Receptor
PDB id Resolution Class Description Source Keywords
4WDG 2.05 Å EC: 3.1.4.37 CATALYTIC DOMAIN OF MOUSE 2',3'-CYCLIC NUCLEOTIDE 3'- PHOSPHODIESTERASE, WITH MUTATION V321A, COMPLEXED WITH 2',5 MUS MUSCULUS HYDROLASE MYELIN NERVOUS SYSTEM
Ref.: DETERMINANTS OF LIGAND BINDING AND CATALYTIC ACTIVI MYELIN ENZYME 2',3'-CYCLIC NUCLEOTIDE 3'-PHOSPHODIE SCI REP V. 5 16520 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
A2P A:401;
Valid;
none;
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427.201 C10 H15 N5 O10 P2 c1nc(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2XMI 1.74 Å EC: 3.1.4.37 CATALYTIC DOMAIN OF MOUSE 2',3'-CYCLIC NUCLEOTIDE 3'-PHOSPHODIESTERASE, COMPLEXED WITH CITRATE MUS MUSCULUS HYDROLASE MYELIN
Ref.: MYELIN 2',3'-CYCLIC NUCLEOTIDE 3'-PHOSPHODIESTERASE SITE LIGAND BINDING AND MOLECULAR CONFORMATION. PLOS ONE V. 7 32336 2012
Members (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4WDD - CIT C6 H8 O7 C(C(=O)O)C....
2 4WFR - 2AM C10 H14 N5 O7 P c1nc(c2c(n....
3 2YPH - QQY C10 H12 N5 O5 P S c1nc(c2c(n....
4 2YP0 - OVE C10 H14 N5 O6 P S c1nc(c2c(n....
5 3ZBS - OVE C10 H14 N5 O6 P S c1nc(c2c(n....
6 2YDB - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
7 2Y1P - CIT C6 H8 O7 C(C(=O)O)C....
8 4WDB - 2AM C10 H14 N5 O7 P c1nc(c2c(n....
9 3ZBR - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
10 2XMI - FLC C6 H5 O7 C(C(=O)[O-....
11 2YPE - ACK C10 H12 N5 O6 P c1nc(c2c(n....
12 4WDG - A2P C10 H15 N5 O10 P2 c1nc(c2c(n....
13 2YQ9 - 2AM C10 H14 N5 O7 P c1nc(c2c(n....
14 4WCA - CIT C6 H8 O7 C(C(=O)O)C....
15 4WDA - 2AM C10 H14 N5 O7 P c1nc(c2c(n....
16 2YOZ - OVE C10 H14 N5 O6 P S c1nc(c2c(n....
17 2YDD - 2AM C10 H14 N5 O7 P c1nc(c2c(n....
18 4WDF - A2P C10 H15 N5 O10 P2 c1nc(c2c(n....
19 2YPC - QQX C10 H12 N5 O5 P S c1nc(c2c(n....
20 3ZBZ - OVE C10 H14 N5 O6 P S c1nc(c2c(n....
70% Homology Family (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4WDD - CIT C6 H8 O7 C(C(=O)O)C....
2 4WFR - 2AM C10 H14 N5 O7 P c1nc(c2c(n....
3 2YPH - QQY C10 H12 N5 O5 P S c1nc(c2c(n....
4 2YP0 - OVE C10 H14 N5 O6 P S c1nc(c2c(n....
5 3ZBS - OVE C10 H14 N5 O6 P S c1nc(c2c(n....
6 2YDB - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
7 2Y1P - CIT C6 H8 O7 C(C(=O)O)C....
8 4WDB - 2AM C10 H14 N5 O7 P c1nc(c2c(n....
9 3ZBR - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
10 2XMI - FLC C6 H5 O7 C(C(=O)[O-....
11 2YPE - ACK C10 H12 N5 O6 P c1nc(c2c(n....
12 4WDG - A2P C10 H15 N5 O10 P2 c1nc(c2c(n....
13 2YQ9 - 2AM C10 H14 N5 O7 P c1nc(c2c(n....
14 4WCA - CIT C6 H8 O7 C(C(=O)O)C....
15 4WDA - 2AM C10 H14 N5 O7 P c1nc(c2c(n....
16 2YOZ - OVE C10 H14 N5 O6 P S c1nc(c2c(n....
