Receptor
PDB id Resolution Class Description Source Keywords
1Z2P 1.22 Å EC: 2.-.-.- INOSITOL 1,3,4-TRISPHOSPHATE 5/6-KINASE IN COMPLEX WITH MG2+ PCP/INS(1,3,4)P3 ENTAMOEBA HISTOLYTICA INOSITOL PHOSPHATE KINASE ATP-GRASP TRANSFERASE
Ref.: SPECIFICITY DETERMINANTS IN INOSITOL POLYPHOSPHATE SYNTHESIS: CRYSTAL STRUCTURE OF INOSITOL 1,3,4-TRIS 5/6-KINASE. MOL.CELL V. 18 201 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACP X:1476;
Valid;
none;
submit data
505.208 C11 H18 N5 O12 P3 c1nc(...
I3S X:500;
Valid;
none;
submit data
420.096 C6 H15 O15 P3 [C@H]...
MG X:1295;
X:1296;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1Z2P 1.22 Å EC: 2.-.-.- INOSITOL 1,3,4-TRISPHOSPHATE 5/6-KINASE IN COMPLEX WITH MG2+ PCP/INS(1,3,4)P3 ENTAMOEBA HISTOLYTICA INOSITOL PHOSPHATE KINASE ATP-GRASP TRANSFERASE
Ref.: SPECIFICITY DETERMINANTS IN INOSITOL POLYPHOSPHATE SYNTHESIS: CRYSTAL STRUCTURE OF INOSITOL 1,3,4-TRIS 5/6-KINASE. MOL.CELL V. 18 201 2005
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 236 families.
1 1Z2P - I3S C6 H15 O15 P3 [C@H]1([C@....
2 1Z2O - I4P C6 H16 O18 P4 C1([C@H]([....
3 1Z2N - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 211 families.
1 1Z2P - I3S C6 H15 O15 P3 [C@H]1([C@....
2 1Z2O - I4P C6 H16 O18 P4 C1([C@H]([....
3 1Z2N - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 166 families.
1 1Z2P - I3S C6 H15 O15 P3 [C@H]1([C@....
2 1Z2O - I4P C6 H16 O18 P4 C1([C@H]([....
3 1Z2N - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ACP; Similar ligands found: 351
No: Ligand ECFP6 Tc MDL keys Tc
1 ACP 1 1
2 ACQ 0.866667 1
3 A2D 0.857143 0.945205
4 BA3 0.833333 0.945205
5 AP5 0.821918 0.945205
6 ADP 0.821918 0.972222
7 B4P 0.821918 0.945205
8 AN2 0.810811 0.958904
9 AP2 0.808219 0.986301
10 A12 0.808219 0.986301
11 M33 0.8 0.932432
12 ATP 0.789474 0.972222
13 5FA 0.779221 0.972222
14 AQP 0.779221 0.972222
15 AR6 0.779221 0.945205
16 APR 0.779221 0.945205
17 AGS 0.769231 0.921053
18 SAP 0.769231 0.921053
19 AD9 0.769231 0.945946
20 A 0.763889 0.944444
21 AMP 0.763889 0.944444
22 APC 0.75641 0.986301
23 CA0 0.753247 0.92
24 ADX 0.753247 0.851852
25 ANP 0.75 0.945946
26 50T 0.74359 0.932432
27 PRX 0.734177 0.87013
28 ABM 0.733333 0.893333
29 ATF 0.731707 0.933333
30 AMP MG 0.72 0.868421
31 SRA 0.706667 0.894737
32 A22 0.705882 0.958904
33 RBY 0.703704 0.959459
34 ADV 0.703704 0.959459
35 5AL 0.698795 0.906667
36 ADQ 0.689655 0.92
37 A1R 0.689655 0.909091
38 AU1 0.6875 0.945946
