 PMO 0.464286 0.873239
251 PA7 0.464286 0.705128
252 QQX 0.4625 0.826667
253 2VA 0.45977 0.797297
254 IMP 0.458824 0.90411
255 NOS 0.458333 0.788732
256 CC5 0.458333 0.84058
257 K15 0.458333 0.698795
258 DDS 0.455556 0.851351
259 V1N 0.455446 0.943662
260 NJP 0.454545 0.918919
261 G7M 0.453488 0.87013
262 93A 0.453488 0.804878
263 3L1 0.453333 0.77027
264 3D1 0.453333 0.77027
265 FB0 0.45082 0.781609
266 NDC 0.45082 0.87013
267 0WD 0.45045 0.894737
268 26A 0.447368 0.76
269 2FA 0.447368 0.810811
270 2BA 0.447059 0.914286
271 CMP 0.447059 0.927536
272 D3Y 0.446809 0.786667
273 APU 0.444444 0.893333
274 FDA 0.443548 0.809524
275 PUA 0.443478 0.858974
276 ODP 0.441441 0.883117
277 6FA 0.44 0.817073
278 RP1 0.439024 0.864865
279 SP1 0.439024 0.864865
280 103 0.439024 0.861111
281 3NZ 0.438776 0.779221
282 U G A 0.436508 0.8375
283 NDP 0.436364 0.894737
284 NPW 0.436364 0.860759
285 MTP 0.434211 0.727273
286 NVA 2AD 0.433333 0.74026
287 FAD 0.433071 0.82716
288 FAS 0.433071 0.82716
289 SFD 0.433071 0.712766
290 IRN 0.432432 0.867647
291 NZQ 0.432432 0.883117
292 ZZB 0.432432 0.792683
293 TXP 0.432432 0.894737
294 FNK 0.430769 0.781609
295 128 0.429907 0.752941
296 PLP AAD 0.429825 0.758621
297 1DA 0.428571 0.842857
298 PAX 0.428571 0.82716
299 6MD 0.428571 0.805556
300 SLU 0.426087 0.767442
301 12D 0.424528 0.761905
302 5F1 0.423077 0.72973
303 ETB 0.422414 0.809524
304 DCA 0.422414 0.8
305 WMP 0.421053 0.864865
306 FAY 0.416667 0.8375
307 COA 0.415254 0.8
308 KH3 0.415094 0.690476
309 FMP 0.413793 0.871429
310 N01 0.413793 0.90411
311 RFL 0.413534 0.797619
312 NMN AMP PO4 0.412281 0.868421
313 GDP 0.408602 0.893333
314 GP2 0.408602 0.858974
315 NAP 0.408333 0.944444
316 NOC 0.407895 0.760563
317 CNV FAD 0.407407 0.770115
318 1PR 0.405941 0.820513
319 2ER 0.405941 0.831169
320 P5F 0.405797 0.8
321 COS 0.404959 0.781609
322 TAP 0.404959 0.906667
323 AMX 0.404959 0.809524
324 CAO 0.404959 0.772727
325 30N 0.404959 0.731183
326 XMP 0.402299 0.891892
327 G2P 0.402062 0.858974
328 CMX 0.401639 0.8
329 SCO 0.401639 0.8
330 NA0 0.401639 0.931507
331 F2N 0.4 0.790698
Ligand no: 2; Ligand: DGP; Similar ligands found: 83
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 5GP 0.60241 0.922078
8 G 0.60241 0.922078
9 CGP 0.596154 0.925926
10 DC DG 0.575472 0.902439
11 GDP 0.516484 0.910256
12 D5M 0.511905 0.894737
13 DA 0.511905 0.894737
14 3GP 0.505747 0.909091
15 2GP 0.505747 0.922078
16 GP3 0.505495 0.8875
17 G3D 0.505263 0.922078
18 GTP 0.5 0.910256
19 GP2 0.5 0.924051
20 DU DU DU DU BRU DG DU 0.495935 0.850575
21 G4P 0.494845 0.922078
22 GNH 0.494624 0.898734
23 P2G 0.494382 0.871795
