Receptor
PDB id Resolution Class Description Source Keywords
1UKE 2.2 Å EC: 2.7.4.14 UMP/CMP KINASE FROM SLIME MOLD DICTYOSTELIUM DISCOIDEUM NMP KINASE NUCLEOTIDE SPECIFICITY PHOSPHORYL TRANSFER BISUBSTRATE INHIBITOR NUCLEOTIDE MONOPHOSPHATE KINASE
Ref.: CRYSTAL STRUCTURE OF THE COMPLEX OF UMP/CMP KINASE FROM DICTYOSTELIUM DISCOIDEUM AND THE BISUBSTRATE INHIBITOR P1-(5'-ADENOSYL) P5-(5'-URIDYL) PENTAPHOSPHATE (UP5A) AND MG2+ AT 2.2 A: IMPLICATIONS FOR WATER-MEDIATED SPECIFICITY. BIOCHEMISTRY
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:196;
Invalid;
none;
submit data
24.305 Mg [Mg+2...
UP5 A:195;
Valid;
none;
submit data
893.327 C19 H28 N7 O24 P5 c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1QF9 1.7 Å EC: 2.7.4.14 PH INFLUENCES FLUORIDE COORDINATION NUMBER OF THE ALFX PHOSP TRANSFER TRANSITION STATE ANALOG IN UMP/CMP KINASE DICTYOSTELIUM DISCOIDEUM NUCLEOSIDE MONOPHOSPHATE KINASE NMP KINASE PHOSPHORYL TRANTRANSITION STATE ANALOG COMPLEX TRANSFERASE KINASE
Ref.: PH INFLUENCES FLUORIDE COORDINATION NUMBER OF THE A PHOSPHORYL TRANSFER TRANSITION STATE ANALOG. NAT.STRUCT.BIOL. V. 6 721 1999
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1UKE - UP5 C19 H28 N7 O24 P5 c1nc(c2c(n....
2 3UKD - AF3 Al F3 F[Al](F)F
3 4UKD - UDP ADP BF2 n/a n/a
4 5UKD - AF3 Al F3 F[Al](F)F
5 1QF9 - ALF Al F4 F[Al-](F)(....
6 2UKD - C5P C9 H14 N3 O8 P C1=CN(C(=O....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1UKE - UP5 C19 H28 N7 O24 P5 c1nc(c2c(n....
2 3UKD - AF3 Al F3 F[Al](F)F
3 4UKD - UDP ADP BF2 n/a n/a
4 5UKD - AF3 Al F3 F[Al](F)F
5 1QF9 - ALF Al F4 F[Al-](F)(....
6 2UKD - C5P C9 H14 N3 O8 P C1=CN(C(=O....
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 1UKE - UP5 C19 H28 N7 O24 P5 c1nc(c2c(n....
2 3UKD - AF3 Al F3 F[Al](F)F
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: UP5; Similar ligands found: 336
No: Ligand ECFP6 Tc MDL keys Tc
1 UP5 1 1
2 4TC 0.881188 0.973684
3 UPA 0.711712 0.986667
4 B4P 0.691489 0.945946
5 AP5 0.691489 0.945946
6 A U 0.690265 0.947368
7 BA3 0.680851 0.945946
8 139 0.678261 0.948718
9 AQP 0.663265 0.92
10 5FA 0.663265 0.92
11 ATP 0.653061 0.92
12 HEJ 0.653061 0.92
13 U A 0.644628 0.960526
14 A2D 0.642105 0.945946
15 SAP 0.623762 0.873418
16 AGS 0.623762 0.873418
17 ADP 0.622449 0.92
18 ACP 0.62 0.896104
19 G5P 0.614035 0.898734
20 U5F 0.612245 0.853333
21 U A A U 0.609375 0.960526
22 T5A 0.608333 0.91358
23 G3A 0.605263 0.898734
24 APU 0.605042 0.947368
25 UTP 0.602041 0.853333
26 AN2 0.6 0.907895
27 AT4 0.6 0.884615
28 APR 0.598039 0.92
29 AR6 0.598039 0.92
30 ACQ 0.596154 0.896104
31 ANP 0.596154 0.896104
32 6YZ 0.59434 0.896104
33 M33 0.594059 0.907895
34 AD9 0.592233 0.896104
35 A4P 0.591667 0.869048
36 ATF 0.584906 0.884615
37 PRX 0.582524 0.848101