39 ADP MG 0.6875 0.881579
40 TAT 0.686747 0.933333
41 SRP 0.682353 0.907895
42 BEF ADP 0.679012 0.858974
43 ADP BEF 0.679012 0.858974
44 OAD 0.674157 0.92
45 4TC 0.673469 0.922078
46 4AD 0.670455 0.921053
47 AMO 0.670455 0.933333
48 00A 0.662921 0.860759
49 ADP PO3 0.662651 0.917808
50 3OD 0.659341 0.92
51 BIS 0.659341 0.909091
52 25A 0.659091 0.945205
53 8QN 0.659091 0.906667
54 5SV 0.659091 0.82716
55 OOB 0.659091 0.906667
56 ATP MG 0.654762 0.881579
57 SON 0.654321 0.933333
58 25L 0.652174 0.958904
59 PAJ 0.651685 0.8625
60 DLL 0.644444 0.906667
61 AHX 0.644444 0.897436
62 TXA 0.641304 0.907895
63 3UK 0.637363 0.894737
64 ADP ALF 0.632184 0.848101
65 ALF ADP 0.632184 0.848101
66 WAQ 0.630435 0.884615
67 LAD 0.630435 0.8625
68 PR8 0.630435 0.851852
69 MAP 0.629214 0.921053
70 GAP 0.627907 0.87013
71 ANP MG 0.625 0.871795
72 ADP VO4 0.625 0.906667
73 VO4 ADP 0.625 0.906667
74 ME8 0.623656 0.841463
75 PTJ 0.623656 0.873418
76 NB8 0.623656 0.897436
77 1ZZ 0.623656 0.819277
78 FYA 0.623656 0.906667
79 UP5 0.62 0.896104
80 G3A 0.618557 0.897436
81 AFH 0.612245 0.886076
82 G5P 0.612245 0.897436
83 9SN 0.610526 0.85
84 GTA 0.606061 0.864198
85 YAP 0.604167 0.896104
86 FA5 0.604167 0.907895
87 TXD 0.60396 0.884615
88 XAH 0.597938 0.841463
89 XYA 0.597222 0.821918
90 ADN 0.597222 0.821918
91 RAB 0.597222 0.821918
92 48N 0.594059 0.897436
93 DAL AMP 0.593407 0.881579
94 2A5 0.593023 0.92
95 AOC 0.592593 0.8
96 4UV 0.591837 0.871795
97 NAI 0.588235 0.884615
98 NXX 0.588235 0.907895
99 NAX 0.588235 0.875
100 DND 0.588235 0.907895
101 6V0 0.588235 0.873418
102 ATR 0.586207 0.944444
103 PAP 0.586207 0.958333
104 ADP BMA 0.585106 0.894737
105 LAQ 0.584158 0.819277
106 5AS 0.583333 0.761364
107 TXE 0.582524 0.884615
108 OMR 0.582524 0.831325
109 5N5 0.581081 0.797297
110 4UU 0.58 0.871795
111 A A 0.578947 0.918919
112 7D3 0.578313 0.881579
113 AP0 0.576923 0.873418
114 A4D 0.573333 0.797297
115 5CD 0.573333 0.783784
116 JB6 0.572917 0.884615
117 4UW 0.572816 0.839506
118 A4P 0.571429 0.823529
119 CNA 0.570093 0.907895
120 7D4 0.569767 0.881579
121 ITT 0.569767 0.917808
122 A2R 0.565217 0.958904
123 M2T 0.564103 0.716049
124 YLP 0.563107 0.821429
125 139 0.560748 0.851852
126 ADJ 0.560748 0.831325
127 T5A 0.560748 0.843373
128 TAD 0.558824 0.910256
129 ATP A A A 0.555556 0.905405
130 A3P 0.552941 0.944444
131 TYM 0.552381 0.907895
132 IOT 0.551402 0.833333
133 EP4 0.551282 0.734177
134 MYR AMP 0.55102 0.797619
135 7D5 0.55 0.855263
