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 1579 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 1312 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 1130 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
Ligand no: 1; Ligand: 7D3; Similar ligands found: 291
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 ATP 0.6375 0.905405
9 HEJ 0.6375 0.905405
10 AV2 0.630952 0.855263
11 5FA 0.62963 0.905405
12 AQP 0.62963 0.905405
13 7D7 0.626866 0.830986
14 A2D 0.623377 0.88
15 B4P 0.620253 0.88
16 AP5 0.620253 0.88
17 DAT 0.617284 0.893333
18 AN2 0.6125 0.893333
19 BA3 0.607595 0.88
20 ACQ 0.607143 0.881579
21 6YZ 0.604651 0.881579
22 AT4 0.592593 0.87013
23 M33 0.585366 0.868421
24 AMP 0.584416 0.878378
25 A 0.584416 0.878378
26 ACP 0.578313 0.881579
27 APR 0.571429 0.88
28 AR6 0.571429 0.88
29 ANP 0.569767 0.881579
30 TAT 0.569767 0.87013
31 T99 0.569767 0.87013
32 3AT 0.569767 0.905405
33 A3P 0.567901 0.90411
34 SAP 0.564706 0.858974
35 AGS 0.564706 0.858974
36 AD9 0.564706 0.881579
37 ADP MG 0.554217 0.853333
38 APC 0.552941 0.894737
39 DTP 0.551724 0.893333
40 3AM 0.551282 0.890411
41 A2P 0.548781 0.890411
42 CA0 0.547619 0.857143
43 ADX 0.547619 0.795181
44 PPS 0.545455 0.817073
45 A2R 0.544444 0.893333
46 HQG 0.544444 0.893333
47 45A 0.54321 0.831169
48 ABM 0.54321 0.831169
49 KG4 0.541176 0.857143
50 50T 0.541176 0.868421
51 ATF 0.539326 0.87013
52 A22 0.538462 0.893333
53 2AM 0.538462 0.90411
54 PRX 0.534884 0.810127
55 25L 0.53125 0.893333
56 A12 0.53012 0.894737
57 AP2 0.53012 0.894737
58 ATP MG 0.528736 0.853333
59 ADP PO3 0.528736 0.853333
60 APC MG 0.528736 0.855263
61 5AL 0.52809 0.844156
62 A1R 0.526882 0.871795
63 ADQ 0.526882 0.881579
64 12D 0.519608 0.755814
65 OVE 0.518519 0.868421
66 SRA 0.518519 0.833333
67 DDS 0.516854 0.891892
68 SRP 0.516484 0.846154
69 NA7 0.515789 0.894737
70 AU1 0.511628 0.881579
71 8LE 0.511111 0.8125
72 A3R 0.510638 0.871795
73 RAB 0.506849 0.783784
74 ADN 0.506849 0.783784
75 XYA 0.506849 0.783784
76 OZV 0.5 0.88
77 OAD 0.5 0.857143
78 25A 0.5 0.88
79 9X8 0.5 0.835443
80 8QN 0.5 0.844156
81 V3L 0.5 0.88
82 8LH 0.5 0.846154
83 128 0.495238 0.747126
84 AMO 0.494737 0.846154
85 RBY 0.494382 0.87013
86 ADV 0.494382 0.87013
87 DA 0.493976 0.866667
88 D5M 0.493976 0.866667
89 BIS 0.489796 0.848101
90 3OD 0.489796 0.857143
91 AHX 0.489583 0.8375
92 00A 0.489583 0.802469
93 GGZ 0.489362 0.771084
94 8LQ 0.489362 0.822785
95 MAP 0.489362 0.858974
96 ALF ADP 0.48913 0.790123
97 ADP ALF 0.48913 0.790123
98 G5P 0.485437 0.8375
99 5SV 0.484211 0.792683
100 OOB 0.484211 0.844156
101 ADP VO4 0.483871 0.844156
102 VO4 ADP 0.483871 0.844156
103 GAP 0.483516 0.833333
104 SON 0.482759 0.87013
105 LAD 0.479592 0.82716
106 B5V 0.479592 0.822785
107 PAJ 0.479167 0.82716
108 4AD 0.479167 0.835443
109 G3A 0.475728 0.8375
110 TXA 0.474747 0.846154
111 FYA 0.474747 0.820513
112 NB8 0.474747 0.814815
113 PTJ 0.474747 0.814815
114 ME8 0.474747 0.764706
115 DLL 0.474227 0.844156
116 5N5 0.473684 0.76
117 48N 0.471698 0.814815
118 LQJ 0.470588 0.88
119 LMS 0.46988 0.752941
120 3UK 0.469388 0.833333
121 ADP BMA 0.469388 0.857143
122 PO4 PO4 A A A A PO4 0.469388 0.84
123 A4D 0.467532 0.76
124 5CD 0.467532 0.723684
125 J4G 0.464646 0.835443
126 WAQ 0.464646 0.825
127 PR8 0.464646 0.817073
128 101 0.464286 0.891892
129 6AD 0.462366 0.82716
130 ATP A 0.460784 0.842105
131 ATP A A A 0.460784 0.842105
132 YAP 0.460784 0.8125
133 FA5 0.460784 0.822785
134 1ZZ 0.46 0.785714
135 A3G 0.458824 0.74359
136 DAL AMP 0.458333 0.820513
137 AFH 0.457143 0.82716
138 SO8 0.456522 0.734177
139 XAH 0.456311 0.807229
140 2VA 0.455556 0.74359
141 TM1 0.455446 0.744186
142 A A A 0.454545 0.844156
143 UP5 0.453704 0.835443
144 NAX 0.453704 0.795181
145 9ZA 0.453608 0.825
