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 (2D)
Ligand no: 1; Ligand: 6YZ; Similar ligands found: 384
No: Ligand ECFP6 Tc MDL keys Tc
1 6YZ 1 1
2 ACQ 0.909091 1
3 ACP 0.833333 1
4 ATP 0.833333 0.972222
5 HEJ 0.833333 0.972222
6 5FA 0.822785 0.972222
7 AQP 0.822785 0.972222
8 ADP 0.818182 0.972222
9 AP5 0.794872 0.945205
10 B4P 0.794872 0.945205
11 BA3 0.782051 0.945205
12 A2D 0.779221 0.945205
13 APC 0.756098 0.986301
14 AN2 0.740741 0.958904
15 AT4 0.740741 0.933333
16 M33 0.731707 0.932432
17 TAT 0.729412 0.933333
18 T99 0.729412 0.933333
19 AGS 0.72619 0.921053
20 AMP 0.717949 0.944444
21 A 0.717949 0.944444
22 APR 0.714286 0.945205
23 AR6 0.714286 0.945205
24 ANP 0.709302 0.945946
25 AD9 0.705882 0.945946
26 A12 0.695122 0.986301
27 AP2 0.695122 0.986301
28 25L 0.691489 0.958904
29 CA0 0.690476 0.92
30 ADX 0.690476 0.851852
31 50T 0.682353 0.932432
32 KG4 0.682353 0.92
33 HQG 0.677778 0.958904
34 PRX 0.674419 0.87013
35 ATF 0.674157 0.933333
36 ABM 0.670732 0.893333
37 45A 0.670732 0.893333
38 A22 0.67033 0.958904
39 AMP MG 0.666667 0.90411
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 ADP BEF 0.658824 0.917808
45 ADQ 0.655914 0.92
46 APC MG 0.647727 0.918919
47 SRA 0.646341 0.894737
48 5AL 0.644444 0.906667
49 8LE 0.644444 0.871795
50 A1R 0.638298 0.909091
51 A3R 0.638298 0.909091
52 7D4 0.632184 0.881579
53 AU1 0.632184 0.945946
54 JNT 0.631579 0.945946
55 8LH 0.630435 0.883117
56 SRP 0.630435 0.907895
57 ATP MG 0.629214 0.917808
58 ADP PO3 0.629214 0.917808
59 25A 0.62766 0.945205
60 OZV 0.62766 0.945205
61 OAD 0.625 0.92
62 9X8 0.625 0.896104
63 4AD 0.621053 0.921053
64 2A5 0.617977 0.92
65 G5P 0.617647 0.897436
66 QA7 0.617021 0.871795
67 8LQ 0.617021 0.907895
68 00A 0.614583 0.860759
69 ITT 0.613636 0.917808
70 3OD 0.612245 0.92
71 BIS 0.612245 0.909091
72 5SV 0.610526 0.82716
73 OOB 0.610526 0.906667
74 8QN 0.610526 0.906667
75 G3A 0.607843 0.897436
76 7D3 0.604651 0.881579
77 BEF ADP 0.604396 0.893333
78 HFD 0.604396 0.921053
79 JSQ 0.604396 0.921053
80 PAJ 0.604167 0.8625
81 AMO 0.604167 0.933333
82 MAP 0.6 0.921053
83 AHX 0.597938 0.897436
84 DLL 0.597938 0.906667
85 GTA 0.596154 0.864198
86 PTJ 0.59596 0.873418
87 UP5 0.59434 0.896104
88 KMQ 0.594059 0.907895
89 PAP 0.593407 0.958333
90 ATR 0.593407 0.944444
91 3UK 0.591837 0.894737
92 V2G 0.591398 0.897436
93 AFH 0.586538 0.886076
94 B5V 0.585859 0.883117
95 PR8 0.585859 0.851852
96 WAQ 0.585859 0.884615
97 LAD 0.585859 0.8625
98 ALF ADP 0.585106 0.848101
99 VO4 ADP 0.585106 0.92