136 A3D 0.54955 0.894737
137 GCP 0.548387 0.922078
138 YLC 0.54717 0.841463
139 YLB 0.54717 0.821429
140 UPA 0.54717 0.884615
141 NAD 0.545455 0.906667
142 COD 0.545455 0.813953
143 G5A 0.544444 0.781609
144 DTA 0.544304 0.766234
145 3DH 0.54321 0.753247
146 DZD 0.540541 0.910256
147 AHZ 0.538462 0.797619
148 MTA 0.5375 0.753247
149 3AM 0.536585 0.90411
150 A2P 0.534884 0.930556
151 TYR AMP 0.534653 0.858974
152 AR6 AR6 0.533981 0.893333
153 6AD 0.532609 0.886076
154 PPS 0.532609 0.851852
155 YLA 0.53211 0.821429
156 AMP DBH 0.529412 0.87013
157 AYB 0.527273 0.811765
158 A5A 0.526882 0.788235
159 TSB 0.526316 0.8
160 6RE 0.52381 0.7625
161 S4M 0.523256 0.670455
162 SSA 0.521277 0.802326
163 NA7 0.520408 0.959459
164 7MD 0.519231 0.864198
165 LPA AMP 0.518868 0.797619
166 BTX 0.517857 0.843373
167 NAE 0.517241 0.871795
168 52H 0.515789 0.761364
169 54H 0.515789 0.770115
170 VMS 0.515789 0.770115
171 BT5 0.513274 0.833333
172 NAQ 0.512821 0.85
173 ZAS 0.511905 0.746835
174 J7C 0.511628 0.772152
175 A3N 0.511628 0.766234
176 IMO 0.511628 0.90411
177 AV2 0.510638 0.893333
178 53H 0.510417 0.761364
179 5CA 0.510417 0.802326
180 ARU 0.510204 0.839506
181 ARG AMP 0.509434 0.831325
182 ALF ADP 3PG 0.509259 0.839506
183 AF3 ADP 3PG 0.509259 0.839506
184 LA8 ALF 3PG 0.509259 0.839506
185 M24 0.508621 0.829268
186 ZID 0.508475 0.894737
187 2AM 0.506024 0.917808
188 V3L 0.505376 0.945205
189 3AT 0.505376 0.972222
190 AVV 0.505155 0.897436
191 MAO 0.5 0.761905
192 LSS 0.5 0.764045
193 NSS 0.5 0.802326
194 DSZ 0.5 0.802326
195 EAD 0.5 0.851852
196 DSH 0.5 0.728395
197 P5A 0.5 0.747253
198 YLY 0.495726 0.811765
199 NVA LMS 0.494949 0.744444
200 5X8 0.494505 0.766234
201 DAT 0.494505 0.906667
202 7MC 0.490909 0.843373
203 LEU LMS 0.49 0.744444
204 SMM 0.489583 0.689655
205 SAM 0.489362 0.694118
206 DTP 0.489362 0.906667
207 7DD 0.488889 0.958333
208 GJV 0.488636 0.753086
209 OVE 0.488372 0.881579
210 5AD 0.486842 0.726027
211 KAA 0.485149 0.755556
212 GSU 0.485149 0.781609
213 P1H 0.483871 0.831325
214 NDE 0.483871 0.907895
215 N0B 0.483333 0.821429
216 A3G 0.482759 0.802632
217 NAD IBO 0.482456 0.848101
218 NAJ PZO 0.478632 0.82716
219 4TA 0.478261 0.809524
220 SFG 0.478261 0.753247
221 YSA 0.47619 0.781609
222 FB0 0.47619 0.827586
223 NDC 0.47619 0.85
224 7DT 0.473118 0.958333
225 A7D 0.472527 0.779221
226 NJP 0.469565 0.921053
227 FDA 0.46875 0.835294
228 A5D 0.468085 0.766234
229 SA8 0.468085 0.710843
230 MHZ 0.467391 0.701149
