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 (2D)
Ligand no: 1; Ligand: UP5; Similar ligands found: 338
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 BA3 0.680851 0.945946
7 139 0.678261 0.948718
8 AQP 0.663265 0.92
9 5FA 0.663265 0.92
10 HEJ 0.653061 0.92
11 ATP 0.653061 0.92
12 A2D 0.642105 0.945946
13 AGS 0.623762 0.873418
14 ADP 0.622449 0.92
15 ACP 0.62 0.896104
16 G5P 0.614035 0.898734
17 U5F 0.612245 0.853333
18 T5A 0.608333 0.91358
19 G3A 0.605263 0.898734
20 APU 0.605042 0.947368
21 UTP 0.602041 0.853333
22 AT4 0.6 0.884615
23 AN2 0.6 0.907895
24 AR6 0.598039 0.92
25 APR 0.598039 0.92
26 ANP 0.596154 0.896104
27 ACQ 0.596154 0.896104
28 6YZ 0.59434 0.896104
29 M33 0.594059 0.907895
30 AD9 0.592233 0.896104
31 A4P 0.591667 0.869048
32 ATF 0.584906 0.884615
33 PRX 0.582524 0.848101
34 GTA 0.581197 0.865854
35 25L 0.575221 0.933333
36 TXE 0.575 0.960526
37 HQG 0.574074 0.907895
38 A3R 0.572727 0.8625
39 ADQ 0.572727 0.921053
40 UDP 0.571429 0.853333
41 A22 0.568807 0.933333
42 NAI 0.566667 0.960526
43 6V0 0.566667 0.948052
44 TAT 0.566038 0.884615
45 T99 0.566038 0.884615
46 AP2 0.564356 0.884615
47 A12 0.564356 0.884615
48 ADX 0.563107 0.831325
49 CA0 0.563107 0.921053
50 AMP 0.561224 0.893333
51 A 0.561224 0.893333
52 A1R 0.558559 0.8625
53 50T 0.557692 0.883117
54 KG4 0.557692 0.921053
55 AP0 0.557377 0.923077
56 TXD 0.553719 0.935065
57 NAX 0.553719 0.924051
58 APC 0.552381 0.884615
59 9X8 0.548673 0.873418
60 PUA 0.546154 0.935897
61 4AD 0.544643 0.897436
62 45A 0.544554 0.87013
63 ABM 0.544554 0.87013
64 AMP MG 0.54 0.88
65 JNT 0.539823 0.896104
66 BIS 0.53913 0.8625
67 UNP 0.538462 0.831169
68 8LH 0.536364 0.884615
69 5SV 0.535714 0.807229
70 OAD 0.535088 0.921053
71 APC MG 0.53271 0.87013
72 5AL 0.53211 0.907895
73 8LE 0.53211 0.873418
74 ADJ 0.531746 0.855422
75 UFM 0.527273 0.855263
76 UPG 0.527273 0.855263
77 GDU 0.527273 0.855263
78 3OD 0.525862 0.921053
79 KMQ 0.525424 0.909091
80 SRA 0.524752 0.848101
81 ADP BEF 0.52381 0.893333
82 ADP MG 0.52381 0.893333
83 80F 0.523077 0.890244
84 SRP 0.522523 0.884615
85 25A 0.522124 0.92
86 OZV 0.522124 0.92
87 8QN 0.522124 0.907895
88 SFB 0.52 0.797753
89 AU1 0.518868 0.896104
90 RBY 0.518519 0.884615
91 ADV 0.518519 0.884615
92 UDH 0.518182 0.792683
93 PR8 0.517241 0.831325
94 4UV 0.516667 0.922078
95 BEF ADP 0.513761 0.87013
96 660 0.513514 0.844156
97 URM 0.513514 0.844156
98 QA7 0.513274 0.873418
99 UPF 0.513274 0.8125
100 U2F 0.513274 0.8125
101 MAP 0.513274 0.873418
102 8LQ 0.513274 0.884615
103 UFG 0.513274 0.8125
104 00A 0.513043 0.886076
105 AHX 0.513043 0.875
106 1ZZ 0.512821 0.821429
107 U5P 0.510204 0.84
108 U 0.510204 0.84
109 OOB 0.508772 0.933333
110 3UC 0.508621 0.8125
111 AFH 0.508197 0.864198
112 4UU 0.508197 0.922078
113 ADP PO3 0.504587 0.893333
114 ATP MG 0.504587 0.893333
115 UPP 0.504505 0.88