100 ANP MG 0.585106 0.906667
101 SON 0.58427 0.933333
102 GAP 0.580645 0.87013
103 ME8 0.58 0.841463
104 FYA 0.58 0.906667
105 TXA 0.58 0.907895
106 NB8 0.58 0.897436
107 1ZZ 0.58 0.819277
108 TXD 0.579439 0.884615
109 A4P 0.577982 0.823529
110 LMS 0.576471 0.807229
111 9SN 0.568627 0.85
112 DQV 0.566038 0.932432
113 NAX 0.564815 0.875
114 RAB 0.564103 0.821918
115 XYA 0.564103 0.821918
116 ADN 0.564103 0.821918
117 FA5 0.563107 0.907895
118 B5M 0.563107 0.871795
119 B5Y 0.563107 0.871795
120 9ZA 0.561224 0.884615
121 9ZD 0.561224 0.884615
122 ADP BMA 0.56 0.894737
123 XAH 0.557692 0.841463
124 GA7 0.556604 0.907895
125 48N 0.555556 0.897436
126 AP0 0.554545 0.873418
127 T5A 0.553571 0.843373
128 4UV 0.552381 0.871795
129 DAL AMP 0.55102 0.881579
130 DND 0.550459 0.907895
131 6V0 0.550459 0.873418
132 NAI 0.550459 0.884615
133 3AT 0.547368 0.972222
134 LAQ 0.546296 0.819277
135 OMR 0.545455 0.831325
136 AOC 0.545455 0.8
137 TXE 0.545455 0.884615
138 4UU 0.542056 0.871795
139 6AD 0.541667 0.886076
140 38V 0.541667 0.911392
141 7D5 0.541176 0.855263
142 A2R 0.540816 0.958904
143 L3W 0.540541 0.907895
144 139 0.539823 0.851852
145 5AS 0.538462 0.761364
146 TAD 0.537037 0.910256
147 4UW 0.536364 0.839506
148 CNA 0.535088 0.907895
149 ATP A 0.533333 0.905405
150 ATP A A A 0.533333 0.905405
151 DTP 0.53125 0.906667
152 5N5 0.530864 0.797297
153 80F 0.529915 0.843373
154 A3P 0.527473 0.944444
155 YLP 0.527273 0.821429
156 UPA 0.526786 0.884615
157 ADJ 0.526316 0.831325
158 NO7 0.525253 0.907895
159 5CD 0.52439 0.783784
160 A4D 0.52439 0.797297
161 DZD 0.521368 0.910256
162 CUU 0.521277 0.972222
163 AV2 0.520408 0.893333
164 JB6 0.519231 0.884615
165 TYM 0.517857 0.907895
166 M2T 0.517647 0.716049
167 IOT 0.517544 0.833333
168 F2R 0.517241 0.865854
169 A3D 0.516949 0.894737
170 7DT 0.515789 0.958333
171 MYR AMP 0.514286 0.797619
172 7MD 0.513761 0.864198
173 AR6 AR6 0.513761 0.893333
174 YLC 0.513274 0.841463
175 YLB 0.513274 0.821429
176 NAD 0.512821 0.906667
177 COD 0.512821 0.813953
178 3AM 0.511364 0.90411
179 A2P 0.51087 0.930556
180 PPS 0.510204 0.851852
181 EP4 0.505882 0.734177
182 DAT 0.505263 0.906667
183 H1Q 0.505263 0.88
184 G5A 0.505155 0.781609
185 AHZ 0.504505 0.797619
186 3DH 0.5 0.753247
187 7DD 0.5 0.958333
188 DDS 0.5 0.855263
189 SSA 0.5 0.802326
190 YLA 0.5 0.821429
191 DTA 0.5 0.766234
192 NA7 0.5 0.959459
193 AYB 0.495726 0.811765
194 AMP DBH 0.495413 0.87013
195 MTA 0.494253 0.753247
196 RGT 0.490741 0.933333
197 TSB 0.490196 0.8