231 71V 0.466667 0.884615
232 0WD 0.465517 0.897436
233 G A A A 0.465517 0.85
234 6FA 0.465116 0.843373
235 GGZ 0.464646 0.804878
236 SAH 0.463158 0.746835
237 6C6 0.463158 0.883117
238 SAI 0.463158 0.7375
239 NAJ PYZ 0.46281 0.829268
240 Y3J 0.4625 0.706667
241 7D7 0.461538 0.723684
242 TXP 0.46087 0.897436
243 PO4 PO4 A A A A PO4 0.460784 0.878378
244 S7M 0.459184 0.694118
245 AMP NAD 0.459016 0.858974
246 6IA 0.458333 0.839506
247 DDS 0.458333 0.855263
248 FAD 0.458015 0.853659
249 SFD 0.458015 0.736842
250 FAS 0.458015 0.853659
251 ODP 0.456897 0.886076
252 A3S 0.456522 0.813333
253 7C5 0.453704 0.797468
254 AAT 0.453608 0.710843
255 EEM 0.453608 0.694118
256 RGT 0.45283 0.933333
257 NPW 0.452174 0.8875
258 NDP 0.452174 0.897436
259 FAY 0.451852 0.864198
260 PGS 0.451613 0.860759
261 D5M 0.449438 0.88
262 DA 0.449438 0.88
263 NEC 0.449438 0.727273
264 U A G G 0.449153 0.860759
265 2SA 0.44898 0.933333
266 NIA 0.448276 0.802469
267 NZQ 0.448276 0.910256
268 A U 0.447368 0.848101
269 A3T 0.446809 0.8
270 A A A 0.446602 0.906667
271 128 0.446429 0.758621
272 6K6 0.445545 0.905405
273 GEK 0.445545 0.740741
274 4YB 0.445455 0.764045
275 AAM 0.444444 0.944444
276 FNK 0.444444 0.806818
277 62F 0.444444 0.864198
278 Z5A 0.443548 0.761364
279 WSA 0.442478 0.790698
280 AMZ 0.44186 0.891892
281 C2R 0.44186 0.88
282 12D 0.441441 0.767442
283 XNP 0.440678 0.851852
284 RFL 0.437956 0.823529
285 N6P 0.436893 0.890411
286 62X 0.436893 0.670455
287 AIR 0.433735 0.876712
288 PLP AAD 0.433333 0.725275
289 GP3 0.43299 0.897436
290 A6D 0.432692 0.705882
291 V1N 0.431193 0.893333
292 649 0.429825 0.747253
293 GP2 0.428571 0.910256
294 NA0 0.428571 0.907895
295 GDP 0.428571 0.896104
296 0UM 0.427184 0.702381
297 DCA 0.42623 0.825581
298 ETB 0.42623 0.835294
299 GNH 0.424242 0.884615
300 NAP 0.424 0.92
301 PUA 0.422764 0.8625
302 APU 0.422414 0.871795
303 101 0.422222 0.855263
304 3AD 0.421687 0.808219
305 FA9 0.42069 0.865854
306 TAP 0.420635 0.884615
307 TM1 0.420561 0.755814
308 P5F 0.41958 0.825581
309 0T1 0.419355 0.825581
310 COA 0.419355 0.825581
311 K15 0.419048 0.686047
312 7RP 0.417582 0.902778
313 S8M 0.417476 0.7625
314 NHD 0.416667 0.881579
315 GTP 0.415842 0.896104
316 FCX 0.414062 0.797753
317 F2N 0.413793 0.816092
318 AS 0.413043 0.835443
319 7RA 0.413043 0.931507
320 G1R 0.411765 0.884615
321 SXZ 0.411215 0.714286
322 QQY 0.411111 0.794872
323 ACK 0.411111 0.837838
324 AMX 0.409449 0.835294
325 30N 0.409449 0.755319