116 PAJ 0.504348 0.864198
117 AMO 0.504348 0.909091
118 WAQ 0.504274 0.8625
119 LAD 0.504274 0.841463
120 DQV 0.504065 0.959459
121 EAD 0.50365 0.924051
122 VO4 ADP 0.5 0.871795
123 ANP MG 0.5 0.883117
124 5AS 0.5 0.744444
125 OMR 0.5 0.833333
126 DLL 0.5 0.933333
127 G3N 0.5 0.857143
128 UPU 0.5 0.853333
129 L3W 0.496063 0.96
130 48N 0.496 0.875
131 XAH 0.495868 0.821429
132 3UK 0.495726 0.921053
133 AWU 0.495575 0.855263
134 SON 0.495327 0.884615
135 44P 0.49505 0.820513
136 CNA 0.492308 0.934211
137 DND 0.492063 0.934211
138 9SN 0.491667 0.875
139 B5V 0.491525 0.909091
140 USQ 0.491379 0.755814
141 V2G 0.491071 0.851852
142 7D4 0.490741 0.835443
143 ITT 0.490741 0.868421
144 P1H 0.489362 0.901235
145 B5Y 0.487603 0.897436
146 B5M 0.487603 0.897436
147 PTJ 0.487395 0.851852
148 ME8 0.487395 0.821429
149 FYA 0.487395 0.883117
150 TXA 0.487395 0.909091
151 NB8 0.487395 0.875
152 UDX 0.486957 0.855263
153 UAD 0.486957 0.855263
154 ALF ADP 0.486726 0.82716
155 LMS 0.485437 0.788235
156 NAJ PZO 0.485075 0.898734
157 GA7 0.483871 0.884615
158 UDM 0.483333 0.833333
159 GAP 0.482143 0.871795
160 4UW 0.480315 0.8875
161 UGA 0.478632 0.866667
162 UGB 0.478632 0.866667
163 PAP 0.477477 0.906667
164 ATR 0.477477 0.893333
165 U2G 0.476923 0.9125
166 2KH 0.476636 0.831169
167 6MZ C U 0.475862 0.9
168 UD2 0.47541 0.844156
169 FA5 0.47541 0.909091
170 UD1 0.47541 0.844156
171 UGF 0.474576 0.822785
172 DAL AMP 0.474138 0.883117
173 0WD 0.473684 0.948052
174 4TA 0.473684 0.878049
175 HFD 0.473214 0.873418
176 JSQ 0.473214 0.873418
177 12V 0.472 0.822785
178 HWU 0.472 0.822785
179 ADP BMA 0.470588 0.896104
180 9ZA 0.470085 0.8625
181 9ZD 0.470085 0.8625
182 2A5 0.468468 0.848101
183 UDP UDP 0.466667 0.826667
184 A2R 0.465517 0.907895
185 YLP 0.460938 0.802326
186 AV2 0.46087 0.846154
187 NAJ PYZ 0.460432 0.855422
188 G 6MZ C U 0.459459 0.911392
189 MYR AMP 0.459016 0.8
190 38V 0.457143 0.865854
191 HP7 0.456 0.855263
192 F2R 0.455224 0.823529
193 Z5A 0.453901 0.847059
194 TYM 0.453846 0.909091
195 7D3 0.453704 0.835443
196 LAQ 0.453125 0.821429
197 MJZ 0.452381 0.881579
198 COD 0.451852 0.795455
199 NAD 0.451852 0.933333
200 NDP 0.451128 0.948052
201 JB6 0.45082 0.8625
202 YLB 0.450382 0.802326
203 UD4 0.448819 0.857143
204 F5P 0.448819 0.857143
205 7MD 0.448819 0.843373
206 AOC 0.448598 0.802632
207 AYB 0.447761 0.793103
208 GP3 0.447368 0.898734
209 EEB 0.44697 0.822785
210 EPU 0.44697 0.822785
211 NA7 0.446281 0.884615
212 A3D 0.445255 0.921053
213 UD7 0.444444 0.844156
214 Y6W 0.444444 0.8125
215 IOT 0.443609 0.793103
216 3AT 0.443478 0.894737
217 DTP 0.443478 0.835443
218 BTX 0.441176 0.823529
219 NPW 0.440298 0.9125
220 ATP A 0.44 0.906667
221 ATP A A A 0.44 0.906667
222 NAQ 0.439716 0.875
223 YLC 0.439394 0.843373
224 EPZ 0.439394 0.833333
225 RAB 0.438776 0.8
226 XYA 0.438776 0.8