198 A5A 0.49 0.788235
199 O02 0.489796 0.947368
200 IMO 0.48913 0.90411
201 NAE 0.487805 0.871795
202 BTX 0.487395 0.843373
203 7MC 0.486957 0.843373
204 LPA AMP 0.486726 0.797619
205 ARG AMP 0.486486 0.831325
206 AVV 0.485437 0.897436
207 V3L 0.484848 0.945205
208 EAD 0.484127 0.851852
209 NAQ 0.483871 0.85
210 6MZ 0.483871 0.905405
211 S4M 0.483871 0.670455
212 6RE 0.483516 0.7625
213 BT5 0.483333 0.833333
214 2AM 0.483146 0.917808
215 128 0.482456 0.758621
216 54H 0.480392 0.770115
217 52H 0.480392 0.761364
218 VMS 0.480392 0.770115
219 GCP 0.480392 0.922078
220 ZID 0.48 0.894737
221 M24 0.479675 0.829268
222 MAO 0.478723 0.761905
223 ALF ADP 3PG 0.478261 0.839506
224 AF3 ADP 3PG 0.478261 0.839506
225 ARU 0.47619 0.839506
226 8X1 0.475728 0.755556
227 53H 0.475728 0.761364
228 5CA 0.475728 0.802326
229 HDV 0.475248 0.87013
230 5X8 0.474227 0.766234
231 NAD TDB 0.474138 0.893333
232 NAD IBO 0.474138 0.893333
233 A3N 0.473118 0.766234
234 J7C 0.473118 0.772152
235 ZAS 0.472527 0.746835
236 GTP 0.470588 0.896104
237 P1H 0.469231 0.831325
238 NDE 0.469231 0.907895
239 N0B 0.468254 0.821429
240 YLY 0.467742 0.811765
241 OVE 0.467391 0.881579
242 P5A 0.46729 0.747253
243 DSZ 0.466667 0.802326
244 LSS 0.466667 0.764045
245 NSS 0.466667 0.802326
246 D4F 0.464 0.819277
247 9K8 0.462963 0.698925
248 AMP NAD 0.46281 0.881579
249 A3G 0.462366 0.802632
250 DSH 0.462366 0.728395
251 NVA LMS 0.462264 0.755556
252 FB0 0.462121 0.827586
253 6C6 0.46 0.883117
254 TXP 0.458333 0.897436
255 LEU LMS 0.457944 0.733333
256 GDP 0.455446 0.896104
257 FDA 0.455224 0.835294
258 NJP 0.454545 0.921053
259 GSU 0.453704 0.781609
260 J4G 0.453704 0.921053
261 KAA 0.453704 0.755556
262 NWW 0.453488 0.739726
263 GJV 0.452632 0.753086
264 12D 0.452174 0.767442
265 6FA 0.451852 0.843373
266 NAJ PZO 0.451613 0.82716
267 NDC 0.451128 0.85
268 QBQ 0.45098 0.883117
269 4TA 0.45082 0.809524
270 0WD 0.45082 0.897436
271 K3K 0.45045 0.782051
272 NPW 0.45 0.8875
273 SA8 0.45 0.710843
274 MHZ 0.44898 0.701149
275 NAJ PYZ 0.448819 0.788235
276 N6P 0.448598 0.890411
277 71V 0.447917 0.884615
278 2SA 0.446602 0.933333
279 YSA 0.446429 0.781609
280 LQJ 0.446429 0.893333
281 NZQ 0.446281 0.910256
282 5AD 0.445783 0.726027
283 FAD 0.445255 0.853659
284 FAS 0.445255 0.853659
285 SFG 0.444444 0.753247
286 PO4 PO4 A A A A PO4 0.444444 0.878378
287 ODP 0.442623 0.886076
288 SMM 0.442308 0.689655
289 J7V 0.44186 0.813953
290 6IA 0.441176 0.839506
291 CZF 0.441176 0.906667
292 SAM 0.441176 0.694118
