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: 339
No: Ligand ECFP6 Tc MDL keys Tc
1 6YZ 1 1
2 ACQ 0.909091 1
3 ACP 0.833333 1
4 HEJ 0.833333 0.972222
5 ATP 0.833333 0.972222
6 AQP 0.822785 0.972222
7 5FA 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 AT4 0.740741 0.933333
15 AN2 0.740741 0.958904
16 M33 0.731707 0.932432
17 TAT 0.729412 0.933333
18 T99 0.729412 0.933333
19 SAP 0.72619 0.921053
20 AGS 0.72619 0.921053
21 AMP 0.717949 0.944444
22 A 0.717949 0.944444
23 APR 0.714286 0.945205
24 AR6 0.714286 0.945205
25 ANP 0.709302 0.945946
26 AD9 0.705882 0.945946
27 A12 0.695122 0.986301
28 AP2 0.695122 0.986301
29 25L 0.691489 0.958904
30 CA0 0.690476 0.92
31 ADX 0.690476 0.851852
32 50T 0.682353 0.932432
33 PRX 0.674419 0.87013
34 ATF 0.674157 0.933333
35 ABM 0.670732 0.893333
36 A22 0.67033 0.958904
37 RBY 0.666667 0.959459
38 ADV 0.666667 0.959459
39 4TC 0.660194 0.922078
40 ADQ 0.655914 0.92
41 SRA 0.646341 0.894737
42 5AL 0.644444 0.906667
43 A3R 0.638298 0.909091
44 A1R 0.638298 0.909091
45 AU1 0.632184 0.945946
46 7D4 0.632184 0.881579
47 SRP 0.630435 0.907895
48 ADP PO3 0.629214 0.917808
49 25A 0.62766 0.945205
50 OAD 0.625 0.92
51 9X8 0.625 0.896104
52 4AD 0.621053 0.921053
53 2A5 0.617977 0.92
54 G5P 0.617647 0.897436
55 00A 0.614583 0.860759
56 ITT 0.613636 0.917808
57 3OD 0.612245 0.92
58 BIS 0.612245 0.909091
59 5SV 0.610526 0.82716
60 OOB 0.610526 0.906667
61 8QN 0.610526 0.906667
62 G3A 0.607843 0.897436
63 7D3 0.604651 0.881579
64 HFD 0.604396 0.921053
65 AMO 0.604167 0.933333
66 PAJ 0.604167 0.8625
67 MAP 0.6 0.921053
68 AHX 0.597938 0.897436
69 DLL 0.597938 0.906667
70 GTA 0.596154 0.864198
71 PTJ 0.59596 0.873418
72 UP5 0.59434 0.896104
73 PAP 0.593407 0.958333
74 ATR 0.593407 0.944444
75 3UK 0.591837 0.894737
76 AFH 0.586538 0.886076
77 B5V 0.585859 0.883117
78 WAQ 0.585859 0.884615
79 LAD 0.585859 0.8625
80 PR8 0.585859 0.851852
81 ADP ALF 0.585106 0.848101
82 ALF ADP 0.585106 0.848101
83 SON 0.58427 0.933333
84 GAP 0.580645 0.87013
85 TXA 0.58 0.907895
86 FYA 0.58 0.906667
87 NB8 0.58 0.897436
88 ME8 0.58 0.841463
89 1ZZ 0.58 0.819277
90 TXD 0.579439 0.884615
91 ADP VO4 0.578947 0.906667
92 VO4 ADP 0.578947 0.906667
93 A4P 0.577982 0.823529
94 LMS 0.576471 0.807229
95 9SN 0.568627 0.85
96 DQV 0.566038 0.932432
97 NAX 0.564815 0.875
98 RAB 0.564103 0.821918
99 ADN 0.564103 0.821918
100 XYA 0.564103 0.821918
101 YAP 0.563107 0.896104
102 FA5 0.563107 0.907895
103 B5Y 0.563107 0.871795
104 B5M 0.563107 0.871795
105 9ZA 0.561224 0.884615
106 9ZD 0.561224 0.884615
107 ADP BMA 0.56 0.894737
108 XAH 0.557692 0.841463
109 GA7 0.556604 0.907895
110 48N 0.555556 0.897436
111 AP0 0.554545 0.873418
112 T5A 0.553571 0.843373
113 4UV 0.552381 0.871795
114 DAL AMP 0.55102 0.881579
115 6V0 0.550459 0.873418
116 NAI 0.550459 0.884615
117 DND 0.550459 0.907895
118 NXX 0.550459 0.907895
119 3AT 0.547368 0.972222
