Receptor
PDB id Resolution Class Description Source Keywords
5LLB 1.92 Å EC: 2.7.4.1 STRUCTURE OF POLYPHOSPHATE KINASE 2 FROM FRANCISELLA TULAREN AMPPCH2PPP AND POLYPHOSPHATE FRANCISELLA TULARENSIS SUBSP. TULARENS(STRAIN SCHU S4 / SCHU 4) COMPLEX WITH NON-HYDROLYSABLE ATP ANALOGUE. POLYPHOSPHATE MENUCLEOTIDE METABOLISM TRANSFERASE
Ref.: SUBSTRATE RECOGNITION AND MECHANISM REVEALED BY LIG POLYPHOSPHATE KINASE 2 STRUCTURES. PROC. NATL. ACAD. SCI. V. 115 3350 2018 U.S.A.
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG B:302;
C:302;
D:302;
A:302;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
CL D:301;
B:301;
C:301;
A:301;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
35.453 Cl [Cl-]
6YZ D:303;
B:303;
A:303;
C:303;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
665.168 C11 H20 N5 O18 P5 c1nc(...
6YW D:304;
A:304;
C:304;
B:304;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
497.895 H8 O19 P6 OP(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5LLB 1.92 Å EC: 2.7.4.1 STRUCTURE OF POLYPHOSPHATE KINASE 2 FROM FRANCISELLA TULAREN AMPPCH2PPP AND POLYPHOSPHATE FRANCISELLA TULARENSIS SUBSP. TULARENS(STRAIN SCHU S4 / SCHU 4) COMPLEX WITH NON-HYDROLYSABLE ATP ANALOGUE. POLYPHOSPHATE MENUCLEOTIDE METABOLISM TRANSFERASE
Ref.: SUBSTRATE RECOGNITION AND MECHANISM REVEALED BY LIG POLYPHOSPHATE KINASE 2 STRUCTURES. PROC. NATL. ACAD. SCI. V. 115 3350 2018 U.S.A.
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5LLB - 6YZ C11 H20 N5 O18 P5 c1nc(c2c(n....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5LLB - 6YZ C11 H20 N5 O18 P5 c1nc(c2c(n....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5LLB - 6YZ C11 H20 N5 O18 P5 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 6YZ; Similar ligands found: 361
No: Ligand ECFP6 Tc MDL keys Tc
1 6YZ 1 1
2 ACQ 0.909091 1
3 HEJ 0.833333 0.972222
4 ATP 0.833333 0.972222
5 ACP 0.833333 1
6 5FA 0.822785 0.972222
7 AQP 0.822785 0.972222
8 ADP 0.818182 0.972222
9 B4P 0.794872 0.945205
10 AP5 0.794872 0.945205
11 BA3 0.782051 0.945205
12 A2D 0.779221 0.945205
13 APC 0.756098 0.986301
14 AT4 0.740741 0.933333
15 AN2 0.740741 0.958904
16 M33 0.731707 0.932432
17 T99 0.729412 0.933333
18 TAT 0.729412 0.933333
19 AGS 0.72619 0.921053
20 SAP 0.72619 0.921053
21 A 0.717949 0.944444
22 AMP 0.717949 0.944444
23 AR6 0.714286 0.945205
24 APR 0.714286 0.945205
25 ANP 0.709302 0.945946
26 AD9 0.705882 0.945946
27 AP2 0.695122 0.986301
28 A12 0.695122 0.986301
29 25L 0.691489 0.958904
30 ADX 0.690476 0.851852
31 CA0 0.690476 0.92
32 KG4 0.682353 0.92
33 50T 0.682353 0.932432
34 HQG 0.677778 0.958904
35 PRX 0.674419 0.87013
36 ATF 0.674157 0.933333
37 45A 0.670732 0.893333
38 ABM 0.670732 0.893333
39 A22 0.67033 0.958904
40 ADV 0.666667 0.959459
41 RBY 0.666667 0.959459
42 4TC 0.660194 0.922078
43 ADP MG 0.658824 0.917808
44 ADQ 0.655914 0.92
45 APC MG 0.647727 0.918919
46 SRA 0.646341 0.894737
