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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 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: 7D3; Similar ligands found: 271
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 AQP 0.62963 0.905405
12 5FA 0.62963 0.905405
13 7D7 0.626866 0.830986
14 A2D 0.623377 0.88
15 AP5 0.620253 0.88
16 B4P 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 T99 0.569767 0.87013
31 TAT 0.569767 0.87013
32 3AT 0.569767 0.905405
33 A3P 0.567901 0.90411
34 AGS 0.564706 0.858974
35 AD9 0.564706 0.881579
36 SAP 0.564706 0.858974
37 APC 0.552941 0.894737
38 DTP 0.551724 0.893333
39 3AM 0.551282 0.890411
40 A2P 0.548781 0.890411
41 ADX 0.547619 0.795181
42 CA0 0.547619 0.857143
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 2AM 0.538462 0.90411
49 A22 0.538462 0.893333
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 12D 0.519608 0.755814
59 SRA 0.518519 0.833333
60 OVE 0.518519 0.868421
61 DDS 0.516854 0.891892
62 SRP 0.516484 0.846154
63 NA7 0.515789 0.894737
64 AU1 0.511628 0.881579
65 A3R 0.510638 0.871795
66 XYA 0.506849 0.783784
67 ADN 0.506849 0.783784
68 RAB 0.506849 0.783784
69 25A 0.5 0.88
70 8QN 0.5 0.844156
71 V3L 0.5 0.88
72 9X8 0.5 0.835443
73 OAD 0.5 0.857143
74 128 0.495238 0.747126
75 AMO 0.494737 0.846154
76 ADV 0.494382 0.87013
77 RBY 0.494382 0.87013
78 DA 0.493976 0.866667
79 D5M 0.493976 0.866667
80 3OD 0.489796 0.857143
81 BIS 0.489796 0.848101
82 AHX 0.489583 0.8375
83 00A 0.489583 0.802469
84 GGZ 0.489362 0.771084
85 MAP 0.489362 0.858974
86 ALF ADP 0.48913 0.790123
87 ADP ALF 0.48913 0.790123
88 G5P 0.485437 0.8375
89 OOB 0.484211 0.844156
90 5SV 0.484211 0.792683
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 B5V 0.479592 0.822785
96 LAD 0.479592 0.82716
97 4AD 0.479167 0.835443
98 PAJ 0.479167 0.82716
99 G3A 0.475728 0.8375
100 ME8 0.474747 0.764706
101 PTJ 0.474747 0.814815
102 NB8 0.474747 0.814815
103 TXA 0.474747 0.846154
104 FYA 0.474747 0.820513
105 DLL 0.474227 0.844156
106 5N5 0.473684 0.76
107 48N 0.471698 0.814815
108 LMS 0.46988 0.752941
109 PO4 PO4 A A A A PO4 0.469388 0.84
110 ADP BMA 0.469388 0.857143
111 3UK 0.469388 0.833333
112 A4D 0.467532 0.76
113 5CD 0.467532 0.723684
114 PR8 0.464646 0.817073
115 WAQ 0.464646 0.825
116 101 0.464286 0.891892
117 6AD 0.462366 0.82716
118 FA5 0.460784 0.822785
119 YAP 0.460784 0.8125
120 ATP A A A 0.460784 0.842105
121 1ZZ 0.46 0.785714
122 A3G 0.458824 0.74359
123 DAL AMP 0.458333 0.820513
124 AFH 0.457143 0.82716
125 SO8 0.456522 0.734177
126 XAH 0.456311 0.807229
127 2VA 0.455556 0.74359
128 TM1 0.455446 0.744186
129 A A A 0.454545 0.844156
130 UP5 0.453704 0.835443
131 NAX 0.453704 0.795181
132 9ZA 0.453608 0.825
133 9ZD 0.453608 0.825
134 DQV 0.45283 0.868421
135 GTA 0.45283 0.807229
136 QQY 0.452381 0.782051
137 ACK 0.452381 0.824324
138 ZAS 0.452381 0.691358
139 9SN 0.45098 0.792683
140 A A 0.45 0.855263
141 EP4 0.45 0.679012
142 A3S 0.449438 0.753247
143 3AD 0.448718 0.77027
144 3L1 0.448718 0.786667
145 3D1 0.448718 0.786667
146 B5Y 0.446602 0.8125
147 B5M 0.446602 0.8125
148 NPW 0.446429 0.807229
149 NVA 2AD 0.445652 0.707317