17 2YDD - 2AM C10 H14 N5 O7 P c1nc(c2c(n....
18 4WDF - A2P C10 H15 N5 O10 P2 c1nc(c2c(n....
19 2YPC - QQX C10 H12 N5 O5 P S c1nc(c2c(n....
20 3ZBZ - OVE C10 H14 N5 O6 P S c1nc(c2c(n....
50% Homology Family (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4WDD - CIT C6 H8 O7 C(C(=O)O)C....
2 4WFR - 2AM C10 H14 N5 O7 P c1nc(c2c(n....
3 2YPH - QQY C10 H12 N5 O5 P S c1nc(c2c(n....
4 2YP0 - OVE C10 H14 N5 O6 P S c1nc(c2c(n....
5 3ZBS - OVE C10 H14 N5 O6 P S c1nc(c2c(n....
6 2YDB - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
7 2Y1P - CIT C6 H8 O7 C(C(=O)O)C....
8 4WDB - 2AM C10 H14 N5 O7 P c1nc(c2c(n....
9 3ZBR - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
10 2XMI - FLC C6 H5 O7 C(C(=O)[O-....
11 2YPE - ACK C10 H12 N5 O6 P c1nc(c2c(n....
12 4WDG - A2P C10 H15 N5 O10 P2 c1nc(c2c(n....
13 2YQ9 - 2AM C10 H14 N5 O7 P c1nc(c2c(n....
14 4WCA - CIT C6 H8 O7 C(C(=O)O)C....
15 4WDA - 2AM C10 H14 N5 O7 P c1nc(c2c(n....
16 2YOZ - OVE C10 H14 N5 O6 P S c1nc(c2c(n....
17 2YDD - 2AM C10 H14 N5 O7 P c1nc(c2c(n....
18 4WDF - A2P C10 H15 N5 O10 P2 c1nc(c2c(n....
19 2YPC - QQX C10 H12 N5 O5 P S c1nc(c2c(n....
20 3ZBZ - OVE C10 H14 N5 O6 P S c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: A2P; Similar ligands found: 307
No: Ligand ECFP6 Tc MDL keys Tc
1 A2P 1 1
2 ATR 0.835616 0.985294
3 2AM 0.80597 0.956522
4 A2R 0.772152 0.943662
5 A22 0.7625 0.943662
6 25A 0.731707 0.957143
7 NA7 0.72619 0.917808
8 V3L 0.7 0.957143
9 A 0.684932 0.956522
10 AMP 0.684932 0.956522
11 A3P 0.684211 0.985294
12 OVE 0.675676 0.916667
13 7D5 0.643836 0.888889
14 3AM 0.626667 0.942029
15 25L 0.626374 0.943662
16 PO4 PO4 A A A A PO4 0.611111 0.942029
17 NPW 0.598039 0.848101
18 NDP 0.598039 0.881579
19 XNP 0.596154 0.858974
20 PAP 0.595238 0.971014
21 NZQ 0.592233 0.87013
22 TXP 0.592233 0.881579
23 NJP 0.586538 0.905405
24 ODP 0.586538 0.87013
25 ABM 0.575 0.902778
26 45A 0.575 0.902778
27 A2D 0.575 0.929577
28 PPS 0.574713 0.858974
29 ADP 0.573171 0.957143
30 AMP MG 0.56962 0.914286
31 SRA 0.56962 0.90411
32 AN2 0.566265 0.943662
33 2A5 0.564706 0.90411
34 AP2 0.560976 0.917808
35 A12 0.560976 0.917808
36 BA3 0.560976 0.929577
37 AGS 0.55814 0.905405
38 B4P 0.554217 0.929577
39 AP5 0.554217 0.929577
40 HEJ 0.552941 0.957143
41 ATP 0.552941 0.957143
42 7D3 0.548781 0.890411
43 AT4 0.547619 0.917808
44 5FA 0.546512 0.957143
45 APC 0.546512 0.917808
46 AQP 0.546512 0.957143
47 RAB 0.541667 0.802817
48 XYA 0.541667 0.802817
49 ADN 0.541667 0.802817
50 AU1 0.541176 0.930556
51 M33 0.541176 0.916667
52 ADX 0.541176 0.835443
53 7D4 0.541176 0.890411
54 CA0 0.541176 0.90411
55 NAP 0.539823 0.930556
56 HQG 0.538462 0.943662
57 1DG 0.535088 0.881579
