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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 1443 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 1205 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 1039 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: 7D5; Similar ligands found: 273
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 A 0.691176 0.902778
6 AMP 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 A2D 0.594595 0.853333
12 ABM 0.594595 0.853333
13 ADP 0.592105 0.878378
14 2AM 0.591549 0.902778
15 AN2 0.584416 0.866667
16 DA 0.581081 0.890411
17 D5M 0.581081 0.890411
18 V3L 0.580247 0.878378
19 AP2 0.578947 0.868421
20 BA3 0.578947 0.853333
21 A12 0.578947 0.868421
22 PAP 0.575 0.890411
23 AP5 0.571429 0.853333
24 B4P 0.571429 0.853333
25 HEJ 0.56962 0.878378
26 ATP 0.56962 0.878378
27 SRA 0.567568 0.855263
28 OVE 0.567568 0.866667
29 AT4 0.564103 0.844156
30 5FA 0.5625 0.878378
31 APC 0.5625 0.868421
32 AQP 0.5625 0.878378
33 ACQ 0.560976 0.855263
34 XYA 0.560606 0.780822
35 RAB 0.560606 0.780822
36 ADN 0.560606 0.780822
37 AU1 0.556962 0.855263
38 M33 0.556962 0.842105
39 CA0 0.556962 0.831169
40 ADX 0.556962 0.771084
41 ATR 0.555556 0.876712
42 PPS 0.554217 0.792683
43 50T 0.55 0.866667
44 ACP 0.55 0.855263
45 AR6 0.54321 0.853333
46 PRX 0.54321 0.831169
47 APR 0.54321 0.853333
48 T99 0.542169 0.844156
49 TAT 0.542169 0.844156
50 6YZ 0.541176 0.855263
51 25A 0.54023 0.878378
52 AGS 0.536585 0.833333
53 AD9 0.536585 0.855263
54 RBY 0.536585 0.844156
55 ADP PO3 0.536585 0.851351
56 ADV 0.536585 0.844156
57 SAP 0.536585 0.833333
58 5AL 0.535714 0.842105
59 AV2 0.529412 0.828947
60 SON 0.525 0.868421
61 ANP 0.52381 0.855263
62 SRP 0.523256 0.844156
63 5N5 0.521739 0.756757
64 A2R 0.517241 0.866667
65 5CD 0.514286 0.743243
66 A4D 0.514286 0.756757
67 LMS 0.513158 0.75
68 DAT 0.512195 0.866667
69 ATF 0.511628 0.844156
70 A22 0.511364 0.866667
71 DTA 0.506849 0.75
72 101 0.506494 0.916667
73 GAP 0.505882 0.831169
74 3AT 0.505882 0.878378
75 8QN 0.505618 0.842105
76 TM1 0.505376 0.741176
77 ADQ 0.5 0.855263
78 MTA 0.5 0.714286
79 AMO 0.5 0.820513
80 A1R 0.5 0.846154
81 A3G 0.5 0.74026
82 PTJ 0.494624 0.8125
83 AHX 0.494505 0.8125
84 MAP 0.494382 0.833333
85 GGZ 0.494382 0.746988
86 ALF ADP 0.494253 0.7875
87 ADP ALF 0.494253 0.7875
88 2VA 0.493976 0.74026
89 5X8 0.493976 0.705128
90 QQY 0.493506 0.802632
91 ACK 0.493506 0.847222
92 EP4 0.493151 0.696203
93 3L1 0.492958 0.783784
94 3AD 0.492958 0.791667
95 3D1 0.492958 0.783784
96 ANZ 0.489796 0.7875
97 NA7 0.48913 0.868421
98 OOB 0.488889 0.842105
99 9ZD 0.488889 0.822785
100 9ZA 0.488889 0.822785
101 5SV 0.488889 0.8125
102 VO4 ADP 0.488636 0.842105
103 ADP VO4 0.488636 0.842105