47 8LE 0.644444 0.871795
48 5AL 0.644444 0.906667
49 A3R 0.638298 0.909091
50 A1R 0.638298 0.909091
51 7D4 0.632184 0.881579
52 AU1 0.632184 0.945946
53 8LH 0.630435 0.883117
54 SRP 0.630435 0.907895
55 ATP MG 0.629214 0.917808
56 ADP PO3 0.629214 0.917808
57 25A 0.62766 0.945205
58 OZV 0.62766 0.945205
59 OAD 0.625 0.92
60 9X8 0.625 0.896104
61 4AD 0.621053 0.921053
62 2A5 0.617977 0.92
63 G5P 0.617647 0.897436
64 8LQ 0.617021 0.907895
65 00A 0.614583 0.860759
66 ITT 0.613636 0.917808
67 BIS 0.612245 0.909091
68 3OD 0.612245 0.92
69 5SV 0.610526 0.82716
70 8QN 0.610526 0.906667
71 OOB 0.610526 0.906667
72 G3A 0.607843 0.897436
73 7D3 0.604651 0.881579
74 HFD 0.604396 0.921053
75 JSQ 0.604396 0.921053
76 PAJ 0.604167 0.8625
77 AMO 0.604167 0.933333
78 MAP 0.6 0.921053
79 DLL 0.597938 0.906667
80 AHX 0.597938 0.897436
81 GTA 0.596154 0.864198
82 PTJ 0.59596 0.873418
83 UP5 0.59434 0.896104
84 PAP 0.593407 0.958333
85 ATR 0.593407 0.944444
86 3UK 0.591837 0.894737
87 AFH 0.586538 0.886076
88 WAQ 0.585859 0.884615
89 B5V 0.585859 0.883117
90 LAD 0.585859 0.8625
91 PR8 0.585859 0.851852
92 ALF ADP 0.585106 0.848101
93 ADP ALF 0.585106 0.848101
94 SON 0.58427 0.933333
95 GAP 0.580645 0.87013
96 NB8 0.58 0.897436
97 TXA 0.58 0.907895
98 FYA 0.58 0.906667
99 1ZZ 0.58 0.819277
100 ME8 0.58 0.841463
101 TXD 0.579439 0.884615
102 ADP VO4 0.578947 0.906667
103 VO4 ADP 0.578947 0.906667
104 A4P 0.577982 0.823529
105 LMS 0.576471 0.807229
106 9SN 0.568627 0.85
107 DQV 0.566038 0.932432
108 NAX 0.564815 0.875
109 ADN 0.564103 0.821918
110 RAB 0.564103 0.821918
111 XYA 0.564103 0.821918
112 FA5 0.563107 0.907895
113 B5M 0.563107 0.871795
114 B5Y 0.563107 0.871795
115 YAP 0.563107 0.896104
116 9ZA 0.561224 0.884615
117 9ZD 0.561224 0.884615
118 ADP BMA 0.56 0.894737
119 XAH 0.557692 0.841463
120 GA7 0.556604 0.907895
121 48N 0.555556 0.897436
122 AP0 0.554545 0.873418
123 T5A 0.553571 0.843373
124 4UV 0.552381 0.871795
125 DAL AMP 0.55102 0.881579
126 NXX 0.550459 0.907895
127 DND 0.550459 0.907895
128 6V0 0.550459 0.873418
129 NAI 0.550459 0.884615
130 3AT 0.547368 0.972222
131 LAQ 0.546296 0.819277
132 OMR 0.545455 0.831325
133 TXE 0.545455 0.884615
134 AOC 0.545455 0.8
135 4UU 0.542056 0.871795
136 6AD 0.541667 0.886076
137 7D5 0.541176 0.855263
138 A2R 0.540816 0.958904
139 139 0.539823 0.851852
140 5AS 0.538462 0.761364
141 TAD 0.537037 0.910256
142 4UW 0.536364 0.839506
143 CNA 0.535088 0.907895
144 ATP A 0.533333 0.905405
145 ATP A A A 0.533333 0.905405
146 DTP 0.53125 0.906667
147 5N5 0.530864 0.797297
148 80F 0.529915 0.843373
149 A3P 0.527473 0.944444
150 YLP 0.527273 0.821429
151 UPA 0.526786 0.884615
152 ADJ 0.526316 0.831325
153 NO7 0.525253 0.907895
154 A4D 0.52439 0.797297
155 5CD 0.52439 0.783784
156 A A 0.524272 0.918919
157 DZD 0.521368 0.910256
158 AV2 0.520408 0.893333
159 JB6 0.519231 0.884615
160 TYM 0.517857 0.907895