146 9ZD 0.453608 0.825
147 GTA 0.45283 0.807229
148 DQV 0.45283 0.868421
149 QQY 0.452381 0.782051
150 ACK 0.452381 0.824324
151 ZAS 0.452381 0.691358
152 9SN 0.45098 0.792683
153 EP4 0.45 0.679012
154 A A 0.45 0.855263
155 A3S 0.449438 0.753247
156 3D1 0.448718 0.786667
157 3L1 0.448718 0.786667
158 3AD 0.448718 0.77027
159 B5M 0.446602 0.8125
160 B5Y 0.446602 0.8125
161 NPW 0.446429 0.807229
162 NVA 2AD 0.445652 0.707317
163 4TC 0.445455 0.814815
164 ITT 0.444444 0.853333
165 M2T 0.444444 0.662651
166 DTA 0.444444 0.730769
167 NZQ 0.442478 0.82716
168 AOC 0.44186 0.74026
169 APU 0.441441 0.858974
170 A4P 0.441441 0.790698
171 JSQ 0.44086 0.858974
172 HFD 0.44086 0.858974
173 VRT 0.44086 0.716049
174 QQX 0.440476 0.772152
175 TXD 0.440367 0.825
176 DND 0.440367 0.846154
177 6V0 0.440367 0.814815
178 NXX 0.440367 0.846154
179 NAI 0.440367 0.825
180 5AD 0.44 0.666667
181 5X8 0.43956 0.6875
182 A3T 0.43956 0.763158
183 MTA 0.439024 0.696203
184 ODP 0.438596 0.82716
185 F2R 0.438596 0.809524
186 5AS 0.438202 0.730337
187 4UV 0.438095 0.8125
188 J7V 0.438017 0.761364
189 AS 0.436782 0.822785
190 OMR 0.436364 0.797619
191 TXE 0.436364 0.825
192 AHZ 0.435185 0.744186
193 LAQ 0.435185 0.785714
194 0WD 0.434783 0.8375
195 T5A 0.433628 0.788235
196 139 0.433628 0.839506
197 NDP 0.433628 0.8375
198 ADJ 0.433628 0.797619
199 NO7 0.43299 0.87013
200 AP0 0.432432 0.814815
201 DCA 0.432203 0.793103
202 ETB 0.432203 0.781609
203 YLP 0.431193 0.788235
204 6RE 0.430233 0.707317
205 ZDA 0.430108 0.828947
206 4UU 0.429907 0.8125
207 AR6 AR6 0.429907 0.831169
208 ANZ 0.429907 0.768293
209 GA7 0.429907 0.846154
210 7MD 0.429907 0.807229
211 TXP 0.429825 0.8375
212 3DH 0.428571 0.696203
213 80F 0.42735 0.767442
214 4UW 0.427273 0.783133
215 MYR AMP 0.427184 0.764706
216 HDV 0.427083 0.857143
217 NJP 0.426087 0.858974
218 NEC 0.425287 0.692308
219 0T1 0.425 0.793103
220 COA 0.425 0.793103
221 H1Q 0.423913 0.818182
222 TYM 0.423423 0.822785
223 XNP 0.422414 0.817073
224 NAD 0.422414 0.844156
225 COD 0.422414 0.781609
226 J7C 0.420455 0.716049
227 YLB 0.419643 0.788235
228 UPA 0.419643 0.848101
229 YLC 0.419643 0.807229
230 103 0.418605 0.802632
231 Y3J 0.417722 0.649351
232 7DD 0.417582 0.891892
233 JB6 0.417476 0.802469
234 CNA 0.417391 0.846154
235 ARG AMP 0.416667 0.776471
236 PUA 0.416667 0.85
237 S4M 0.41573 0.640449
238 CC5 0.415584 0.733333
239 A3D 0.415254 0.833333
240 CAO 0.414634 0.766667
241 COS 0.414634 0.775281
242 AMX 0.414634 0.802326
243 30N 0.414634 0.726316
244 TSB 0.414141 0.747126
245 9BG 0.413793 0.860759
246 A5A 0.412371 0.735632
247 CMX 0.41129 0.793103
248 SCO 0.41129 0.793103
249 AMP DBH 0.411215 0.810127
250 TYR AMP 0.411215 0.790123
251 MAO 0.411111 0.709302
252 G5A 0.410526 0.730337
253 NAQ 0.409836 0.792683
254 N5O 0.409091 0.708861
255 DSH 0.409091 0.695122
256 YLA 0.408696 0.788235
257 SFG 0.408602 0.696203
258 SSA 0.408163 0.75
259 ACO 0.408 0.766667
260 FAM 0.408 0.775281
261 FCX 0.408 0.766667
262 7MC 0.40708 0.788235
263 NAP 0.406504 0.857143
264 NMX 0.40625 0.734043
265 SAM 0.40625 0.643678
266 LPA AMP 0.405405 0.764706
267 AYB 0.405172 0.77907
268 ZZB 0.405172 0.764706
269 HAX 0.404762 0.775281
270 A3N 0.404494 0.730769
271 54H 0.40404 0.719101
272 VMS 0.40404 0.719101
273 A U 0.403509 0.8125
274 DG1 0.403226 0.8375
275 1DG 0.403226 0.8375
276 TAP 0.403226 0.825
277 NAE 0.401639 0.8125
278 FYN 0.401575 0.793103
279 3KK 0.401575 0.775281
280 7L1 0.4 0.766667
281 NA0 0.4 0.846154
282 TAD 0.4 0.82716
283 53H 0.4 0.711111
284 5CA 0.4 0.75
285 KGJ 0.4 0.726316
286 IOT 0.4 0.8
287 GJV 0.4 0.698795
288 EAD 0.4 0.795181
289 N5A 0.4 0.683544
290 D3Y 0.4 0.734177
291 SA8 0.4 0.658824
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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