293 7D7 0.440476 0.723684
294 A3S 0.438776 0.813333
295 A7D 0.438776 0.779221
296 7C5 0.438596 0.797468
297 NDP 0.438017 0.897436
298 8PZ 0.4375 0.802326
299 AAT 0.436893 0.710843
300 RFL 0.43662 0.823529
301 A5D 0.435644 0.766234
302 SFD 0.434783 0.736842
303 PGS 0.434343 0.860759
304 GGZ 0.433962 0.804878
305 G2P 0.433962 0.910256
306 B1U 0.433628 0.72043
307 MGP 0.432692 0.8625
308 FNK 0.432624 0.806818
309 62F 0.432624 0.864198
310 DA 0.431579 0.88
311 D5M 0.431579 0.88
312 NEC 0.431579 0.727273
313 SAI 0.431373 0.7375
314 SAH 0.431373 0.746835
315 GP3 0.431373 0.897436
316 A3T 0.43 0.8
317 6K6 0.429907 0.905405
318 K3E 0.429825 0.772152
319 FAY 0.429577 0.864198
320 6G0 0.428571 0.8625
321 S7M 0.428571 0.694118
322 XNP 0.427419 0.851852
323 AAM 0.427083 0.944444
324 Y3J 0.425287 0.706667
325 AMZ 0.423913 0.891892
326 C2R 0.423913 0.88
327 KOY 0.423729 0.782051
328 O05 0.423423 0.86747
329 K2R 0.423423 0.881579
330 EEM 0.423077 0.694118
331 K2H 0.422018 0.7375
332 K3H 0.421053 0.731707
333 Z5A 0.419847 0.761364
334 NWQ 0.419355 0.72
335 4YB 0.418803 0.764045
336 PLP AAD 0.417323 0.717391
337 GEK 0.416667 0.740741
338 QXP 0.416667 0.767442
339 NA0 0.416667 0.907895
340 N5O 0.416667 0.766234
341 WSA 0.416667 0.790698
342 AIR 0.41573 0.876712
343 V47 0.415094 0.763158
344 NIA 0.414894 0.802469
345 DCA 0.414062 0.825581
346 ETB 0.414062 0.835294
347 GAV 0.412844 0.8625
348 NAP 0.412214 0.92
349 PUA 0.410853 0.8625
350 APU 0.409836 0.871795
351 GNH 0.409524 0.884615
352 DZ4 0.409524 0.883117
353 TAP 0.409091 0.884615
354 62X 0.409091 0.670455
355 K2W 0.408696 0.743902
356 N5A 0.408163 0.74026
357 9BG 0.408 0.873418
358 ZDA 0.407767 0.842105
359 IDP 0.407767 0.894737
360 0T1 0.407692 0.825581
361 COA 0.407692 0.825581
362 GNP 0.407407 0.873418
363 9GM 0.407407 0.873418
364 GSP 0.407407 0.851852
365 TM1 0.40708 0.755814
366 101 0.40625 0.855263
367 9JJ 0.405405 0.841463
368 QXG 0.405405 0.758621
369 A6D 0.405405 0.705882
370 K15 0.405405 0.686047
371 V1N 0.405172 0.893333
372 649 0.404959 0.747253
373 F2N 0.403974 0.816092
374 K38 0.403509 0.759494
375 FCX 0.402985 0.797753
376 7RP 0.402062 0.902778
377 MGO 0.401869 0.839506
378 R2V 0.401786 0.767442
379 Q34 0.401639 0.678161
380 8Q2 0.401639 0.775281
381 FA9 0.401316 0.865854
382 P5F 0.4 0.825581
383 KYB 0.4 0.73494
384 0UM 0.4 0.702381
Similar Ligands (3D)
Ligand no: 1; Ligand: 6YZ; Similar ligands found: 0
No: Ligand Similarity coefficient
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
APoc FAQ
Feedback