120 LAQ 0.546296 0.819277
121 OMR 0.545455 0.831325
122 TXE 0.545455 0.884615
123 AOC 0.545455 0.8
124 4UU 0.542056 0.871795
125 6AD 0.541667 0.886076
126 7D5 0.541176 0.855263
127 A2R 0.540816 0.958904
128 139 0.539823 0.851852
129 5AS 0.538462 0.761364
130 TAD 0.537037 0.910256
131 4UW 0.536364 0.839506
132 CNA 0.535088 0.907895
133 ATP A A A 0.533333 0.905405
134 DTP 0.53125 0.906667
135 5N5 0.530864 0.797297
136 80F 0.529915 0.843373
137 A3P 0.527473 0.944444
138 YLP 0.527273 0.821429
139 UPA 0.526786 0.884615
140 ADJ 0.526316 0.831325
141 A4D 0.52439 0.797297
142 5CD 0.52439 0.783784
143 A A 0.524272 0.918919
144 DZD 0.521368 0.910256
145 AV2 0.520408 0.893333
146 JB6 0.519231 0.884615
147 TYM 0.517857 0.907895
148 M2T 0.517647 0.716049
149 IOT 0.517544 0.833333
150 F2R 0.517241 0.865854
151 A3D 0.516949 0.894737
152 7DT 0.515789 0.958333
153 MYR AMP 0.514286 0.797619
154 AR6 AR6 0.513761 0.893333
155 7MD 0.513761 0.864198
156 YLC 0.513274 0.841463
157 YLB 0.513274 0.821429
158 COD 0.512821 0.813953
159 NAD 0.512821 0.906667
160 3AM 0.511364 0.90411
161 A2P 0.51087 0.930556
162 PPS 0.510204 0.851852
163 EP4 0.505882 0.734177
164 DAT 0.505263 0.906667
165 G5A 0.505155 0.781609
166 AHZ 0.504505 0.797619
167 DDS 0.5 0.855263
168 YLA 0.5 0.821429
169 NA7 0.5 0.959459
170 DTA 0.5 0.766234
171 SSA 0.5 0.802326
172 3DH 0.5 0.753247
173 7DD 0.5 0.958333
174 AYB 0.495726 0.811765
175 TYR AMP 0.495413 0.871795
176 AMP DBH 0.495413 0.87013
177 MTA 0.494253 0.753247
178 RGT 0.490741 0.933333
179 TSB 0.490196 0.8
180 A5A 0.49 0.788235
181 IMO 0.48913 0.90411
182 NAE 0.487805 0.871795
183 BTX 0.487395 0.843373
184 7MC 0.486957 0.843373
185 LPA AMP 0.486726 0.797619
186 ARG AMP 0.486486 0.831325
187 AVV 0.485437 0.897436
188 V3L 0.484848 0.945205
189 EAD 0.484127 0.851852
190 NAQ 0.483871 0.85
191 S4M 0.483871 0.670455
192 6RE 0.483516 0.7625
193 BT5 0.483333 0.833333
194 2AM 0.483146 0.917808
195 128 0.482456 0.758621
196 54H 0.480392 0.770115
197 VMS 0.480392 0.770115
198 GCP 0.480392 0.922078
199 52H 0.480392 0.761364
200 ZID 0.48 0.894737
201 M24 0.479675 0.829268
202 MAO 0.478723 0.761905
203 AF3 ADP 3PG 0.478261 0.839506
204 ARU 0.47619 0.839506
205 5CA 0.475728 0.802326
206 53H 0.475728 0.761364
207 8X1 0.475728 0.755556
208 HDV 0.475248 0.87013
209 5X8 0.474227 0.766234
210 A3N 0.473118 0.766234
211 J7C 0.473118 0.772152
212 ZAS 0.472527 0.746835
213 GTP 0.470588 0.896104
214 NDE 0.469231 0.907895
215 P1H 0.469231 0.831325
216 N0B 0.468254 0.821429
217 YLY 0.467742 0.811765
218 OVE 0.467391 0.881579
219 P5A 0.46729 0.747253
220 LSS 0.466667 0.764045
221 NSS 0.466667 0.802326
222 DSZ 0.466667 0.802326
223 9K8 0.462963 0.698925
224 G A A A 0.46281 0.85
225 AMP NAD 0.46281 0.881579
226 DSH 0.462366 0.728395
227 A3G 0.462366 0.802632
228 NVA LMS 0.462264 0.755556
229 FB0 0.462121 0.827586
230 6C6 0.46 0.883117