38 GTA 0.581197 0.865854
39 25L 0.575221 0.933333
40 TXE 0.575 0.960526
41 A U C C 0.574627 0.923077
42 HQG 0.574074 0.907895
43 A3R 0.572727 0.8625
44 ADQ 0.572727 0.921053
45 UDP 0.571429 0.853333
46 A G U 0.569343 0.888889
47 A22 0.568807 0.933333
48 6V0 0.566667 0.948052
49 NAI 0.566667 0.960526
50 T99 0.566038 0.884615
51 TAT 0.566038 0.884615
52 A12 0.564356 0.884615
53 AP2 0.564356 0.884615
54 CA0 0.563107 0.921053
55 ADX 0.563107 0.831325
56 AMP 0.561224 0.893333
57 A 0.561224 0.893333
58 A1R 0.558559 0.8625
59 50T 0.557692 0.883117
60 KG4 0.557692 0.921053
61 AP0 0.557377 0.923077
62 TXD 0.553719 0.935065
63 NAX 0.553719 0.924051
64 APC 0.552381 0.884615
65 A G U U 0.549296 0.888889
66 9X8 0.548673 0.873418
67 PUA 0.546154 0.935897
68 4AD 0.544643 0.897436
69 ABM 0.544554 0.87013
70 45A 0.544554 0.87013
71 BIS 0.53913 0.8625
72 UNP 0.538462 0.831169
73 8LH 0.536364 0.884615
74 5SV 0.535714 0.807229
75 OAD 0.535088 0.921053
76 APC MG 0.53271 0.87013
77 5AL 0.53211 0.907895
78 8LE 0.53211 0.873418
79 ADJ 0.531746 0.855422
80 GDU 0.527273 0.855263
81 GUD 0.527273 0.855263
82 UFM 0.527273 0.855263
83 UPG 0.527273 0.855263
84 3OD 0.525862 0.921053
85 SRA 0.524752 0.848101
86 ADP MG 0.52381 0.893333
87 80F 0.523077 0.890244
88 SRP 0.522523 0.884615
89 OZV 0.522124 0.92
90 25A 0.522124 0.92
91 8QN 0.522124 0.907895
92 SFB 0.52 0.797753
93 AU1 0.518868 0.896104
94 ADV 0.518519 0.884615
95 RBY 0.518519 0.884615
96 UDH 0.518182 0.792683
97 PR8 0.517241 0.831325
98 4UV 0.516667 0.922078
99 660 0.513514 0.844156
100 URM 0.513514 0.844156
101 MAP 0.513274 0.873418
102 U2F 0.513274 0.8125
103 UFG 0.513274 0.8125
104 8LQ 0.513274 0.884615
105 UPF 0.513274 0.8125
106 AHX 0.513043 0.875
107 00A 0.513043 0.886076
108 1ZZ 0.512821 0.821429
109 U5P 0.510204 0.84
110 U 0.510204 0.84
111 OOB 0.508772 0.933333
112 3UC 0.508621 0.8125
113 4UU 0.508197 0.922078
114 AFH 0.508197 0.864198
115 ADP PO3 0.504587 0.893333
116 ATP MG 0.504587 0.893333
117 UPP 0.504505 0.88
118 AMO 0.504348 0.909091
119 PAJ 0.504348 0.864198
120 WAQ 0.504274 0.8625
121 LAD 0.504274 0.841463
122 DQV 0.504065 0.959459
123 EAD 0.50365 0.924051
124 UPU 0.5 0.853333
125 DLL 0.5 0.933333
126 5AS 0.5 0.744444
127 OMR 0.5 0.833333
128 G3N 0.5 0.857143
129 48N 0.496 0.875
130 XAH 0.495868 0.821429
131 3UK 0.495726 0.921053
132 SON 0.495327 0.884615
133 44P 0.49505 0.820513
134 CNA 0.492308 0.934211
135 NXX 0.492063 0.934211
136 DND 0.492063 0.934211
137 9SN 0.491667 0.875
138 B5V 0.491525 0.909091
139 USQ 0.491379 0.755814
140 7D4 0.490741 0.835443
141 ITT 0.490741 0.868421
142 P1H 0.489362 0.901235
143 B5M 0.487603 0.897436
144 B5Y 0.487603 0.897436
145 NB8 0.487395 0.875
146 TXA 0.487395 0.909091
147 PTJ 0.487395 0.851852
148 FYA 0.487395 0.883117
149 ME8 0.487395 0.821429
