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 PHOSPHORYL TRANSFER TRANSITION STATE ANALOG IN UMP/CMP K INASE DICTYOSTELIUM DISCOIDEUM NUCLEOSIDE MONOPHOSPHATE KINASE NMP KINASE PHOSPHORYL TRANSFER TRANSITION STATE ANALOG COMPLEX TRANSFERASE
Ref.: PH INFLUENCES FLUORIDE COORDINATION NUMBER OF THE ALFX 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: 318
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 5FA 0.663265 0.92
10 AQP 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 U A A U 0.609375 0.960526
21 T5A 0.608333 0.91358
22 G3A 0.605263 0.898734
23 APU 0.605042 0.947368
24 UTP 0.602041 0.853333
25 AN2 0.6 0.907895
26 AT4 0.6 0.884615
27 AR6 0.598039 0.92
28 APR 0.598039 0.92
29 ACQ 0.596154 0.896104
30 ANP 0.596154 0.896104
31 6YZ 0.59434 0.896104
32 M33 0.594059 0.907895
33 AD9 0.592233 0.896104
34 A4P 0.591667 0.869048
35 ATF 0.584906 0.884615
36 PRX 0.582524 0.848101
37 GTA 0.581197 0.865854
38 25L 0.575221 0.933333
39 TXE 0.575 0.960526
40 A U C C 0.574627 0.923077
41 A3R 0.572727 0.8625
42 ADQ 0.572727 0.921053
43 UDP 0.571429 0.853333
44 A G U 0.569343 0.888889
45 A22 0.568807 0.933333
46 6V0 0.566667 0.948052
47 NAI 0.566667 0.960526
48 T99 0.566038 0.884615
49 TAT 0.566038 0.884615
50 AP2 0.564356 0.884615
51 A12 0.564356 0.884615
52 ADX 0.563107 0.831325
53 CA0 0.563107 0.921053
54 AMP 0.561224 0.893333
55 A 0.561224 0.893333
56 A1R 0.558559 0.8625
57 50T 0.557692 0.883117
58 AP0 0.557377 0.923077
59 NAX 0.553719 0.924051
60 TXD 0.553719 0.935065
61 APC 0.552381 0.884615
62 A G U U 0.549296 0.888889
63 9X8 0.548673 0.873418
64 PUA 0.546154 0.935897
65 4AD 0.544643 0.897436
66 ABM 0.544554 0.87013
67 BIS 0.53913 0.8625
68 UNP 0.538462 0.831169
69 5SV 0.535714 0.807229
70 OAD 0.535088 0.921053
71 5AL 0.53211 0.907895
72 ADJ 0.531746 0.855422
73 UFM 0.527273 0.855263
74 GDU 0.527273 0.855263
75 UPG 0.527273 0.855263
76 GUD 0.527273 0.855263
77 3OD 0.525862 0.921053
78 SRA 0.524752 0.848101
79 80F 0.523077 0.890244
80 SRP 0.522523 0.884615
81 8QN 0.522124 0.907895
82 25A 0.522124 0.92
83 SFB 0.52 0.797753
84 AU1 0.518868 0.896104
85 RBY 0.518519 0.884615
86 ADV 0.518519 0.884615
87 UDH 0.518182 0.792683
88 PR8 0.517241 0.831325
89 4UV 0.516667 0.922078
90 660 0.513514 0.844156
91 URM 0.513514 0.844156
92 UPF 0.513274 0.8125
93 MAP 0.513274 0.873418
94 U2F 0.513274 0.8125
95 UFG 0.513274 0.8125
96 00A 0.513043 0.886076
97 AHX 0.513043 0.875
98 1ZZ 0.512821 0.821429
99 U 0.510204 0.84
100 U5P 0.510204 0.84
101 OOB 0.508772 0.933333
102 3UC 0.508621 0.8125
103 AFH 0.508197 0.864198
104 4UU 0.508197 0.922078
105 ADP PO3 0.504587 0.893333
106 UPP 0.504505 0.88
107 AMO 0.504348 0.909091
108 PAJ 0.504348 0.864198
109 WAQ 0.504274 0.8625
110 LAD 0.504274 0.841463
