Receptor
PDB id Resolution Class Description Source Keywords
5TK6 1.92 Å NON-ENZYME: OTHER STRUCTURE OF THE HD-DOMAIN PHOSPHOHYDROLASE OXSA WITH OXETAN DIPHOSPHATE BOUND BACILLUS MEGATERIUM METALLOPROTEIN METAL BINDING PROTEIN
Ref.: AN HD DOMAIN PHOSPHOHYDROLASE ACTIVE SITE TAILORED OXETANOCIN-A BIOSYNTHESIS. PROC. NATL. ACAD. SCI. V. 113 13750 2016 U.S.A.
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:202;
A:201;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
7D3 A:203;
Valid;
none;
submit data
411.202 C10 H15 N5 O9 P2 c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5TK8 1.64 Å NON-ENZYME: OTHER STRUCTURE OF THE HD-DOMAIN PHOSPHOHYDROLASE OXSA WITH OXETAN MONOPHOSPHATE BOUND BACILLUS MEGATERIUM METALLOPROTEIN METAL BINDING PROTEIN
Ref.: AN HD DOMAIN PHOSPHOHYDROLASE ACTIVE SITE TAILORED OXETANOCIN-A BIOSYNTHESIS. PROC. NATL. ACAD. SCI. V. 113 13750 2016 U.S.A.
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 5TK7 - 7D4 C10 H16 N5 O12 P3 c1nc(c2c(n....
2 5TK8 - 7D5 C10 H14 N5 O6 P c1nc(c2c(n....
3 5TK9 - 7D7 C10 H13 N5 O3 c1nc(c2c(n....
4 5TK6 - 7D3 C10 H15 N5 O9 P2 c1nc(c2c(n....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 5TK7 - 7D4 C10 H16 N5 O12 P3 c1nc(c2c(n....
2 5TK8 - 7D5 C10 H14 N5 O6 P c1nc(c2c(n....
3 5TK9 - 7D7 C10 H13 N5 O3 c1nc(c2c(n....
4 5TK6 - 7D3 C10 H15 N5 O9 P2 c1nc(c2c(n....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 5TK7 - 7D4 C10 H16 N5 O12 P3 c1nc(c2c(n....
2 5TK8 - 7D5 C10 H14 N5 O6 P c1nc(c2c(n....
3 5TK9 - 7D7 C10 H13 N5 O3 c1nc(c2c(n....
4 5TK6 - 7D3 C10 H15 N5 O9 P2 c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 7D3; Similar ligands found: 298
No: Ligand ECFP6 Tc MDL keys Tc
1 7D3 1 1
2 7D4 0.884058 1
3 7D5 0.830769 0.971831
4 2A5 0.714286 0.906667
5 ADP 0.706667 0.905405
6 PAP 0.683544 0.917808
7 ATR 0.6625 0.90411
8 CUU 0.6375 0.905405
9 ATP 0.6375 0.905405
10 HEJ 0.6375 0.905405
11 AV2 0.630952 0.855263
12 5FA 0.62963 0.905405
13 AQP 0.62963 0.905405
14 7D7 0.626866 0.830986
15 A2D 0.623377 0.88
16 AP5 0.620253 0.88
17 B4P 0.620253 0.88
18 DAT 0.617284 0.893333
19 AN2 0.6125 0.893333
20 BA3 0.607595 0.88
21 ACQ 0.607143 0.881579
22 6YZ 0.604651 0.881579
23 AT4 0.592593 0.87013
24 M33 0.585366 0.868421
25 AMP 0.584416 0.878378
26 A 0.584416 0.878378
27 ACP 0.578313 0.881579
28 AR6 0.571429 0.88
29 APR 0.571429 0.88
30 ANP 0.569767 0.881579
31 3AT 0.569767 0.905405
32 TAT 0.569767 0.87013
33 T99 0.569767 0.87013
34 A3P 0.567901 0.90411
35 AGS 0.564706 0.858974
36 AD9 0.564706 0.881579
37 AMP MG 0.556962 0.84
38 ADP BEF 0.554217 0.853333
39 ADP MG 0.554217 0.853333
40 APC 0.552941 0.894737
41 DTP 0.551724 0.893333
42 3AM 0.551282 0.890411
43 A2P 0.548781 0.890411
44 ADX 0.547619 0.795181
45 CA0 0.547619 0.857143
46 PPS 0.545455 0.817073
47 HQG 0.544444 0.893333
48 A2R 0.544444 0.893333
49 ABM 0.54321 0.831169
50 45A 0.54321 0.831169
51 50T 0.541176 0.868421
52 KG4 0.541176 0.857143
53 ATF 0.539326 0.87013
54 A22 0.538462 0.893333
55 2AM 0.538462 0.90411
56 PRX 0.534884 0.810127
57 25L 0.53125 0.893333
58 A12 0.53012 0.894737
59 AP2 0.53012 0.894737
60 ADP PO3 0.528736 0.853333
61 ATP MG 0.528736 0.853333
62 APC MG 0.528736 0.855263
63 5AL 0.52809 0.844156
64 A1R 0.526882 0.871795
