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 1256 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 1068 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 922 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: 259
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 AV2 0.630952 0.855263
10 5FA 0.62963 0.905405
11 AQP 0.62963 0.905405
12 7D7 0.626866 0.830986
13 A2D 0.623377 0.88
14 B4P 0.620253 0.88
15 AP5 0.620253 0.88
16 DAT 0.617284 0.893333
17 AN2 0.6125 0.893333
18 BA3 0.607595 0.88
19 ACQ 0.607143 0.881579
20 M33 0.585366 0.868421
21 A 0.584416 0.878378
22 AMP 0.584416 0.878378
23 ACP 0.578313 0.881579
24 AR6 0.571429 0.88
25 APR 0.571429 0.88
26 ANP 0.569767 0.881579
27 TAT 0.569767 0.87013
28 3AT 0.569767 0.905405
29 A3P 0.567901 0.90411
30 SAP 0.564706 0.858974
31 AD9 0.564706 0.881579
32 AGS 0.564706 0.858974
33 BEF ADP 0.559524 0.8
34 ADP BEF 0.559524 0.8
35 APC 0.552941 0.894737
36 DTP 0.551724 0.893333
37 3AM 0.551282 0.890411
38 AMP MG 0.55 0.807692
39 A2P 0.548781 0.890411
40 ADX 0.547619 0.795181
41 CA0 0.547619 0.857143
42 ADP MG 0.547619 0.820513
43 PPS 0.545455 0.817073
44 A2R 0.544444 0.893333
45 ABM 0.54321 0.831169
46 50T 0.541176 0.868421
47 ATF 0.539326 0.87013
48 A22 0.538462 0.893333
49 2AM 0.538462 0.90411
50 PRX 0.534884 0.810127
51 25L 0.53125 0.893333
52 A12 0.53012 0.894737
53 AP2 0.53012 0.894737
54 ADP PO3 0.528736 0.853333
55 5AL 0.52809 0.844156
56 ADQ 0.526882 0.881579
57 A1R 0.526882 0.871795
58 ATP MG 0.522727 0.820513
59 12D 0.519608 0.755814
60 OVE 0.518519 0.868421
61 SRA 0.518519 0.833333
62 DDS 0.516854 0.891892
63 SRP 0.516484 0.846154
64 NA7 0.515789 0.894737
65 AU1 0.511628 0.881579
66 ADN 0.506849 0.783784
67 XYA 0.506849 0.783784
68 RAB 0.506849 0.783784
69 V3L 0.5 0.88
70 OAD 0.5 0.857143
71 25A 0.5 0.88
72 8QN 0.5 0.844156
73 128 0.495238 0.747126
74 AMO 0.494737 0.846154
75 ADV 0.494382 0.87013
76 RBY 0.494382 0.87013
77 D5M 0.493976 0.866667
78 DA 0.493976 0.866667
79 3OD 0.489796 0.857143
80 BIS 0.489796 0.848101
81 00A 0.489583 0.802469
82 AHX 0.489583 0.8375
83 MAP 0.489362 0.858974
84 GGZ 0.489362 0.771084
85 ADP ALF 0.48913 0.790123
86 ALF ADP 0.48913 0.790123
87 G5P 0.485437 0.8375
88 5SV 0.484211 0.792683
89 OOB 0.484211 0.844156
90 ANP MG 0.483871 0.8125
91 VO4 ADP 0.483871 0.844156
92 ADP VO4 0.483871 0.844156
93 GAP 0.483516 0.833333
94 SON 0.482759 0.87013
95 LAD 0.479592 0.82716
96 PAJ 0.479167 0.82716
97 4AD 0.479167 0.835443
98 G3A 0.475728 0.8375
99 FYA 0.474747 0.820513
100 NB8 0.474747 0.814815
101 PTJ 0.474747 0.814815
102 TXA 0.474747 0.846154
103 ME8 0.474747 0.764706
104 DLL 0.474227 0.844156
105 5N5 0.473684 0.76
106 48N 0.471698 0.814815
107 ADP BMA 0.469388 0.857143
108 PO4 PO4 A A A A PO4 0.469388 0.84
109 3UK 0.469388 0.833333
110 A4D 0.467532 0.76
111 5CD 0.467532 0.723684
112 PR8 0.464646 0.817073
113 WAQ 0.464646 0.825
114 101 0.464286 0.891892
115 6AD 0.462366 0.82716
116 ATP A A A 0.460784 0.842105
117 FA5 0.460784 0.822785
118 YAP 0.460784 0.8125
119 1ZZ 0.46 0.785714
120 A3G 0.458824 0.74359
121 DAL AMP 0.458333 0.820513
122 AFH 0.457143 0.82716
123 SO8 0.456522 0.734177
124 XAH 0.456311 0.807229
125 2VA 0.455556 0.74359
126 TM1 0.455446 0.744186
127 A A A 0.454545 0.844156
128 NAX 0.453704 0.795181
129 UP5 0.453704 0.835443
130 GTA 0.45283 0.807229
131 ZAS 0.452381 0.691358