161 M2T 0.517647 0.716049
162 IOT 0.517544 0.833333
163 F2R 0.517241 0.865854
164 A3D 0.516949 0.894737
165 7DT 0.515789 0.958333
166 MYR AMP 0.514286 0.797619
167 7MD 0.513761 0.864198
168 AR6 AR6 0.513761 0.893333
169 YLC 0.513274 0.841463
170 YLB 0.513274 0.821429
171 COD 0.512821 0.813953
172 NAD 0.512821 0.906667
173 3AM 0.511364 0.90411
174 A2P 0.51087 0.930556
175 PPS 0.510204 0.851852
176 EP4 0.505882 0.734177
177 H1Q 0.505263 0.88
178 DAT 0.505263 0.906667
179 G5A 0.505155 0.781609
180 AHZ 0.504505 0.797619
181 YLA 0.5 0.821429
182 SSA 0.5 0.802326
183 3DH 0.5 0.753247
184 7DD 0.5 0.958333
185 DTA 0.5 0.766234
186 NA7 0.5 0.959459
187 DDS 0.5 0.855263
188 AYB 0.495726 0.811765
189 TYR AMP 0.495413 0.871795
190 AMP DBH 0.495413 0.87013
191 MTA 0.494253 0.753247
192 RGT 0.490741 0.933333
193 TSB 0.490196 0.8
194 A5A 0.49 0.788235
195 IMO 0.48913 0.90411
196 NAE 0.487805 0.871795
197 BTX 0.487395 0.843373
198 7MC 0.486957 0.843373
199 LPA AMP 0.486726 0.797619
200 ARG AMP 0.486486 0.831325
201 AVV 0.485437 0.897436
202 V3L 0.484848 0.945205
203 EAD 0.484127 0.851852
204 S4M 0.483871 0.670455
205 6MZ 0.483871 0.905405
206 NAQ 0.483871 0.85
207 6RE 0.483516 0.7625
208 BT5 0.483333 0.833333
209 2AM 0.483146 0.917808
210 128 0.482456 0.758621
211 54H 0.480392 0.770115
212 VMS 0.480392 0.770115
213 52H 0.480392 0.761364
214 GCP 0.480392 0.922078
215 ZID 0.48 0.894737
216 M24 0.479675 0.829268
217 MAO 0.478723 0.761905
218 AF3 ADP 3PG 0.478261 0.839506
219 ARU 0.47619 0.839506
220 8X1 0.475728 0.755556
221 5CA 0.475728 0.802326
222 53H 0.475728 0.761364
223 HDV 0.475248 0.87013
224 5X8 0.474227 0.766234
225 J7C 0.473118 0.772152
226 A3N 0.473118 0.766234
227 ZAS 0.472527 0.746835
228 GTP 0.470588 0.896104
229 P1H 0.469231 0.831325
230 NDE 0.469231 0.907895
231 N0B 0.468254 0.821429
232 YLY 0.467742 0.811765
233 OVE 0.467391 0.881579
234 P5A 0.46729 0.747253
235 LSS 0.466667 0.764045
236 NSS 0.466667 0.802326
237 DSZ 0.466667 0.802326
238 9K8 0.462963 0.698925
239 G A A A 0.46281 0.85
240 AMP NAD 0.46281 0.881579
241 A3G 0.462366 0.802632
242 DSH 0.462366 0.728395
243 NVA LMS 0.462264 0.755556
244 FB0 0.462121 0.827586
245 6C6 0.46 0.883117
246 TXP 0.458333 0.897436
247 LEU LMS 0.457944 0.755556
248 GDP 0.455446 0.896104
249 FDA 0.455224 0.835294
250 NJP 0.454545 0.921053
251 GSU 0.453704 0.781609
252 J4G 0.453704 0.921053
253 KAA 0.453704 0.755556
254 GJV 0.452632 0.753086
255 12D 0.452174 0.767442
256 6FA 0.451852 0.843373
257 NAJ PZO 0.451613 0.82716
258 NDC 0.451128 0.85
259 4TA 0.45082 0.809524
260 0WD 0.45082 0.897436
261 SA8 0.45 0.710843
262 NPW 0.45 0.8875
263 MHZ 0.44898 0.701149
264 NAJ PYZ 0.448819 0.788235
265 N6P 0.448598 0.890411
266 71V 0.447917 0.884615
267 2SA 0.446602 0.933333
268 YSA 0.446429 0.781609
269 LQJ 0.446429 0.893333
270 NZQ 0.446281 0.910256
271 5AD 0.445783 0.726027
272 FAD 0.445255 0.853659
273 FAS 0.445255 0.853659