150 4TC 0.445455 0.814815
151 ITT 0.444444 0.853333
152 M2T 0.444444 0.662651
153 DTA 0.444444 0.730769
154 NZQ 0.442478 0.82716
155 AOC 0.44186 0.74026
156 A4P 0.441441 0.790698
157 APU 0.441441 0.858974
158 VRT 0.44086 0.716049
159 HFD 0.44086 0.858974
160 QQX 0.440476 0.772152
161 DND 0.440367 0.846154
162 TXD 0.440367 0.825
163 NXX 0.440367 0.846154
164 NAI 0.440367 0.825
165 6V0 0.440367 0.814815
166 5AD 0.44 0.666667
167 5X8 0.43956 0.6875
168 A3T 0.43956 0.763158
169 MTA 0.439024 0.696203
170 ODP 0.438596 0.82716
171 F2R 0.438596 0.809524
172 5AS 0.438202 0.730337
173 4UV 0.438095 0.8125
174 J7V 0.438017 0.761364
175 AS 0.436782 0.822785
176 OMR 0.436364 0.797619
177 TXE 0.436364 0.825
178 AHZ 0.435185 0.744186
179 LAQ 0.435185 0.785714
180 0WD 0.434783 0.8375
181 T5A 0.433628 0.788235
182 NDP 0.433628 0.8375
183 ADJ 0.433628 0.797619
184 139 0.433628 0.839506
185 AP0 0.432432 0.814815
186 DCA 0.432203 0.793103
187 ETB 0.432203 0.781609
188 YLP 0.431193 0.788235
189 6RE 0.430233 0.707317
190 ZDA 0.430108 0.828947
191 ANZ 0.429907 0.768293
192 4UU 0.429907 0.8125
193 7MD 0.429907 0.807229
194 GA7 0.429907 0.846154
195 AR6 AR6 0.429907 0.831169
196 TXP 0.429825 0.8375
197 3DH 0.428571 0.696203
198 80F 0.42735 0.767442
199 4UW 0.427273 0.783133
200 MYR AMP 0.427184 0.764706
201 HDV 0.427083 0.857143
202 NJP 0.426087 0.858974
203 NEC 0.425287 0.692308
204 COA 0.425 0.793103
205 0T1 0.425 0.793103
206 TYM 0.423423 0.822785
207 XNP 0.422414 0.817073
208 NAD 0.422414 0.844156
209 COD 0.422414 0.781609
210 J7C 0.420455 0.716049
211 YLB 0.419643 0.788235
212 UPA 0.419643 0.848101
213 YLC 0.419643 0.807229
214 103 0.418605 0.802632
215 Y3J 0.417722 0.649351
216 7DD 0.417582 0.891892
217 JB6 0.417476 0.802469
218 CNA 0.417391 0.846154
219 PUA 0.416667 0.85
220 ARG AMP 0.416667 0.776471
221 S4M 0.41573 0.640449
222 CC5 0.415584 0.733333
223 A3D 0.415254 0.833333
224 30N 0.414634 0.726316
225 AMX 0.414634 0.802326
226 CAO 0.414634 0.766667
227 COS 0.414634 0.775281
228 TSB 0.414141 0.747126
229 A5A 0.412371 0.735632
230 SCO 0.41129 0.793103
231 CMX 0.41129 0.793103
232 AMP DBH 0.411215 0.810127
233 TYR AMP 0.411215 0.790123
234 MAO 0.411111 0.709302
235 G5A 0.410526 0.730337
236 NAQ 0.409836 0.792683
237 DSH 0.409091 0.695122
238 YLA 0.408696 0.788235
239 SFG 0.408602 0.696203
240 SSA 0.408163 0.75
241 FCX 0.408 0.766667
242 ACO 0.408 0.766667
243 FAM 0.408 0.775281
244 7MC 0.40708 0.788235
245 NAP 0.406504 0.857143
246 NMX 0.40625 0.734043
247 SAM 0.40625 0.643678
248 LPA AMP 0.405405 0.764706
249 AYB 0.405172 0.77907
250 ZZB 0.405172 0.764706
251 HAX 0.404762 0.775281
252 A3N 0.404494 0.730769
253 54H 0.40404 0.719101
254 VMS 0.40404 0.719101
255 A U 0.403509 0.8125
256 1DG 0.403226 0.8375
257 TAP 0.403226 0.825
258 DG1 0.403226 0.8375
259 NAE 0.401639 0.8125
260 3KK 0.401575 0.775281
261 FYN 0.401575 0.793103
262 7L1 0.4 0.766667
263 GJV 0.4 0.698795
264 5CA 0.4 0.75
265 53H 0.4 0.711111
266 D3Y 0.4 0.734177
267 TAD 0.4 0.82716
268 SA8 0.4 0.658824
269 EAD 0.4 0.795181
270 IOT 0.4 0.8
271 NA0 0.4 0.846154
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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