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Receptor
PDB id Resolution Class Description Source Keywords
5TK7 1.9 Å NON-ENZYME: OTHER STRUCTURE OF THE HD-DOMAIN PHOSPHOHYDROLASE OXSA WITH OXETAN TRIPHOSPHATE BOUND BACILLUS MEGATERIUM PHOSPHOHYDROLASE 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
7D4 A:203;
Valid;
none;
submit data
491.182 C10 H16 N5 O12 P3 c1nc(...
MG A:202;
A:201;
Part of Protein;
Part of Protein;
none;
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: 7D4; Similar ligands found: 250
No: Ligand ECFP6 Tc MDL keys Tc
1 7D4 1 1
2 7D3 0.884058 1
3 7D5 0.782609 0.971831
4 ATP 0.730769 0.905405
5 HEJ 0.730769 0.905405
6 AQP 0.721519 0.905405
7 5FA 0.721519 0.905405
8 AP5 0.670886 0.88
9 B4P 0.670886 0.88
10 2A5 0.658537 0.906667
11 BA3 0.658228 0.88
12 3AT 0.654762 0.905405
13 ADP 0.65 0.905405
14 DTP 0.635294 0.893333
15 A2D 0.632911 0.88
16 6YZ 0.632184 0.881579
17 SAP 0.611765 0.858974
18 PAP 0.611765 0.917808
19 AGS 0.611765 0.858974
20 ATR 0.611765 0.90411
21 25L 0.606383 0.893333
22 AN2 0.60241 0.893333
23 ACQ 0.597701 0.881579
24 DDS 0.597701 0.891892
25 TAT 0.597701 0.87013
26 T99 0.597701 0.87013
27 7D7 0.591549 0.830986
28 AT4 0.583333 0.87013
29 APR 0.581395 0.88
30 AR6 0.581395 0.88
31 M33 0.576471 0.868421
32 AMP 0.575 0.878378
33 A 0.575 0.878378
34 AD9 0.574713 0.881579
35 ACP 0.569767 0.881579
36 AV2 0.566667 0.855263
37 ANP 0.561798 0.881579
38 A2R 0.554348 0.893333
39 DAT 0.551724 0.893333
40 A22 0.548387 0.893333
41 128 0.548077 0.747126
42 APC 0.545455 0.894737
43 A2P 0.541176 0.890411
44 A3P 0.541176 0.90411
45 CA0 0.54023 0.857143
46 ADX 0.54023 0.795181
47 A3R 0.536842 0.871795
48 A1R 0.536842 0.871795
49 ADQ 0.536842 0.881579
50 ABM 0.535714 0.831169
51 50T 0.534091 0.868421
52 ATF 0.532609 0.87013
53 PRX 0.52809 0.810127
54 NA7 0.525773 0.894737
55 3AM 0.52439 0.890411
56 G5P 0.524272 0.8375
57 AP2 0.523256 0.894737
58 A12 0.523256 0.894737
59 ITT 0.522727 0.853333
60 PPS 0.521739 0.817073
61 5AL 0.521739 0.844156
62 HFD 0.516484 0.858974
63 G3A 0.514563 0.8375
64 2AM 0.512195 0.90411
65 SRA 0.511905 0.833333
66 SRP 0.510638 0.846154
67 OAD 0.510204 0.857143
68 9X8 0.510204 0.835443
69 AU1 0.505618 0.881579
70 ADP PO3 0.505495 0.853333
71 3OD 0.5 0.857143
72 HDV 0.5 0.857143
73 25A 0.494845 0.88
74 8QN 0.494845 0.844156
75 V3L 0.494624 0.88
76 OVE 0.494118 0.868421
77 UP5 0.490741 0.835443
78 GTA 0.490566 0.807229
79 4AD 0.489796 0.835443
80 AMO 0.489796 0.846154
81 ADV 0.48913 0.87013
82 RBY 0.48913 0.87013
83 BIS 0.485149 0.848101
84 AHX 0.484848 0.8375
85 00A 0.484848 0.802469
86 MAP 0.484536 0.858974
87 48N 0.481481 0.814815
88 RAB 0.480519 0.783784
89 ADN 0.480519 0.783784
90 XYA 0.480519 0.783784
91 5SV 0.479592 0.792683
92 OOB 0.479592 0.844156
93 SON 0.477778 0.87013
94 A4P 0.477477 0.790698
95 LAD 0.475248 0.82716
96 B5V 0.475248 0.822785
97 PAJ 0.474747 0.82716
98 ZDA 0.473118 0.828947
99 12D 0.472222 0.755814
100 DA 0.471264 0.866667
101 D5M 0.471264 0.866667
102 FYA 0.470588 0.820513
103 ME8 0.470588 0.764706
104 PTJ 0.470588 0.814815
105 TXA 0.470588 0.846154
106 NB8 0.470588 0.814815
107 DLL 0.47 0.844156
108 GGZ 0.469388 0.771084
109 T5A 0.469027 0.788235
110 ALF ADP 0.46875 0.790123
111 ADP ALF 0.46875 0.790123
112 AFH 0.46729 0.82716
113 3UK 0.465347 0.833333
114 LMS 0.465116 0.752941
115 VO4 ADP 0.463918 0.844156
116 ADP VO4 0.463918 0.844156
117 NAX 0.463636 0.795181
118 GAP 0.463158 0.833333