24 G2P 0.489583 0.924051
25 GMP 0.487805 0.797468
26 ALF 5GP 0.484211 0.833333
27 GMV 0.484211 0.8875
28 P1G 0.483516 0.884615
29 G2R 0.48 0.948718
30 GAV 0.479592 0.876543
31 GCP 0.479167 0.911392
32 G1R 0.479167 0.898734
33 0O2 0.475248 0.922078
34 GNP 0.474227 0.8875
35 GSP 0.474227 0.865854
36 GDP MG 0.473684 0.864198
37 3PD UM3 0.473214 0.878049
38 DOI 0.47191 0.87013
39 DG DA DC DG 0.469697 0.891566
40 DG DC 0.466667 0.9375
41 DA DC DG DA 0.466165 0.891566
42 GPG 0.460784 0.876543
43 GPX 0.46 0.909091
44 GDP ALF 0.455446 0.833333
45 BEF GDP 0.454545 0.833333
46 GTP MG 0.454545 0.864198
47 CF2 0.451613 0.811765
48 3ZE 0.451613 0.897436
49 DA DU DG DA 0.451327 0.845238
50 GCP G 0.45 0.875
51 GPD 0.449541 0.890244
52 Y9Z 0.443396 0.869048
53 GDD 0.443396 0.876543
54 GDC 0.443396 0.876543
55 GKE 0.443396 0.876543
56 GDP AF3 0.441176 0.833333
57 DG DT DC 0.439024 0.860465
58 G3A 0.435185 0.8875
59 YGP 0.433962 0.845238
60 DC DG DA DC 0.431818 0.91358
61 G5P 0.431193 0.8875
62 SGP 0.430108 0.817073
63 JB2 0.427273 0.876543
64 G G U 0.427273 0.898734
65 GDR 0.425926 0.876543
66 G G 0.425926 0.8875
67 GTG 0.425926 0.855422
68 GFB 0.425926 0.876543
69 DAT 0.425532 0.896104
70 DT DA DC DG 0.42069 0.870588
71 DC DG DT DA 0.417808 0.870588
72 GKD 0.414414 0.876543
73 U2G 0.413793 0.855422
74 BGO 0.413793 0.865854
75 GDX 0.410714 0.8875
76 DTP 0.408163 0.896104
77 CG2 0.40678 0.855422
78 GDP 7MG 0.405405 0.853659
79 JB3 0.405172 0.865854
80 8OG 0.404255 0.855422
81 NGD 0.401709 0.876543
82 FEG 0.401709 0.869048
83 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: 32
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)
1 3KO0 TFP 0.005595 0.43351
2 1MZC SUC 0.004708 0.43246
3 3WUR O4B 0.007906 0.43237
4 2GMP NAG MAN 0.007049 0.43131
5 3BU1 HSM 0.01 0.42949
6 3WUR O4B 0.008562 0.42937
7 3CQL NAG 0.007853 0.42709
8 3CQL NAG 0.008207 0.426
9 3KO0 TFP 0.009514 0.42259
10 3KO0 TFP 0.009132 0.42076
11 3K4Z CBI 0.00846 0.42027
12 3KO0 TFP 0.009751 0.41966
13 1T0S BML 0.01086 0.4196
14 1T0S BML 0.01086 0.4196
15 2V5E SCR 0.0214 0.41797
16 4Q86 AMP 0.005325 0.41651
17 4Q86 AMP 0.005576 0.41559
18 2GMP NAG MAN 0.01075 0.41468
19 2Y69 CHD 0.01782 0.41217
20 1SQL GUN 0.01815 0.40788
21 3HP9 CF1 0.01995 0.40721
22 2Q89 6CS 0.01585 0.40629
23 1KDO C 0.007576 0.40568
24 3PMA SCR 0.02939 0.40453
25 4OKD GLC GLC GLC 0.02474 0.404
26 2Y69 CHD 0.02416 0.40361
27 1SQL GUN 0.02158 0.40357
28 2V95 HCY 0.02342 0.40339
29 3PD6 PMP 0.01518 0.40308
30 1G0N PHH 0.02375 0.40288
31 3NUG NAD 0.01585 0.40086
32 2PHU MAN MAN 0.0252 0.40056
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)
Feedback