104 DTP 0.488372 0.866667
105 A3S 0.487805 0.75
106 3DH 0.486842 0.714286
107 M2T 0.486486 0.679012
108 5AD 0.485294 0.684932
109 LAD 0.483871 0.825
110 B5V 0.483871 0.820513
111 A3R 0.483516 0.846154
112 PAJ 0.483516 0.802469
113 4AD 0.483516 0.810127
114 AOC 0.481013 0.76
115 QQX 0.480519 0.792208
116 NB8 0.478723 0.790123
117 TXA 0.478723 0.820513
118 ME8 0.478723 0.761905
119 FYA 0.478723 0.842105
120 00A 0.478261 0.8
121 DLL 0.478261 0.842105
122 DAL AMP 0.477778 0.818182
123 SO8 0.476744 0.730769
124 VRT 0.476744 0.7125
125 A3T 0.47619 0.76
126 5AS 0.47561 0.727273
127 AS 0.475 0.844156
128 ZAS 0.474359 0.708861
129 25L 0.473684 0.866667
130 OAD 0.473118 0.831169
131 3UK 0.473118 0.831169
132 9X8 0.473118 0.810127
133 ADP BMA 0.473118 0.831169
134 A A A 0.473118 0.842105
135 PO4 PO4 A A A A PO4 0.473118 0.837838
136 6RE 0.468354 0.725
137 WAQ 0.468085 0.822785
138 PR8 0.468085 0.814815
139 A A 0.468085 0.878378
140 NVA 2AD 0.465116 0.703704
141 YAP 0.463918 0.810127
142 ATP A A A 0.463918 0.84
143 FA5 0.463918 0.820513
144 1ZZ 0.463158 0.783133
145 BIS 0.463158 0.822785
146 3OD 0.463158 0.831169
147 DSH 0.4625 0.7125
148 XAH 0.459184 0.804878
149 Y3J 0.458333 0.666667
150 CC5 0.457143 0.753425
151 J7C 0.45679 0.734177
152 103 0.455696 0.824324
153 DDS 0.454545 0.864865
154 9SN 0.453608 0.790123
155 8BR 0.451219 0.844156
156 S4M 0.451219 0.655172
157 G3A 0.45 0.8125
158 B5M 0.44898 0.810127
159 B5Y 0.44898 0.810127
160 JB6 0.447917 0.8
161 48N 0.446602 0.790123
162 MAO 0.445783 0.72619
163 TSB 0.445652 0.724138
164 G5P 0.445545 0.8125
165 7MD 0.445545 0.783133
166 A5A 0.444444 0.732558
167 NEC 0.444444 0.688312
168 APU 0.443396 0.857143
169 MYR AMP 0.443299 0.761905
170 G5A 0.443182 0.727273
171 SAH 0.443182 0.708861
172 SFG 0.44186 0.714286
173 38Y 0.440367 0.77381
174 4UV 0.44 0.810127
175 SSA 0.43956 0.727273
176 A3N 0.439024 0.727273
177 IMO 0.439024 0.837838
178 12D 0.436893 0.732558
179 LAQ 0.436893 0.783133
180 AHZ 0.436893 0.741176
181 A7D 0.435294 0.763158
182 54H 0.434783 0.715909
183 VMS 0.434783 0.715909
184 GJV 0.433735 0.716049
185 YLP 0.432692 0.785714
186 WMP 0.432432 0.828947
187 SA8 0.431818 0.674699
188 A5D 0.431818 0.75
189 AR6 AR6 0.431373 0.828947
190 AFH 0.431373 0.802469
191 4UU 0.431373 0.810127
192 GA7 0.431373 0.844156
193 ARG AMP 0.431373 0.77381
194 ZZB 0.431193 0.783133
195 53H 0.430108 0.707865
196 5CA 0.430108 0.727273
197 D3Y 0.430108 0.730769
198 4UW 0.428571 0.780488
199 NAX 0.428571 0.771084
200 128 0.428571 0.724138
201 GTA 0.427184 0.783133
202 TAD 0.427184 0.802469
203 DQV 0.427184 0.842105
204 SAI 0.426966 0.7
205 AFX 0.426667 0.64557
206 TYR AMP 0.425743 0.7875
207 AMP DBH 0.425743 0.807692
208 TYM 0.424528 0.820513
