Receptor
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.
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
7D5 A:201;
Valid;
none;
submit data
331.222 C10 H14 N5 O6 P c1nc(...
MG A:202;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
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: 7D5; Similar ligands found: 295
No: Ligand ECFP6 Tc MDL keys Tc
1 7D5 1 1
2 7D3 0.830769 0.971831
3 7D4 0.782609 0.971831
4 7D7 0.7 0.855072
5 AMP 0.691176 0.902778
6 A 0.691176 0.902778
7 A3P 0.666667 0.902778
8 A2P 0.643836 0.888889
9 3AM 0.605634 0.915493
10 2A5 0.602564 0.88
11 45A 0.594595 0.853333
12 ABM 0.594595 0.853333
13 A2D 0.594595 0.853333
14 ADP 0.592105 0.878378
15 2AM 0.591549 0.902778
16 AMP MG 0.589041 0.863014
17 AN2 0.584416 0.866667
18 D5M 0.581081 0.890411
19 DA 0.581081 0.890411
20 V3L 0.580247 0.878378
21 BA3 0.578947 0.853333
22 AP2 0.578947 0.868421
23 A12 0.578947 0.868421
24 PAP 0.575 0.890411
25 AP5 0.571429 0.853333
26 B4P 0.571429 0.853333
27 HEJ 0.56962 0.878378
28 ATP 0.56962 0.878378
29 SRA 0.567568 0.855263
30 OVE 0.567568 0.866667
31 AT4 0.564103 0.844156
32 ADP MG 0.564103 0.851351
33 ADP BEF 0.564103 0.851351
34 AQP 0.5625 0.878378
35 5FA 0.5625 0.878378
36 APC 0.5625 0.868421
37 ACQ 0.560976 0.855263
38 XYA 0.560606 0.780822
39 RAB 0.560606 0.780822
40 ADN 0.560606 0.780822
41 AU1 0.556962 0.855263
42 ADX 0.556962 0.771084
43 M33 0.556962 0.842105
44 CA0 0.556962 0.831169
45 ATR 0.555556 0.876712
46 PPS 0.554217 0.792683
47 ACP 0.55 0.855263
48 KG4 0.55 0.831169
49 50T 0.55 0.866667
50 PRX 0.54321 0.831169
51 APR 0.54321 0.853333
52 AR6 0.54321 0.853333
53 T99 0.542169 0.844156
54 TAT 0.542169 0.844156
55 6YZ 0.541176 0.855263
56 25A 0.54023 0.878378
57 ATP MG 0.536585 0.851351
58 RBY 0.536585 0.844156
59 AD9 0.536585 0.855263
60 AGS 0.536585 0.833333
61 APC MG 0.536585 0.853333
62 ADV 0.536585 0.844156
63 ADP PO3 0.536585 0.851351
64 V2G 0.535714 0.835443
65 5AL 0.535714 0.842105
66 J4G 0.533333 0.833333
67 CUU 0.530864 0.878378
68 AV2 0.529412 0.828947
69 SON 0.525 0.868421
70 ANP 0.52381 0.855263
71 SRP 0.523256 0.844156
72 5N5 0.521739 0.756757
73 8LE 0.517647 0.810127
74 A2R 0.517241 0.866667
75 HQG 0.517241 0.866667
76 A4D 0.514286 0.756757
77 5CD 0.514286 0.743243
78 LMS 0.513158 0.75
79 DAT 0.512195 0.866667
80 BEF ADP 0.511905 0.828947
81 ATF 0.511628 0.844156
82 A22 0.511364 0.866667
83 QA7 0.511364 0.810127
84 DTA 0.506849 0.75
85 101 0.506494 0.916667
86 3AT 0.505882 0.878378
87 GAP 0.505882 0.831169
88 8LH 0.505747 0.844156
89 8QN 0.505618 0.842105
90 TM1 0.505376 0.741176
91 MTA 0.5 0.714286
92 A3G 0.5 0.74026
93 ADQ 0.5 0.855263
94 AMO 0.5 0.820513
95 KL2 0.5 0.824324
96 A1R 0.5 0.846154
97 PTJ 0.494624 0.8125
98 AHX 0.494505 0.8125
99 MAP 0.494382 0.833333
100 8LQ 0.494382 0.820513
101 GGZ 0.494382 0.746988
102 VO4 ADP 0.494253 0.855263
103 ALF ADP 0.494253 0.7875
104 ANP MG 0.494253 0.842105