227 ADN 0.438776 0.8
228 BT5 0.437956 0.813953
229 DZD 0.437956 0.8875
230 ARG AMP 0.4375 0.790698
231 F5G 0.4375 0.844156
232 NZQ 0.437037 0.935897
233 TXP 0.437037 0.923077
234 8X1 0.436975 0.73913
235 TSB 0.436975 0.802326
236 UDP GAL 0.436975 0.831169
237 A3P 0.436364 0.893333
238 FDA 0.436242 0.880952
239 CSV 0.435484 0.825
240 CSQ 0.435484 0.825
241 UDZ 0.435115 0.783133
242 G5A 0.434783 0.764045
243 TAD 0.434109 0.864198
244 6FA 0.433333 0.86747
245 AMP DBH 0.433071 0.871795
246 D4F 0.432624 0.843373
247 NAE 0.432624 0.897436
248 CTP 0.432432 0.857143
249 HF4 0.432432 0.857143
250 GTP 0.432203 0.873418
251 SSA 0.432203 0.784091
252 AF3 ADP 3PG 0.431818 0.819277
253 P5A 0.430894 0.731183
254 IUG 0.430769 0.788235
255 AHZ 0.430769 0.8
256 5N5 0.43 0.776316
257 NSS 0.429752 0.784091
258 YLA 0.42963 0.823529
259 PRT 0.428571 0.858974
260 54H 0.428571 0.772727
261 VMS 0.428571 0.772727
262 FAS 0.427632 0.878049
263 FAD 0.427632 0.878049
264 SFD 0.427632 0.757895
265 6AD 0.42735 0.841463
266 PPS 0.42735 0.809524
267 ZID 0.426573 0.921053
268 AR6 AR6 0.426357 0.894737
269 ARU 0.42623 0.797619
270 NVA LMS 0.42623 0.73913
271 5CD 0.425743 0.763158
272 A4D 0.425743 0.776316
273 YLY 0.425532 0.793103
274 3DH 0.424528 0.734177
275 A5A 0.423729 0.790698
276 A2P 0.423423 0.88
277 ODP 0.423358 0.935897
278 M2T 0.423077 0.698795
279 FAY 0.423077 0.888889
280 FB0 0.422819 0.788889
281 LEU LMS 0.422764 0.717391
282 O02 0.422414 0.851852
283 AVV 0.421488 0.851852
284 H1Q 0.421053 0.857143
285 ALF ADP 3PG 0.421053 0.819277
286 3AM 0.420561 0.855263
287 NAD TDB 0.41791 0.92
288 7MC 0.41791 0.823529
289 NAD IBO 0.41791 0.92
290 7DT 0.417391 0.906667
291 RGT 0.417323 0.884615
292 FNK 0.416667 0.850575
293 52H 0.416667 0.764045
294 62F 0.416667 0.865854
295 NO7 0.416667 0.884615
296 GCP 0.416667 0.851852
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 53H 0.413223 0.764045
306 5CA 0.413223 0.784091
307 GSP 0.413223 0.831325
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 CUU 0.408696 0.894737
316 URI 0.408163 0.76
317 KAA 0.408 0.73913
318 7C5 0.407692 0.8
319 N0B 0.406897 0.845238
320 TPG 0.406897 0.8
321 DDS 0.40678 0.810127
322 CZF 0.40678 0.907895
323 GDP 0.40678 0.873418
324 LSS 0.406504 0.747253
325 DSZ 0.406504 0.784091
326 LPA AMP 0.406015 0.8
327 MTA 0.40566 0.734177
328 CDP 0.405405 0.857143
329 7XL 0.405172 0.835443
330 QBQ 0.403361 0.860759
331 B1U 0.403101 0.741935
332 NJP 0.402878 0.922078
333 6MZ 0.401786 0.857143
334 91P 0.40146 0.890244
335 UMA 0.401408 0.833333
336 AMP NAD 0.4 0.907895
337 6RE 0.4 0.702381
338 NMN AMP PO4 0.4 0.922078
Similar Ligands (3D)
Ligand no: 1; Ligand: UP5; Similar ligands found: 1
No: Ligand Similarity coefficient
1 UDP ADP BF2 0.9662
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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