119 DQV 0.462963 0.868421
120 PR8 0.460784 0.817073
121 WAQ 0.460784 0.825
122 YAP 0.457143 0.8125
123 FA5 0.457143 0.822785
124 1ZZ 0.456311 0.785714
125 NPW 0.45614 0.807229
126 AP0 0.455357 0.814815
127 DAL AMP 0.454545 0.820513
128 XAH 0.45283 0.807229
129 NZQ 0.452174 0.82716
130 ADP BMA 0.45098 0.857143
131 PO4 PO4 A A A A PO4 0.45098 0.84
132 NXX 0.45045 0.846154
133 NAI 0.45045 0.825
134 6V0 0.45045 0.814815
135 DND 0.45045 0.846154
136 TXD 0.45045 0.825
137 9ZA 0.45 0.825
138 9ZD 0.45 0.825
139 5N5 0.45 0.76
140 HF7 0.44898 0.881579
141 9SN 0.447619 0.792683
142 7DT 0.446809 0.891892
143 TXE 0.446429 0.825
144 OMR 0.446429 0.797619
145 0WD 0.444444 0.8375
146 A4D 0.444444 0.76
147 5CD 0.444444 0.723684
148 ADJ 0.443478 0.797619
149 139 0.443478 0.839506
150 NDP 0.443478 0.8375
151 ATP A A A 0.443396 0.842105
152 B5M 0.443396 0.8125
153 B5Y 0.443396 0.8125
154 101 0.443182 0.891892
155 4TC 0.442478 0.814815
156 NVA 2AD 0.442105 0.707317
157 TXP 0.439655 0.8375
158 CNA 0.439655 0.846154
159 AOC 0.438202 0.74026
160 A3G 0.438202 0.74359
161 SO8 0.4375 0.734177
162 80F 0.436975 0.767442
163 2VA 0.43617 0.74359
164 ODP 0.435897 0.82716
165 NJP 0.435897 0.858974
166 F2R 0.435897 0.809524
167 4UV 0.435185 0.8125
168 5AS 0.434783 0.730337
169 A A 0.432692 0.855263
170 AHZ 0.432432 0.744186
171 LAQ 0.432432 0.785714
172 XNP 0.432203 0.817073
173 ACK 0.431818 0.824324
174 QQY 0.431818 0.782051
175 A3S 0.430108 0.753247
176 RGT 0.429907 0.87013
177 DCA 0.429752 0.793103
178 ETB 0.429752 0.781609
179 EP4 0.428571 0.679012
180 YLP 0.428571 0.788235
181 6AD 0.428571 0.82716
182 4UU 0.427273 0.8125
183 7MD 0.427273 0.807229
184 GA7 0.427273 0.846154
185 3AD 0.426829 0.77027
186 3L1 0.426829 0.786667
187 3D1 0.426829 0.786667
188 PUA 0.42623 0.85
189 APU 0.426087 0.858974
190 4UW 0.424779 0.783133
191 TM1 0.424528 0.744186
192 DG1 0.424 0.8375
193 1DG 0.424 0.8375
194 DTA 0.423529 0.730769
195 M2T 0.423529 0.662651
196 A A A 0.423077 0.844156
197 0T1 0.422764 0.793103
198 COA 0.422764 0.793103
199 VRT 0.42268 0.716049
200 NEC 0.422222 0.692308
201 TYM 0.421053 0.822785
202 5X8 0.421053 0.6875
203 A3T 0.421053 0.763158
204 QQX 0.420455 0.772152
205 COD 0.420168 0.781609
206 GTP 0.42 0.835443
207 SSA 0.42 0.75
208 MTA 0.418605 0.696203
209 5AD 0.417722 0.666667
210 AS 0.417582 0.822785
211 YLC 0.417391 0.807229
212 YLB 0.417391 0.788235
213 UPA 0.417391 0.848101
214 ZAS 0.41573 0.691358
215 JB6 0.415094 0.802469
216 ARG AMP 0.414414 0.776471
217 AR6 AR6 0.414414 0.831169
218 ANZ 0.414414 0.768293
219 COS 0.412698 0.775281
220 CAO 0.412698 0.766667
221 AMX 0.412698 0.802326
222 30N 0.412698 0.726316
223 TSB 0.411765 0.747126
224 MYR AMP 0.411215 0.764706
225 6RE 0.411111 0.707317
226 A5A 0.41 0.735632
227 H6Y 0.41 0.857143
228 EAD 0.409449 0.795181
229 CMX 0.409449 0.793103
230 SCO 0.409449 0.793103
231 3DH 0.409091 0.696203
232 TYR AMP 0.409091 0.790123
233 NAD 0.408333 0.844156
234 G5A 0.408163 0.730337
235 YLA 0.40678 0.788235
236 FCX 0.40625 0.766667
237 FAM 0.40625 0.775281
238 ACO 0.40625 0.766667
239 7MC 0.405172 0.788235
240 AYB 0.403361 0.77907
241 HAX 0.403101 0.775281
242 J7C 0.402174 0.716049
243 VMS 0.401961 0.719101
244 DGT 0.401961 0.814815
245 54H 0.401961 0.719101
246 A3D 0.401639 0.833333
247 J7V 0.401575 0.761364
248 103 0.4 0.802632
249 3KK 0.4 0.775281
250 FYN 0.4 0.793103
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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