326 CAO 0.409449 0.797753
327 J7V 0.409449 0.813953
328 COS 0.409449 0.806818
329 1DG 0.409449 0.897436
330 DG1 0.409449 0.897436
331 NAD BBN 0.408759 0.821429
332 8BR 0.408602 0.883117
333 GNP 0.407767 0.873418
334 GSP 0.407767 0.851852
335 D3Y 0.407767 0.792208
336 G2P 0.407767 0.910256
337 CC5 0.407407 0.819444
338 KB1 0.407407 0.702381
339 N01 0.406504 0.881579
340 CMX 0.40625 0.825581
341 SCO 0.40625 0.825581
342 CMP 0.404255 0.876712
343 2BA 0.404255 0.890411
344 ACO 0.403101 0.797753
345 FAM 0.403101 0.806818
346 NAD CJ3 0.402878 0.793103
347 2VA 0.402062 0.779221
348 3NZ 0.401869 0.78481
349 26A 0.4 0.74359
350 HAX 0.4 0.806818
351 QQX 0.4 0.78481
Ligand no: 2; Ligand: I3S; Similar ligands found: 16
No: Ligand ECFP6 Tc MDL keys Tc
1 I3P 1 1
2 I3S 1 1
3 4IP 0.724138 0.966667
4 2IP 0.692308 1
5 I0P 0.678571 0.966667
6 ITP 0.655172 1
7 I4P 0.653846 0.933333
8 IP2 0.642857 1
9 5MY 0.6 0.933333
10 IP5 0.6 0.933333
11 5IP 0.6 0.933333
12 I5P 0.6 0.933333
13 I4D 0.566667 0.966667
14 IBS 0.511111 0.789474
15 I6P 0.481481 0.933333
16 IHP 0.481481 0.933333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1Z2P; Ligand: ACP; Similar sites found: 40
This union binding pocket(no: 1) in the query (biounit: 1z2p.bio1) has 37 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4U98 ACP 0.00001321 0.40013 1.85185
2 5VZ0 ADP 0.000003914 0.42336 2.16049
3 3TII ANP 0.000001382 0.40679 2.16049
4 3V4S ADP 0.00002238 0.46511 2.32558
5 3V4S ATP 0.000002486 0.44792 2.32558
6 3KAL ADP 0.00003158 0.45234 2.46914
7 5EQY 5RA 0.001167 0.41902 2.46914
8 5W2I ADP 0.0001496 0.40152 2.72374
9 5W2I I3P 0.0001496 0.40152 2.72374
10 2IO8 ADP 0.0000114 0.43668 3.08642
11 1PK8 ATP 0.00002745 0.4285 3.08642
12 1I7L ATP 0.00002406 0.4268 3.55987
13 3ETH ATP 0.000001393 0.45022 4.01235
14 1T36 ADP 0.0002224 0.40957 4.01235
15 2VPQ ANP 0.000005588 0.44383 4.32099
16 2YW2 ATP 0.000009585 0.42244 4.32099
17 3WVR AMP 0.000003715 0.40261 4.47427
18 5K2M ADP 0.000003851 0.45245 4.7619
19 5C1P DAL DAL 0.0001359 0.40755 5.22876
20 3W0O HY0 0.0003501 0.40769 5.24691
21 3W0O ADP 0.0003501 0.40769 5.24691
22 1KJ8 ATP 0.0002094 0.43387 5.55556
23 1KJ8 GAR 0.0002522 0.43373 5.55556
24 4O4F ATP 0.0001453 0.4078 5.64516
25 4O4F IHP 0.0001926 0.40728 5.64516
26 1IOW ADP 0.00003307 0.45589 6.20915
27 1IOW PHY 0.00003307 0.45589 6.20915
28 2VQD AP2 0.0000831 0.4023 6.79012
29 3K5I AIR 0.0001186 0.43174 7.40741
30 3ORQ ADP 0.000007335 0.43088 7.40741