132 QQY 0.452381 0.782051
133 ACK 0.452381 0.824324
134 9SN 0.45098 0.792683
135 EP4 0.45 0.679012
136 A A 0.45 0.855263
137 A3S 0.449438 0.753247
138 3L1 0.448718 0.786667
139 3D1 0.448718 0.786667
140 3AD 0.448718 0.77027
141 NPW 0.446429 0.807229
142 4TC 0.445455 0.814815
143 ITT 0.444444 0.853333
144 DTA 0.444444 0.730769
145 M2T 0.444444 0.662651
146 NZQ 0.442478 0.82716
147 AOC 0.44186 0.74026
148 A4P 0.441441 0.790698
149 APU 0.441441 0.858974
150 VRT 0.44086 0.716049
151 QQX 0.440476 0.772152
152 DND 0.440367 0.846154
153 NXX 0.440367 0.846154
154 NAI 0.440367 0.825
155 TXD 0.440367 0.825
156 6V0 0.440367 0.814815
157 5AD 0.44 0.666667
158 A3T 0.43956 0.763158
159 5X8 0.43956 0.6875
160 MTA 0.439024 0.696203
161 ODP 0.438596 0.82716
162 5AS 0.438202 0.730337
163 4UV 0.438095 0.8125
164 J7V 0.438017 0.761364
165 AS 0.436782 0.822785
166 TXE 0.436364 0.825
167 OMR 0.436364 0.797619
168 AHZ 0.435185 0.744186
169 LAQ 0.435185 0.785714
170 0WD 0.434783 0.8375
171 T5A 0.433628 0.788235
172 139 0.433628 0.839506
173 NDP 0.433628 0.8375
174 ADJ 0.433628 0.797619
175 AP0 0.432432 0.814815
176 DCA 0.432203 0.793103
177 ETB 0.432203 0.781609
178 YLP 0.431193 0.788235
179 6RE 0.430233 0.707317
180 ZDA 0.430108 0.828947
181 4UU 0.429907 0.8125
182 7MD 0.429907 0.807229
183 AR6 AR6 0.429907 0.831169
184 ANZ 0.429907 0.768293
185 TXP 0.429825 0.8375
186 3DH 0.428571 0.696203
187 4UW 0.427273 0.783133
188 MYR AMP 0.427184 0.764706
189 NJP 0.426087 0.858974
190 NEC 0.425287 0.692308
191 0T1 0.425 0.793103
192 COA 0.425 0.793103
193 TYM 0.423423 0.822785
194 COD 0.422414 0.781609
195 XNP 0.422414 0.817073
196 NAD 0.422414 0.844156
197 J7C 0.420455 0.716049
198 YLB 0.419643 0.788235
199 UPA 0.419643 0.848101
200 YLC 0.419643 0.807229
201 103 0.418605 0.802632
202 Y3J 0.417722 0.649351
203 7DD 0.417582 0.891892
204 JB6 0.417476 0.802469
205 CNA 0.417391 0.846154
206 PUA 0.416667 0.85
207 S4M 0.41573 0.640449
208 CC5 0.415584 0.733333
209 A3D 0.415254 0.833333
210 TYR AMP 0.415094 0.8
211 30N 0.414634 0.726316
212 COS 0.414634 0.775281
213 AMX 0.414634 0.802326
214 CAO 0.414634 0.766667
215 TSB 0.414141 0.747126
216 A5A 0.412371 0.735632
217 SCO 0.41129 0.793103
218 CMX 0.41129 0.793103
219 AMP DBH 0.411215 0.810127
220 MAO 0.411111 0.709302
221 LA8 ALF 3PG 0.410714 0.761905
222 ALF ADP 3PG 0.410714 0.761905
223 G5A 0.410526 0.730337
224 NAQ 0.409836 0.792683
225 DSH 0.409091 0.695122
226 YLA 0.408696 0.788235
227 SFG 0.408602 0.696203
228 SSA 0.408163 0.75
229 FCX 0.408 0.766667
230 FAM 0.408 0.775281
231 ACO 0.408 0.766667
232 7MC 0.40708 0.788235
233 NAP 0.406504 0.857143
234 SAM 0.40625 0.643678
235 NMX 0.40625 0.734043
236 LPA AMP 0.405405 0.764706
237 ZZB 0.405172 0.764706
238 AYB 0.405172 0.77907
239 HAX 0.404762 0.775281
240 A3N 0.404494 0.730769
241 54H 0.40404 0.719101
242 VMS 0.40404 0.719101
243 A U 0.403509 0.8125
244 1DG 0.403226 0.8375
245 TAP 0.403226 0.825
246 DG1 0.403226 0.8375
247 NAE 0.401639 0.8125
248 FYN 0.401575 0.793103
249 3KK 0.401575 0.775281
250 IOT 0.4 0.8
251 GJV 0.4 0.698795
252 D3Y 0.4 0.734177
253 EAD 0.4 0.795181
254 NVA 2AD 0.4 0.7125
255 NA0 0.4 0.846154
256 5CA 0.4 0.75
257 53H 0.4 0.711111
258 TAD 0.4 0.82716
259 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: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
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