111 DQV 0.504065 0.959459
112 EAD 0.50365 0.924051
113 G3N 0.5 0.857143
114 DLL 0.5 0.933333
115 5AS 0.5 0.744444
116 UPU 0.5 0.853333
117 OMR 0.5 0.833333
118 48N 0.496 0.875
119 XAH 0.495868 0.821429
120 3UK 0.495726 0.921053
121 SON 0.495327 0.884615
122 44P 0.49505 0.820513
123 CNA 0.492308 0.934211
124 NXX 0.492063 0.934211
125 DND 0.492063 0.934211
126 9SN 0.491667 0.875
127 B5V 0.491525 0.909091
128 USQ 0.491379 0.755814
129 7D4 0.490741 0.835443
130 ITT 0.490741 0.868421
131 P1H 0.489362 0.901235
132 B5Y 0.487603 0.897436
133 B5M 0.487603 0.897436
134 FYA 0.487395 0.883117
135 ME8 0.487395 0.821429
136 PTJ 0.487395 0.851852
137 TXA 0.487395 0.909091
138 NB8 0.487395 0.875
139 UAD 0.486957 0.855263
140 UDX 0.486957 0.855263
141 ALF ADP 0.486726 0.82716
142 ADP ALF 0.486726 0.82716
143 LMS 0.485437 0.788235
144 NAJ PZO 0.485075 0.898734
145 GA7 0.483871 0.884615
146 UDM 0.483333 0.833333
147 ADP VO4 0.482456 0.883117
148 VO4 ADP 0.482456 0.883117
149 GAP 0.482143 0.871795
150 4UW 0.480315 0.8875
151 UGA 0.478632 0.866667
152 UGB 0.478632 0.866667
153 PAP 0.477477 0.906667
154 ATR 0.477477 0.893333
155 U2G 0.476923 0.9125
156 2KH 0.476636 0.831169
157 YAP 0.47541 0.897436
158 UD2 0.47541 0.844156
159 UD1 0.47541 0.844156
160 FA5 0.47541 0.909091
161 DAL AMP 0.474138 0.883117
162 A C A C 0.474074 0.923077
163 4TA 0.473684 0.878049
164 0WD 0.473684 0.948052
165 G U 0.473282 0.876543
166 HFD 0.473214 0.873418
167 HWU 0.472 0.822785
168 12V 0.472 0.822785
169 ADP BMA 0.470588 0.896104
170 9ZD 0.470085 0.8625
171 9ZA 0.470085 0.8625
172 2A5 0.468468 0.848101
173 UDP UDP 0.466667 0.826667
174 A2R 0.465517 0.907895
175 U A C C 0.463235 0.935065
176 YLP 0.460938 0.802326
177 AV2 0.46087 0.846154
178 NAJ PYZ 0.460432 0.855422
179 MYR AMP 0.459016 0.8
180 HP7 0.456 0.855263
181 F2R 0.455224 0.823529
182 A A 0.454545 0.894737
183 Z5A 0.453901 0.847059
184 TYM 0.453846 0.909091
185 7D3 0.453704 0.835443
186 LAQ 0.453125 0.821429
187 MJZ 0.452381 0.881579
188 COD 0.451852 0.795455
189 NAD 0.451852 0.933333
190 NDP 0.451128 0.948052
191 JB6 0.45082 0.8625
192 YLB 0.450382 0.802326
193 UD4 0.448819 0.857143
194 F5P 0.448819 0.857143
195 7MD 0.448819 0.843373
196 AOC 0.448598 0.802632
197 AYB 0.447761 0.793103
198 GP3 0.447368 0.898734
199 EEB 0.44697 0.822785
200 EPU 0.44697 0.822785
201 NA7 0.446281 0.884615
202 A3D 0.445255 0.921053
203 TYR AMP 0.444444 0.873418
204 UD7 0.444444 0.844156
205 Y6W 0.444444 0.8125
206 IOT 0.443609 0.793103
207 3AT 0.443478 0.894737
208 DTP 0.443478 0.835443
209 BTX 0.441176 0.823529
210 NPW 0.440298 0.9125
211 ATP A A A 0.44 0.906667
212 NAQ 0.439716 0.875
213 EPZ 0.439394 0.833333
214 YLC 0.439394 0.843373
215 RAB 0.438776 0.8
216 XYA 0.438776 0.8