105 5X8 0.493976 0.705128
106 2VA 0.493976 0.74026
107 QQY 0.493506 0.802632
108 ACK 0.493506 0.847222
109 EP4 0.493151 0.696203
110 3L1 0.492958 0.783784
111 NWW 0.492958 0.675676
112 3AD 0.492958 0.791667
113 3D1 0.492958 0.783784
114 ANZ 0.489796 0.7875
115 NA7 0.48913 0.868421
116 9ZD 0.488889 0.822785
117 OZV 0.488889 0.853333
118 5SV 0.488889 0.8125
119 9ZA 0.488889 0.822785
120 OOB 0.488889 0.842105
121 DTP 0.488372 0.866667
122 A3S 0.487805 0.75
123 3DH 0.486842 0.714286
124 M2T 0.486486 0.679012
125 5AD 0.485294 0.684932
126 LAD 0.483871 0.825
127 B5V 0.483871 0.820513
128 4AD 0.483516 0.810127
129 PAJ 0.483516 0.802469
130 A3R 0.483516 0.846154
131 AOC 0.481013 0.76
132 QQX 0.480519 0.792208
133 NB8 0.478723 0.790123
134 TXA 0.478723 0.820513
135 FYA 0.478723 0.842105
136 ME8 0.478723 0.761905
137 00A 0.478261 0.8
138 DLL 0.478261 0.842105
139 JNT 0.478261 0.855263
140 DAL AMP 0.477778 0.818182
141 VRT 0.476744 0.7125
142 SO8 0.476744 0.730769
143 A3T 0.47619 0.76
144 5AS 0.47561 0.727273
145 AS 0.475 0.844156
146 ZAS 0.474359 0.708861
147 LQJ 0.474227 0.878378
148 25L 0.473684 0.866667
149 3UK 0.473118 0.831169
150 ADP BMA 0.473118 0.831169
151 PO4 PO4 A A A A PO4 0.473118 0.837838
152 OAD 0.473118 0.831169
153 9X8 0.473118 0.810127
154 6RE 0.468354 0.725
155 WAQ 0.468085 0.822785
156 PR8 0.468085 0.814815
157 DZ4 0.465909 0.844156
158 NVA 2AD 0.465116 0.703704
159 FA5 0.463918 0.820513
160 ATP A 0.463918 0.84
161 ATP A A A 0.463918 0.84
162 1ZZ 0.463158 0.783133
163 BIS 0.463158 0.822785
164 3OD 0.463158 0.831169
165 DSH 0.4625 0.7125
166 XAH 0.459184 0.804878
167 Y3J 0.458333 0.666667
168 CC5 0.457143 0.753425
169 J7C 0.45679 0.734177
170 103 0.455696 0.824324
171 DDS 0.454545 0.864865
172 9SN 0.453608 0.790123
173 S4M 0.451219 0.655172
174 8BR 0.451219 0.844156
175 G3A 0.45 0.8125
176 B5Y 0.44898 0.810127
177 KMQ 0.44898 0.820513
178 B5M 0.44898 0.810127
179 JB6 0.447917 0.8
180 48N 0.446602 0.790123
181 MAO 0.445783 0.72619
182 TSB 0.445652 0.724138
183 7MD 0.445545 0.783133
184 G5P 0.445545 0.8125
185 A5A 0.444444 0.732558
186 NEC 0.444444 0.688312
187 APU 0.443396 0.857143
188 MYR AMP 0.443299 0.761905
189 SAH 0.443182 0.708861
190 G5A 0.443182 0.727273
191 SFG 0.44186 0.714286
192 H1Q 0.44186 0.84
193 38Y 0.440367 0.77381
194 4UV 0.44 0.810127
195 SSA 0.43956 0.727273
196 A3N 0.439024 0.727273
197 IMO 0.439024 0.837838
198 LAQ 0.436893 0.783133
199 AHZ 0.436893 0.741176
200 12D 0.436893 0.732558
201 A7D 0.435294 0.763158
202 54H 0.434783 0.715909
203 VMS 0.434783 0.715909
204 GJV 0.433735 0.716049
205 6MZ 0.433735 0.864865
206 YLP 0.432692 0.785714
207 WMP 0.432432 0.828947
208 A5D 0.431818 0.75
209 SA8 0.431818 0.674699
210 4UU 0.431373 0.810127
211 GA7 0.431373 0.844156
212 AFH 0.431373 0.802469
213 ARG AMP 0.431373 0.77381
214 AR6 AR6 0.431373 0.828947
215 ZZB 0.431193 0.783133
216 NWQ 0.43038 0.657895