58 DG1 0.535088 0.881579
59 TAP 0.535088 0.893333
60 ACP 0.534884 0.930556
61 KG4 0.534884 0.90411
62 50T 0.534884 0.916667
63 7L1 0.530435 0.761364
64 NA0 0.530435 0.917808
65 ADP BEF 0.529412 0.928571
66 ADP MG 0.529412 0.928571
67 APR 0.528736 0.929577
68 AR6 0.528736 0.929577
69 PRX 0.528736 0.878378
70 ACQ 0.52809 0.930556
71 T99 0.52809 0.917808
72 TAT 0.52809 0.917808
73 D5M 0.52439 0.915493
74 DA 0.52439 0.915493
75 ADV 0.522727 0.891892
76 RBY 0.522727 0.891892
77 AD9 0.522727 0.930556
78 ADQ 0.521277 0.90411
79 LMS 0.518519 0.8125
80 SON 0.511628 0.917808
81 ANP 0.511111 0.930556
82 6YZ 0.51087 0.930556
83 NMN AMP PO4 0.509091 0.855263
84 7D7 0.506849 0.75
85 ATP MG 0.505618 0.928571
86 ADP PO3 0.505618 0.928571
87 APC MG 0.505618 0.902778
88 V2G 0.505495 0.881579
89 5AL 0.505495 0.916667
90 8LE 0.505495 0.88
91 J4G 0.505155 0.905405
92 ATF 0.5 0.917808
93 AV2 0.5 0.929577
94 BEF ADP 0.5 0.902778
95 CO7 0.495935 0.770115
96 AR6 AR6 0.495146 0.902778
97 ENP 0.494845 0.878378
98 OAD 0.494845 0.90411
99 9X8 0.494845 0.88
100 ADP BMA 0.494845 0.878378
101 5SV 0.494737 0.833333
102 SRP 0.494624 0.891892
103 8LH 0.494624 0.891892
104 GAP 0.494505 0.878378
105 101 0.493976 0.888889
106 5N5 0.486842 0.777778
107 KMQ 0.485149 0.891892
108 BIS 0.484848 0.893333
109 PTJ 0.484848 0.881579
110 00A 0.484536 0.868421
111 8LQ 0.484211 0.891892
112 QA7 0.484211 0.88
113 MAP 0.484211 0.905405
114 ANP MG 0.483871 0.916667
115 ALF ADP 0.483871 0.855263
116 VO4 ADP 0.483871 0.930556
117 CUU 0.483146 0.957143
118 5AS 0.482759 0.764706
119 N01 0.482456 0.890411
120 5CD 0.480519 0.788732
121 A4D 0.480519 0.777778
122 OZV 0.479167 0.929577
123 9ZD 0.479167 0.893333
124 8QN 0.479167 0.916667
125 OOB 0.479167 0.916667
126 9ZA 0.479167 0.893333
127 3AT 0.478261 0.957143
128 DTA 0.475 0.77027
129 A3R 0.474227 0.868421
130 PAJ 0.474227 0.846154
131 AMO 0.474227 0.891892
132 A1R 0.474227 0.868421
133 4AD 0.474227 0.88
134 9BG 0.473214 0.881579
135 AOC 0.470588 0.805556
136 A3G 0.470588 0.76
137 1ZZ 0.47 0.825
138 FYA 0.47 0.890411
139 3OD 0.47 0.90411
140 JNT 0.469388 0.90411
141 AHX 0.469388 0.857143
142 DLL 0.469388 0.916667
143 MTA 0.469136 0.756757
144 0WD 0.469027 0.881579
145 DAL AMP 0.46875 0.890411
146 UPA 0.46789 0.868421
147 5X8 0.466667 0.746667
148 DAT 0.466667 0.916667
149 2VA 0.466667 0.76
150 LQJ 0.466019 0.929577
151 TM1 0.465347 0.802469
152 3UK 0.464646 0.90411
153 APU 0.463636 0.905405
154 EP4 0.4625 0.736842
155 DTP 0.462366 0.916667
156 NWW 0.461538 0.742857
157 9SN 0.460784 0.857143
158 LAD 0.46 0.846154
159 WAQ 0.46 0.868421
160 B5V 0.46 0.891892
161 PR8 0.46 0.835443
162 6RE 0.458824 0.74359
163 3DH 0.457831 0.756757