231 TXP 0.458333 0.897436
232 LEU LMS 0.457944 0.755556
233 GDP 0.455446 0.896104
234 FDA 0.455224 0.835294
235 NJP 0.454545 0.921053
236 GSU 0.453704 0.781609
237 KAA 0.453704 0.755556
238 GJV 0.452632 0.753086
239 12D 0.452174 0.767442
240 6FA 0.451852 0.843373
241 NAJ PZO 0.451613 0.82716
242 NDC 0.451128 0.85
243 4TA 0.45082 0.809524
244 0WD 0.45082 0.897436
245 NPW 0.45 0.8875
246 SA8 0.45 0.710843
247 MHZ 0.44898 0.701149
248 NAJ PYZ 0.448819 0.788235
249 N6P 0.448598 0.890411
250 71V 0.447917 0.884615
251 2SA 0.446602 0.933333
252 YSA 0.446429 0.781609
253 NZQ 0.446281 0.910256
254 5AD 0.445783 0.726027
255 FAS 0.445255 0.853659
256 FAD 0.445255 0.853659
257 SFG 0.444444 0.753247
258 PO4 PO4 A A A A PO4 0.444444 0.878378
259 ODP 0.442623 0.886076
260 SMM 0.442308 0.689655
261 J7V 0.44186 0.813953
262 6IA 0.441176 0.839506
263 SAM 0.441176 0.694118
264 7D7 0.440476 0.723684
265 A G 0.439024 0.860759
266 A7D 0.438776 0.779221
267 A3S 0.438776 0.813333
268 7C5 0.438596 0.797468
269 NDP 0.438017 0.897436
270 8PZ 0.4375 0.802326
271 AAT 0.436893 0.710843
272 RFL 0.43662 0.823529
273 A5D 0.435644 0.766234
274 U A G G 0.435484 0.860759
275 SFD 0.434783 0.736842
276 PGS 0.434343 0.860759
277 G2P 0.433962 0.910256
278 GGZ 0.433962 0.804878
279 MGP 0.432692 0.8625
280 62F 0.432624 0.864198
281 FNK 0.432624 0.806818
282 D5M 0.431579 0.88
283 NEC 0.431579 0.727273
284 DA 0.431579 0.88
285 GP3 0.431373 0.897436
286 SAH 0.431373 0.746835
287 SAI 0.431373 0.7375
288 A3T 0.43 0.8
289 6K6 0.429907 0.905405
290 FAY 0.429577 0.864198
291 U A 0.428571 0.884615
292 6G0 0.428571 0.8625
293 S7M 0.428571 0.694118
294 XNP 0.427419 0.851852
295 AAM 0.427083 0.944444
296 Y3J 0.425287 0.706667
297 AMZ 0.423913 0.891892
298 C2R 0.423913 0.88
299 EEM 0.423077 0.694118
300 A U 0.421488 0.848101
301 Z5A 0.419847 0.761364
302 4YB 0.418803 0.764045
303 A A A 0.418182 0.906667
304 GEK 0.416667 0.740741
305 NA0 0.416667 0.907895
306 WSA 0.416667 0.790698
307 AIR 0.41573 0.876712
308 NIA 0.414894 0.802469
309 ETB 0.414062 0.835294
310 DCA 0.414062 0.825581
311 GAV 0.412844 0.8625
312 NAP 0.412214 0.92
313 PUA 0.410853 0.8625
314 APU 0.409836 0.871795
315 GNH 0.409524 0.884615
316 TAP 0.409091 0.884615
317 62X 0.409091 0.670455
318 ZDA 0.407767 0.842105
319 IDP 0.407767 0.894737
320 0T1 0.407692 0.825581
321 COA 0.407692 0.825581
322 9GM 0.407407 0.873418
323 GSP 0.407407 0.851852
324 GNP 0.407407 0.873418
325 TM1 0.40708 0.755814
326 101 0.40625 0.855263
327 A6D 0.405405 0.705882
328 K15 0.405405 0.686047
329 9JJ 0.405405 0.841463
330 V1N 0.405172 0.893333
331 649 0.404959 0.747253
332 F2N 0.403974 0.816092
333 FCX 0.402985 0.797753
334 7RP 0.402062 0.902778
335 MGO 0.401869 0.839506
336 8Q2 0.401639 0.775281
337 FA9 0.401316 0.865854
338 0UM 0.4 0.702381
339 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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