217 ADN 0.438776 0.8
218 DZD 0.437956 0.8875
219 BT5 0.437956 0.813953
220 ARG AMP 0.4375 0.790698
221 F5G 0.4375 0.844156
222 NZQ 0.437037 0.935897
223 TXP 0.437037 0.923077
224 TSB 0.436975 0.802326
225 8X1 0.436975 0.73913
226 A3P 0.436364 0.893333
227 FDA 0.436242 0.880952
228 CSQ 0.435484 0.825
229 CSV 0.435484 0.825
230 UDZ 0.435115 0.783133
231 G5A 0.434783 0.764045
232 TAD 0.434109 0.864198
233 6FA 0.433333 0.86747
234 AMP DBH 0.433071 0.871795
235 NAE 0.432624 0.897436
236 CTP 0.432432 0.857143
237 HF4 0.432432 0.857143
238 SSA 0.432203 0.784091
239 GTP 0.432203 0.873418
240 AF3 ADP 3PG 0.431818 0.819277
241 P5A 0.430894 0.731183
242 IUG 0.430769 0.788235
243 AHZ 0.430769 0.8
244 G A A A 0.430657 0.851852
245 5N5 0.43 0.776316
246 NSS 0.429752 0.784091
247 YLA 0.42963 0.823529
248 PRT 0.428571 0.858974
249 54H 0.428571 0.772727
250 VMS 0.428571 0.772727
251 FAD 0.427632 0.878049
252 FAS 0.427632 0.878049
253 SFD 0.427632 0.757895
254 PPS 0.42735 0.809524
255 6AD 0.42735 0.841463
256 ZID 0.426573 0.921053
257 AR6 AR6 0.426357 0.894737
258 NVA LMS 0.42623 0.73913
259 ARU 0.42623 0.797619
260 A4D 0.425743 0.776316
261 5CD 0.425743 0.763158
262 YLY 0.425532 0.793103
263 3DH 0.424528 0.734177
264 A5A 0.423729 0.790698
265 A2P 0.423423 0.88
266 ODP 0.423358 0.935897
267 M2T 0.423077 0.698795
268 FAY 0.423077 0.888889
269 FB0 0.422819 0.788889
270 LEU LMS 0.422764 0.73913
271 AVV 0.421488 0.851852
272 3AM 0.420561 0.855263
273 A G 0.42029 0.8625
274 7MC 0.41791 0.823529
275 7DT 0.417391 0.906667
276 RGT 0.417323 0.884615
277 U A G G 0.417266 0.8625
278 FNK 0.416667 0.850575
279 62F 0.416667 0.865854
280 GCP 0.416667 0.851852
281 52H 0.416667 0.764045
282 9K8 0.416 0.72043
283 M24 0.415493 0.853659
284 7D5 0.415094 0.810127
285 S4M 0.414414 0.637363
286 DG1 0.413793 0.948052
287 1DG 0.413793 0.948052
288 EP4 0.413462 0.716049
289 NDC 0.413333 0.875
290 GSP 0.413223 0.831325
291 5CA 0.413223 0.784091
292 53H 0.413223 0.764045
293 H6Y 0.411765 0.921053
294 RFL 0.411392 0.847059
295 MAO 0.410714 0.724138
296 DTA 0.409524 0.769231
297 NDE 0.409396 0.909091
298 DAT 0.408696 0.835443
299 URI 0.408163 0.76
300 KAA 0.408 0.73913
301 7C5 0.407692 0.8
302 TPG 0.406897 0.8
303 N0B 0.406897 0.845238
304 DDS 0.40678 0.810127
305 GDP 0.40678 0.873418
306 DSZ 0.406504 0.784091
307 LSS 0.406504 0.747253
308 LPA AMP 0.406015 0.8
309 MTA 0.40566 0.734177
310 CDP 0.405405 0.857143
311 7XL 0.405172 0.835443
312 U U 0.404959 0.842105
313 NJP 0.402878 0.922078
314 91P 0.40146 0.890244
315 UMA 0.401408 0.833333
316 NMN AMP PO4 0.4 0.922078
317 AMP NAD 0.4 0.907895
318 6RE 0.4 0.702381
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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