31 3K5I ADP 0.00002856 0.41663 7.40741
32 2BPM 529 0.004023 0.40037 8.73786
33 2V58 LZJ 0.0001607 0.44807 8.95062
34 2JDR GLY ARG PRO ARG THR THR SER PHE ALA GLU 0.005372 0.40155 9.25926
35 2JDR L20 0.005372 0.40155 9.25926
36 4NZN ANP 0.00000000557 0.60725 10.4938
37 4NZN 2OU 0.00000000557 0.60725 10.4938
38 3VPB ADP 0.00004769 0.42582 18.7943
39 5LXT ACP 0.0000001051 0.48744 24.4755
40 2Q7D ANP 0.000000000009895 0.62091 45.0617
Pocket No.: 2; Query (leader) PDB : 1Z2P; Ligand: I3S; Similar sites found: 45
This union binding pocket(no: 2) in the query (biounit: 1z2p.bio1) has 37 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4U98 ACP 0.00001321 0.40013 1.85185
2 1GSA ADP 0.000009904 0.43111 1.89873
3 5VZ0 ADP 0.000003914 0.42336 2.16049
4 3TII ANP 0.000001382 0.40679 2.16049
5 3V4S ADP 0.00002238 0.46511 2.32558
6 3V4S ATP 0.000002486 0.44792 2.32558
7 3KAL ADP 0.00003158 0.45234 2.46914
8 5EQY 5RA 0.001167 0.41902 2.46914
9 5W2I ADP 0.0001496 0.40152 2.72374
10 5W2I I3P 0.0001496 0.40152 2.72374
11 1AUX AGS 0.000005814 0.41716 2.89389
12 2IO8 ADP 0.0000114 0.43668 3.08642
13 1PK8 ATP 0.00002745 0.4285 3.08642
14 1I7L ATP 0.00002406 0.4268 3.55987
15 3ETH ATP 0.000001393 0.45022 4.01235
16 1T36 ADP 0.0002224 0.40957 4.01235
17 2VPQ ANP 0.000005588 0.44383 4.32099
18 2YW2 ATP 0.000009585 0.42244 4.32099
19 3WVR AMP 0.000003715 0.40261 4.47427
20 5K2M ADP 0.000003851 0.45245 4.7619
21 5C1P DAL DAL 0.0001359 0.40755 5.22876
22 3W0O ADP 0.0003501 0.40769 5.24691
23 3W0O HY0 0.0003501 0.40769 5.24691
24 1KJ8 ATP 0.0002094 0.43387 5.55556
25 1KJ8 GAR 0.0002522 0.43373 5.55556
26 4O4F ATP 0.0001453 0.4078 5.64516
27 4O4F IHP 0.0001926 0.40728 5.64516
28 1IOW PHY 0.00003307 0.45589 6.20915
29 1IOW ADP 0.00003307 0.45589 6.20915
30 3WO0 ALA 0.0003265 0.42978 6.48148
31 2VQD AP2 0.0000831 0.4023 6.79012
32 3K5I AIR 0.0001186 0.43174 7.40741
33 3ORQ ADP 0.000007335 0.43088 7.40741
34 3K5I ADP 0.00002856 0.41663 7.40741
35 2BPM 529 0.004023 0.40037 8.73786
36 2V58 LZJ 0.0001607 0.44807 8.95062
37 2JDR L20 0.005372 0.40155 9.25926
38 2JDR GLY ARG PRO ARG THR THR SER PHE ALA GLU 0.005372 0.40155 9.25926
39 4NZN ANP 0.00000000557 0.60725 10.4938
40 4NZN 2OU 0.00000000557 0.60725 10.4938
41 2R7K AMZ 0.0001289 0.42074 11.1111
42 3VPD ANP 0.0000001934 0.47543 14.2349
43 3VPB ADP 0.00004769 0.42582 18.7943
44 5LXT ACP 0.0000001051 0.48744 24.4755
45 2Q7D ANP 0.000000000009895 0.62091 45.0617
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