209 SMM 0.423913 0.655172
210 3NZ 0.42268 0.725
211 SAM 0.422222 0.658824
212 NPW 0.422018 0.783133
213 DSZ 0.421053 0.707865
214 5F1 0.421053 0.72
215 LSS 0.421053 0.692308
216 YLB 0.420561 0.785714
217 7MC 0.420561 0.764706
218 4TC 0.420561 0.790123
219 UPA 0.420561 0.822785
220 YLC 0.420561 0.804878
221 52H 0.419355 0.707865
222 LPA AMP 0.419048 0.761905
223 NZQ 0.418182 0.802469
224 EEM 0.417582 0.658824
225 PUA 0.417391 0.825
226 A U 0.416667 0.810127
227 DND 0.415094 0.820513
228 TXD 0.415094 0.8
229 NXX 0.415094 0.820513
230 6V0 0.415094 0.790123
231 NAI 0.415094 0.8
232 UP5 0.415094 0.810127
233 8X1 0.414894 0.741573
234 MHZ 0.413793 0.686047
235 71V 0.411765 0.822785
236 TXE 0.411215 0.8
237 OMR 0.411215 0.77381
238 G A A A 0.410714 0.8125
239 XNP 0.410714 0.792683
240 0WD 0.410714 0.8125
241 139 0.409091 0.814815
242 YLA 0.409091 0.785714
243 ADJ 0.409091 0.77381
244 NDP 0.409091 0.8125
245 S7M 0.408602 0.658824
246 P5A 0.408163 0.714286
247 KAA 0.408163 0.722222
248 GSU 0.408163 0.707865
249 ARJ 0.407895 0.712329
250 AP0 0.407407 0.790123
251 NSS 0.40625 0.707865
252 NOC 0.405405 0.702703
253 TXP 0.405405 0.8125
254 AYB 0.405405 0.776471
255 AAM 0.404762 0.902778
256 9K8 0.40404 0.648936
257 A4P 0.40367 0.767442
258 80F 0.403509 0.744186
259 PAX 0.403361 0.795181
260 SP1 0.402439 0.805195
261 RP1 0.402439 0.805195
262 AAT 0.402174 0.695122
263 NVA LMS 0.402062 0.684783
264 YSA 0.401961 0.707865
265 NJP 0.401786 0.833333
266 F2R 0.401786 0.785714
267 ODP 0.401786 0.802469
268 C2R 0.4 0.792208
269 AMZ 0.4 0.802632
270 A C A C 0.4 0.790123
271 IOT 0.4 0.797619
272 APC G U 0.4 0.8
273 ZDA 0.4 0.802632
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: 41
This union binding pocket(no: 1) in the query (biounit: 5tk8.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 5UGW GSH None
2 4WG0 CHD None
3 1Y4C GLC GLC 1.03093
4 2O5L MNR 1.96078
5 1OAA OAA 2.06186
6 2QES ADE 2.06186
7 2GMH FAD 2.57732
8 4RW3 PLM 2.57732
9 4XCP PLM 3.52941
10 3BPX SAL 4.05405
11 1S7G APR 4.12371
12 1BZL GCG 4.63918
13 2BHW NEX 4.63918
14 2C0U FAD NBT 4.63918
15 1SQL GUN 4.79452
16 4J56 FAD 5.15464
17 4JNE ATP 5.6701
18 1XF1 CIT 5.6701
19 5LX9 OLB 6.18557
20 1BRW URA 6.18557
21 5CKS GAL 6.18557
22 4TV1 36M 6.18557
23 4IFP MAL 6.70103
24 5LWY OLB 6.72269
25 3QDW NDG 7.69231
26 4NJS G08 8.08081
27 1T0S BML 8.13953
28 5BJZ MAL 8.76289
29 4O4K 2PK 8.76289
30 2YFB SIN 8.91473
31 3V49 PK0 9.27835
32 1JGS SAL 9.42029
33 4WGF HX2 9.79381
34 4FGC PQ0 10.303
35 3NB0 G6P 10.3093
36 4XR8 MAL 11.9205
37 1ZOY UQ1 12.8866
38 4MG9 27K 14.9485
39 3EYK EYK 15.4639
40 5C1M OLC 22.4
41 2PAR TMP 46.9072
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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