65 ADQ 0.526882 0.881579
66 12D 0.519608 0.755814
67 SRA 0.518519 0.833333
68 OVE 0.518519 0.868421
69 DDS 0.516854 0.891892
70 SRP 0.516484 0.846154
71 NA7 0.515789 0.894737
72 AU1 0.511628 0.881579
73 8LE 0.511111 0.8125
74 A3R 0.510638 0.871795
75 ADN 0.506849 0.783784
76 XYA 0.506849 0.783784
77 RAB 0.506849 0.783784
78 BEF ADP 0.505618 0.831169
79 QA7 0.505376 0.8125
80 JNT 0.505263 0.881579
81 8QN 0.5 0.844156
82 OZV 0.5 0.88
83 V3L 0.5 0.88
84 9X8 0.5 0.835443
85 OAD 0.5 0.857143
86 8LH 0.5 0.846154
87 25A 0.5 0.88
88 128 0.495238 0.747126
89 AMO 0.494737 0.846154
90 V2G 0.494505 0.8375
91 RBY 0.494382 0.87013
92 ADV 0.494382 0.87013
93 D5M 0.493976 0.866667
94 DA 0.493976 0.866667
95 BIS 0.489796 0.848101
96 3OD 0.489796 0.857143
97 00A 0.489583 0.802469
98 AHX 0.489583 0.8375
99 GGZ 0.489362 0.771084
100 MAP 0.489362 0.858974
101 8LQ 0.489362 0.822785
102 ALF ADP 0.48913 0.790123
103 ANP MG 0.48913 0.844156
104 VO4 ADP 0.48913 0.857143
105 G5P 0.485437 0.8375
106 5SV 0.484211 0.792683
107 OOB 0.484211 0.844156
108 GAP 0.483516 0.833333
109 SON 0.482759 0.87013
110 LAD 0.479592 0.82716
111 B5V 0.479592 0.822785
112 4AD 0.479167 0.835443
113 PAJ 0.479167 0.82716
114 G3A 0.475728 0.8375
115 KMQ 0.475248 0.846154
116 ME8 0.474747 0.764706
117 TXA 0.474747 0.846154
118 NB8 0.474747 0.814815
119 PTJ 0.474747 0.814815
120 FYA 0.474747 0.820513
121 DLL 0.474227 0.844156
122 5N5 0.473684 0.76
123 48N 0.471698 0.814815
124 LQJ 0.470588 0.88
125 LMS 0.46988 0.752941
126 PO4 PO4 A A A A PO4 0.469388 0.84
127 ADP BMA 0.469388 0.857143
128 3UK 0.469388 0.833333
129 5CD 0.467532 0.723684
130 A4D 0.467532 0.76
131 WAQ 0.464646 0.825
132 J4G 0.464646 0.835443
133 PR8 0.464646 0.817073
134 101 0.464286 0.891892
135 6AD 0.462366 0.82716
136 DZ4 0.462366 0.87013
137 ATP A 0.460784 0.842105
138 ATP A A A 0.460784 0.842105
139 FA5 0.460784 0.822785
140 1ZZ 0.46 0.785714
141 A3G 0.458824 0.74359
142 DAL AMP 0.458333 0.820513
143 AFH 0.457143 0.82716
144 KL2 0.45679 0.802632
145 SO8 0.456522 0.734177
146 XAH 0.456311 0.807229
147 2VA 0.455556 0.74359
148 TM1 0.455446 0.744186
149 NAX 0.453704 0.795181
150 UP5 0.453704 0.835443
151 9ZA 0.453608 0.825
152 9ZD 0.453608 0.825
153 DQV 0.45283 0.868421
154 GTA 0.45283 0.807229
155 ACK 0.452381 0.824324
156 QQY 0.452381 0.782051
157 ZAS 0.452381 0.691358
158 9SN 0.45098 0.792683
159 EP4 0.45 0.679012
160 A3S 0.449438 0.753247
161 3AD 0.448718 0.77027
162 3L1 0.448718 0.786667
163 NWW 0.448718 0.68
164 3D1 0.448718 0.786667
165 B5Y 0.446602 0.8125
166 B5M 0.446602 0.8125
167 NPW 0.446429 0.807229
168 NVA 2AD 0.445652 0.707317
169 4TC 0.445455 0.814815
170 L3W 0.445455 0.846154
171 M2T 0.444444 0.662651
172 DTA 0.444444 0.730769
173 ITT 0.444444 0.853333
174 NZQ 0.442478 0.82716
175 AOC 0.44186 0.74026
176 APU 0.441441 0.858974
177 A4P 0.441441 0.790698
178 JSQ 0.44086 0.858974
179 VRT 0.44086 0.716049
180 HFD 0.44086 0.858974
181 QQX 0.440476 0.772152
182 TXD 0.440367 0.825
183 NAI 0.440367 0.825
184 6V0 0.440367 0.814815
185 DND 0.440367 0.846154
186 5AD 0.44 0.666667
187 5X8 0.43956 0.6875
188 A3T 0.43956 0.763158
189 MTA 0.439024 0.696203
190 F2R 0.438596 0.809524
191 ODP 0.438596 0.82716
192 5AS 0.438202 0.730337