150 UDX 0.486957 0.855263
151 UAD 0.486957 0.855263
152 ADP ALF 0.486726 0.82716
153 ALF ADP 0.486726 0.82716
154 LMS 0.485437 0.788235
155 NAJ PZO 0.485075 0.898734
156 GA7 0.483871 0.884615
157 UDM 0.483333 0.833333
158 VO4 ADP 0.482456 0.883117
159 ADP VO4 0.482456 0.883117
160 GAP 0.482143 0.871795
161 4UW 0.480315 0.8875
162 UGA 0.478632 0.866667
163 UGB 0.478632 0.866667
164 ATR 0.477477 0.893333
165 PAP 0.477477 0.906667
166 U2G 0.476923 0.9125
167 2KH 0.476636 0.831169
168 FA5 0.47541 0.909091
169 UD1 0.47541 0.844156
170 UD2 0.47541 0.844156
171 YAP 0.47541 0.897436
172 DAL AMP 0.474138 0.883117
173 A C A C 0.474074 0.923077
174 4TA 0.473684 0.878049
175 0WD 0.473684 0.948052
176 G U 0.473282 0.876543
177 JSQ 0.473214 0.873418
178 HFD 0.473214 0.873418
179 HWU 0.472 0.822785
180 12V 0.472 0.822785
181 ADP BMA 0.470588 0.896104
182 9ZD 0.470085 0.8625
183 9ZA 0.470085 0.8625
184 2A5 0.468468 0.848101
185 UDP UDP 0.466667 0.826667
186 A2R 0.465517 0.907895
187 U A C C 0.463235 0.935065
188 YLP 0.460938 0.802326
189 AV2 0.46087 0.846154
190 NAJ PYZ 0.460432 0.855422
191 MYR AMP 0.459016 0.8
192 HP7 0.456 0.855263
193 F2R 0.455224 0.823529
194 A A 0.454545 0.894737
195 Z5A 0.453901 0.847059
196 TYM 0.453846 0.909091
197 7D3 0.453704 0.835443
198 LAQ 0.453125 0.821429
199 MJZ 0.452381 0.881579
200 COD 0.451852 0.795455
201 NAD 0.451852 0.933333
202 NDP 0.451128 0.948052
203 JB6 0.45082 0.8625
204 YLB 0.450382 0.802326
205 7MD 0.448819 0.843373
206 UD4 0.448819 0.857143
207 F5P 0.448819 0.857143
208 AOC 0.448598 0.802632
209 AYB 0.447761 0.793103
210 GP3 0.447368 0.898734
211 EPU 0.44697 0.822785
212 EEB 0.44697 0.822785
213 NA7 0.446281 0.884615
214 A3D 0.445255 0.921053
215 UD7 0.444444 0.844156
216 TYR AMP 0.444444 0.873418
217 Y6W 0.444444 0.8125
218 IOT 0.443609 0.793103
219 3AT 0.443478 0.894737
220 DTP 0.443478 0.835443
221 BTX 0.441176 0.823529
222 NPW 0.440298 0.9125
223 ATP A A A 0.44 0.906667
224 ATP A 0.44 0.906667
225 NAQ 0.439716 0.875
226 EPZ 0.439394 0.833333
227 YLC 0.439394 0.843373
228 ADN 0.438776 0.8
229 XYA 0.438776 0.8
230 RAB 0.438776 0.8
231 DZD 0.437956 0.8875
232 BT5 0.437956 0.813953
233 ARG AMP 0.4375 0.790698
234 F5G 0.4375 0.844156
235 TXP 0.437037 0.923077
236 NZQ 0.437037 0.935897
237 8X1 0.436975 0.73913
238 TSB 0.436975 0.802326
239 A3P 0.436364 0.893333
240 FDA 0.436242 0.880952
241 CSV 0.435484 0.825
242 CSQ 0.435484 0.825
243 UDZ 0.435115 0.783133
244 G5A 0.434783 0.764045
245 TAD 0.434109 0.864198
246 6FA 0.433333 0.86747
247 AMP DBH 0.433071 0.871795
248 NAE 0.432624 0.897436
249 HF4 0.432432 0.857143
250 CTP 0.432432 0.857143
251 GTP 0.432203 0.873418
252 SSA 0.432203 0.784091
253 AF3 ADP 3PG 0.431818 0.819277
254 P5A 0.430894 0.731183
255 AHZ 0.430769 0.8