217 53H 0.430108 0.707865
218 D3Y 0.430108 0.730769
219 5CA 0.430108 0.727273
220 4UW 0.428571 0.780488
221 NAX 0.428571 0.771084
222 128 0.428571 0.724138
223 DQV 0.427184 0.842105
224 GTA 0.427184 0.783133
225 TAD 0.427184 0.802469
226 SAI 0.426966 0.7
227 N5O 0.426829 0.705128
228 AFX 0.426667 0.64557
229 AMP DBH 0.425743 0.807692
230 TYM 0.424528 0.820513
231 SMM 0.423913 0.655172
232 3NZ 0.42268 0.725
233 SAM 0.422222 0.658824
234 NPW 0.422018 0.783133
235 5F1 0.421053 0.72
236 LSS 0.421053 0.692308
237 DSZ 0.421053 0.707865
238 7MC 0.420561 0.764706
239 L3W 0.420561 0.820513
240 YLB 0.420561 0.785714
241 YLC 0.420561 0.804878
242 4TC 0.420561 0.790123
243 UPA 0.420561 0.822785
244 52H 0.419355 0.707865
245 LPA AMP 0.419048 0.761905
246 NZQ 0.418182 0.802469
247 EEM 0.417582 0.658824
248 PUA 0.417391 0.825
249 N5A 0.416667 0.679487
250 NAI 0.415094 0.8
251 UP5 0.415094 0.810127
252 6V0 0.415094 0.790123
253 DND 0.415094 0.820513
254 TXD 0.415094 0.8
255 8X1 0.414894 0.741573
256 9BG 0.414414 0.835443
257 MHZ 0.413793 0.686047
258 71V 0.411765 0.822785
259 TXE 0.411215 0.8
260 OMR 0.411215 0.77381
261 ALF ADP 3PG 0.411215 0.759036
262 KF5 0.410959 0.608108
263 0WD 0.410714 0.8125
264 XNP 0.410714 0.792683
265 139 0.409091 0.814815
266 YLA 0.409091 0.785714
267 NDP 0.409091 0.8125
268 ADJ 0.409091 0.77381
269 S7M 0.408602 0.658824
270 KAA 0.408163 0.722222
271 P5A 0.408163 0.714286
272 GSU 0.408163 0.707865
273 ARJ 0.407895 0.712329
274 AP0 0.407407 0.790123
275 NSS 0.40625 0.707865
276 NOC 0.405405 0.702703
277 AYB 0.405405 0.776471
278 TXP 0.405405 0.8125
279 AAM 0.404762 0.902778
280 9K8 0.40404 0.648936
281 A4P 0.40367 0.767442
282 80F 0.403509 0.744186
283 PAX 0.403361 0.795181
284 RP1 0.402439 0.805195
285 SP1 0.402439 0.805195
286 AAT 0.402174 0.695122
287 NVA LMS 0.402062 0.684783
288 YSA 0.401961 0.707865
289 NJP 0.401786 0.833333
290 ODP 0.401786 0.802469
291 F2R 0.401786 0.785714
292 ZDA 0.4 0.802632
293 AMZ 0.4 0.802632
294 C2R 0.4 0.792208
295 IOT 0.4 0.797619
Similar Ligands (3D)
Ligand no: 1; Ligand: 7D5; Similar ligands found: 49
No: Ligand Similarity coefficient
1 IMP 0.9489
2 6MA 0.9370
3 4X2 0.9273
4 IRP 0.9261
5 FMP 0.9245
6 CMP 0.9238
7 DGP 0.9225
8 5GP 0.9218
9 8OP 0.9179
10 DG 0.9173
11 TMP 0.9156
12 XMP 0.9134
13 G 0.9128
14 UMP 0.9123
15 G7M 0.9109
16 UFP 0.9094
17 IMU 0.9069
18 6OG 0.9063
19 FNU 0.9062
20 DU 0.9028
21 EO7 0.8965
22 U5P 0.8963
23 PFU 0.8961
24 8OG 0.8955
25 5IU 0.8902
26 T3S 0.8901
27 6SW 0.8896
28 TKW 0.8889
29 NIA 0.8881
30 U 0.8861
31 6CG 0.8848
32 9L3 0.8809
33 5FU 0.8785
34 NUP 0.8768
35 5CM 0.8765
36 BRU 0.8751
37 NCN 0.8746
38 7CH 0.8744
39 5BU 0.8730
40 5HU 0.8729
41 NMN 0.8726
42 2DT 0.8714
43 16B 0.8712
44 CNU 0.8637
45 QBT 0.8624
46 MZP 0.8618
47 CAR 0.8608
48 MTE 0.8575
49 IGP 0.8544
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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