274 PO4 PO4 A A A A PO4 0.444444 0.878378
275 SFG 0.444444 0.753247
276 ODP 0.442623 0.886076
277 SMM 0.442308 0.689655
278 J7V 0.44186 0.813953
279 SAM 0.441176 0.694118
280 6IA 0.441176 0.839506
281 7D7 0.440476 0.723684
282 A G 0.439024 0.860759
283 A7D 0.438776 0.779221
284 A3S 0.438776 0.813333
285 7C5 0.438596 0.797468
286 NDP 0.438017 0.897436
287 8PZ 0.4375 0.802326
288 AAT 0.436893 0.710843
289 RFL 0.43662 0.823529
290 A5D 0.435644 0.766234
291 U A G G 0.435484 0.860759
292 SFD 0.434783 0.736842
293 PGS 0.434343 0.860759
294 GGZ 0.433962 0.804878
295 G2P 0.433962 0.910256
296 B1U 0.433628 0.72043
297 MGP 0.432692 0.8625
298 62F 0.432624 0.864198
299 FNK 0.432624 0.806818
300 DA 0.431579 0.88
301 D5M 0.431579 0.88
302 NEC 0.431579 0.727273
303 GP3 0.431373 0.897436
304 SAI 0.431373 0.7375
305 SAH 0.431373 0.746835
306 A3T 0.43 0.8
307 6K6 0.429907 0.905405
308 FAY 0.429577 0.864198
309 S7M 0.428571 0.694118
310 U A 0.428571 0.884615
311 6G0 0.428571 0.8625
312 XNP 0.427419 0.851852
313 AAM 0.427083 0.944444
314 Y3J 0.425287 0.706667
315 AMZ 0.423913 0.891892
316 C2R 0.423913 0.88
317 KOY 0.423729 0.782051
318 EEM 0.423077 0.694118
319 A U 0.421488 0.848101
320 Z5A 0.419847 0.761364
321 4YB 0.418803 0.764045
322 A A A 0.418182 0.906667
323 NA0 0.416667 0.907895
324 WSA 0.416667 0.790698
325 GEK 0.416667 0.740741
326 N5O 0.416667 0.766234
327 AIR 0.41573 0.876712
328 NIA 0.414894 0.802469
329 ETB 0.414062 0.835294
330 DCA 0.414062 0.825581
331 GAV 0.412844 0.8625
332 NAP 0.412214 0.92
333 PUA 0.410853 0.8625
334 APU 0.409836 0.871795
335 GNH 0.409524 0.884615
336 62X 0.409091 0.670455
337 TAP 0.409091 0.884615
338 N5A 0.408163 0.74026
339 9BG 0.408 0.873418
340 ZDA 0.407767 0.842105
341 IDP 0.407767 0.894737
342 COA 0.407692 0.825581
343 0T1 0.407692 0.825581
344 GSP 0.407407 0.851852
345 GNP 0.407407 0.873418
346 9GM 0.407407 0.873418
347 TM1 0.40708 0.755814
348 101 0.40625 0.855263
349 A6D 0.405405 0.705882
350 9JJ 0.405405 0.841463
351 K15 0.405405 0.686047
352 V1N 0.405172 0.893333
353 649 0.404959 0.747253
354 F2N 0.403974 0.816092
355 FCX 0.402985 0.797753
356 7RP 0.402062 0.902778
357 MGO 0.401869 0.839506
358 8Q2 0.401639 0.775281
359 FA9 0.401316 0.865854
360 0UM 0.4 0.702381
361 P5F 0.4 0.825581
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5LLB; Ligand: 6YZ; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5llb.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5LLB; Ligand: 6YZ; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5llb.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5LLB; Ligand: 6YZ; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5llb.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5LLB; Ligand: 6YZ; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5llb.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
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