256 IUG 0.430769 0.788235
257 G A A A 0.430657 0.851852
258 5N5 0.43 0.776316
259 NSS 0.429752 0.784091
260 YLA 0.42963 0.823529
261 PRT 0.428571 0.858974
262 54H 0.428571 0.772727
263 VMS 0.428571 0.772727
264 SFD 0.427632 0.757895
265 FAS 0.427632 0.878049
266 FAD 0.427632 0.878049
267 PPS 0.42735 0.809524
268 6AD 0.42735 0.841463
269 ZID 0.426573 0.921053
270 AR6 AR6 0.426357 0.894737
271 ARU 0.42623 0.797619
272 NVA LMS 0.42623 0.73913
273 A4D 0.425743 0.776316
274 5CD 0.425743 0.763158
275 YLY 0.425532 0.793103
276 3DH 0.424528 0.734177
277 A5A 0.423729 0.790698
278 A2P 0.423423 0.88
279 ODP 0.423358 0.935897
280 FAY 0.423077 0.888889
281 M2T 0.423077 0.698795
282 FB0 0.422819 0.788889
283 LEU LMS 0.422764 0.73913
284 AVV 0.421488 0.851852
285 H1Q 0.421053 0.857143
286 3AM 0.420561 0.855263
287 A G 0.42029 0.8625
288 7MC 0.41791 0.823529
289 7DT 0.417391 0.906667
290 RGT 0.417323 0.884615
291 U A G G 0.417266 0.8625
292 NO7 0.416667 0.884615
293 GCP 0.416667 0.851852
294 52H 0.416667 0.764045
295 62F 0.416667 0.865854
296 FNK 0.416667 0.850575
297 9K8 0.416 0.72043
298 M24 0.415493 0.853659
299 7D5 0.415094 0.810127
300 S4M 0.414414 0.637363
301 1DG 0.413793 0.948052
302 DG1 0.413793 0.948052
303 EP4 0.413462 0.716049
304 NDC 0.413333 0.875
305 5CA 0.413223 0.784091
306 GSP 0.413223 0.831325
307 53H 0.413223 0.764045
308 H6Y 0.411765 0.921053
309 RFL 0.411392 0.847059
310 MAO 0.410714 0.724138
311 LRM 0.409836 0.870588
312 DTA 0.409524 0.769231
313 NDE 0.409396 0.909091
314 DAT 0.408696 0.835443
315 URI 0.408163 0.76
316 KAA 0.408 0.73913
317 7C5 0.407692 0.8
318 TPG 0.406897 0.8
319 N0B 0.406897 0.845238
320 DDS 0.40678 0.810127
321 GDP 0.40678 0.873418
322 DSZ 0.406504 0.784091
323 LSS 0.406504 0.747253
324 LPA AMP 0.406015 0.8
325 MTA 0.40566 0.734177
326 CDP 0.405405 0.857143
327 7XL 0.405172 0.835443
328 U U 0.404959 0.842105
329 B1U 0.403101 0.741935
330 NJP 0.402878 0.922078
331 6MZ 0.401786 0.857143
332 91P 0.40146 0.890244
333 UMA 0.401408 0.833333
334 AMP NAD 0.4 0.907895
335 6RE 0.4 0.702381
336 NMN AMP PO4 0.4 0.922078
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1QF9; Ligand: C5P; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 1qf9.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
1 1LVG ADP 7.73196
Pocket No.: 2; Query (leader) PDB : 1QF9; Ligand: ADP; Similar sites found with APoc: 1
This union binding pocket(no: 2) in the query (biounit: 1qf9.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
1 1LVG ADP 7.73196
Pocket No.: 3; Query (leader) PDB : 1QF9; Ligand: ALF; Similar sites found with APoc: 1
This union binding pocket(no: 3) in the query (biounit: 1qf9.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
1 1LVG ADP 7.73196
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