193 4UV 0.438095 0.8125
194 J7V 0.438017 0.761364
195 AS 0.436782 0.822785
196 TXE 0.436364 0.825
197 OMR 0.436364 0.797619
198 LAQ 0.435185 0.785714
199 AHZ 0.435185 0.744186
200 0WD 0.434783 0.8375
201 NDP 0.433628 0.8375
202 139 0.433628 0.839506
203 ADJ 0.433628 0.797619
204 T5A 0.433628 0.788235
205 NO7 0.43299 0.87013
206 AP0 0.432432 0.814815
207 DCA 0.432203 0.793103
208 ETB 0.432203 0.781609
209 YLP 0.431193 0.788235
210 6RE 0.430233 0.707317
211 ZDA 0.430108 0.828947
212 7MD 0.429907 0.807229
213 4UU 0.429907 0.8125
214 ANZ 0.429907 0.768293
215 GA7 0.429907 0.846154
216 AR6 AR6 0.429907 0.831169
217 TXP 0.429825 0.8375
218 3DH 0.428571 0.696203
219 80F 0.42735 0.767442
220 4UW 0.427273 0.783133
221 MYR AMP 0.427184 0.764706
222 HDV 0.427083 0.857143
223 NJP 0.426087 0.858974
224 NEC 0.425287 0.692308
225 0T1 0.425 0.793103
226 COA 0.425 0.793103
227 H1Q 0.423913 0.818182
228 TYM 0.423423 0.822785
229 COD 0.422414 0.781609
230 XNP 0.422414 0.817073
231 NAD 0.422414 0.844156
232 J7C 0.420455 0.716049
233 YLB 0.419643 0.788235
234 UPA 0.419643 0.848101
235 YLC 0.419643 0.807229
236 103 0.418605 0.802632
237 Y3J 0.417722 0.649351
238 7DD 0.417582 0.891892
239 JB6 0.417476 0.802469
240 CNA 0.417391 0.846154
241 ARG AMP 0.416667 0.776471
242 PUA 0.416667 0.85
243 S4M 0.41573 0.640449
244 CC5 0.415584 0.733333
245 A3D 0.415254 0.833333
246 CAO 0.414634 0.766667
247 AMX 0.414634 0.802326
248 30N 0.414634 0.726316
249 COS 0.414634 0.775281
250 TSB 0.414141 0.747126
251 9BG 0.413793 0.860759
252 A5A 0.412371 0.735632
253 NWQ 0.411765 0.662338
254 CMX 0.41129 0.793103
255 SCO 0.41129 0.793103
256 AMP DBH 0.411215 0.810127
257 MAO 0.411111 0.709302
258 ALF ADP 3PG 0.410714 0.761905
259 G5A 0.410526 0.730337
260 NAQ 0.409836 0.792683
261 N5O 0.409091 0.708861
262 DSH 0.409091 0.695122
263 YLA 0.408696 0.788235
264 SFG 0.408602 0.696203
265 SSA 0.408163 0.75
266 ACO 0.408 0.766667
267 FAM 0.408 0.775281
268 FCX 0.408 0.766667
269 7MC 0.40708 0.788235
270 NAP 0.406504 0.857143
271 38V 0.406504 0.829268
272 SAM 0.40625 0.643678
273 NMX 0.40625 0.734043
274 LPA AMP 0.405405 0.764706
275 AYB 0.405172 0.77907
276 ZZB 0.405172 0.764706
277 HAX 0.404762 0.775281
278 A3N 0.404494 0.730769
279 VMS 0.40404 0.719101
280 54H 0.40404 0.719101
281 TAP 0.403226 0.825
282 DG1 0.403226 0.8375
283 1DG 0.403226 0.8375
284 NAE 0.401639 0.8125
285 3KK 0.401575 0.775281
286 FYN 0.401575 0.793103
287 GJV 0.4 0.698795
288 EAD 0.4 0.795181
289 NA0 0.4 0.846154
290 53H 0.4 0.711111
291 N5A 0.4 0.683544
292 KGJ 0.4 0.726316
293 5CA 0.4 0.75
294 IOT 0.4 0.8
295 D3Y 0.4 0.734177
296 SA8 0.4 0.658824
297 TAD 0.4 0.82716
298 7L1 0.4 0.766667
Similar Ligands (3D)
Ligand no: 1; Ligand: 7D3; Similar ligands found: 7
No: Ligand Similarity coefficient
1 GDP 0.8915
2 UDP 0.8915
3 DUD 0.8807
4 GNH 0.8761
5 M7G 0.8710
6 CDP 0.8672
7 DGI 0.8620
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5TK8; Ligand: 7D5; 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: 5tk8.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5TK8; Ligand: 7D5; 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: 5tk8.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
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