164 M2T 0.45679 0.717949
165 NVA 2AD 0.456522 0.721519
166 ATP A A A 0.456311 0.915493
167 ATP A 0.456311 0.915493
168 TXA 0.455446 0.891892
169 ME8 0.455446 0.825
170 JB6 0.455446 0.868421
171 NB8 0.455446 0.857143
172 GGZ 0.453608 0.833333
173 5AD 0.453333 0.753623
174 ANZ 0.45283 0.831169
175 VRT 0.451613 0.730769
176 G5A 0.451613 0.764706
177 SO8 0.451613 0.75
178 KL2 0.451219 0.873239
179 MYR AMP 0.45098 0.802469
180 PUA 0.449153 0.87013
181 Y3J 0.448718 0.732394
182 AS 0.448276 0.866667
183 IMO 0.448276 0.914286
184 ACK 0.447059 0.898551
185 103 0.447059 0.847222
186 QQY 0.447059 0.849315
187 OMR 0.445455 0.814815
188 NDP DTT 0.444444 0.783133
189 A3S 0.444444 0.77027
190 6MZ 0.443182 0.915493
191 3AD 0.443038 0.814286
192 B5Y 0.442308 0.88
193 FA5 0.442308 0.891892
194 B5M 0.442308 0.88
195 AFH 0.439252 0.846154
196 TSB 0.438776 0.783133
197 XAH 0.438095 0.825
198 A5A 0.4375 0.792683
199 DSH 0.436782 0.708861
200 NAX 0.436364 0.835443
201 NAI 0.436364 0.868421
202 QQX 0.435294 0.837838
203 H1Q 0.434783 0.888889
204 A3T 0.434783 0.780822
205 4UV 0.433962 0.88
206 SSA 0.43299 0.764706
207 J7C 0.431818 0.753247
208 DDS 0.431579 0.888889
209 LAQ 0.431193 0.825
210 ZAS 0.430233 0.75
211 G3A 0.429907 0.881579
212 AP0 0.428571 0.857143
213 CC5 0.428571 0.8
214 52H 0.428571 0.764706
215 DCA 0.428571 0.788235
216 VMS 0.428571 0.77381
217 54H 0.428571 0.77381
218 ETB 0.428571 0.797619
219 48N 0.427273 0.857143
220 DZ4 0.427083 0.891892
221 S4M 0.426966 0.651163
222 8BR 0.426966 0.891892
223 G5P 0.425926 0.881579
224 7MD 0.425926 0.825
225 GA7 0.425926 0.866667
226 4UU 0.425926 0.88
227 ARG AMP 0.425926 0.814815
228 3D1 0.425 0.756757
229 3L1 0.425 0.756757
230 53H 0.424242 0.764706
231 8X1 0.424242 0.738636
232 5CA 0.424242 0.764706
233 6V0 0.423423 0.857143
234 TXD 0.423423 0.868421
235 4UW 0.423423 0.846154
236 UP5 0.423423 0.88
237 PAX 0.422764 0.8375
238 MAO 0.422222 0.743902
239 71V 0.422222 0.868421
240 GTA 0.422018 0.848101
241 TAD 0.422018 0.846154
242 DQV 0.422018 0.916667
243 0T1 0.421488 0.788235
244 COA 0.421488 0.788235
245 SAH 0.421053 0.727273
246 AMP DBH 0.420561 0.853333
247 NEC 0.420455 0.72973
248 TYM 0.419643 0.891892
249 ALF ADP 3PG 0.419643 0.822785
250 TXE 0.419643 0.868421
251 SFG 0.419355 0.733333
252 NDO 0.418033 0.90411
253 P5A 0.417476 0.730337
254 139 0.417391 0.835443
255 4TC 0.415929 0.857143
256 LSS 0.415842 0.747126
257 NSS 0.415842 0.764706
258 DSZ 0.415842 0.764706
259 AAM 0.41573 0.956522
260 A3N 0.41573 0.746667
261 WMP 0.415254 0.876712
262 YLP 0.414414 0.804878
263 LPA AMP 0.414414 0.802469
264 ZZB 0.413793 0.802469
265 A7D 0.413043 0.76
266 C2R 0.411765 0.863014
267 AMZ 0.411765 0.875
268 NVA LMS 0.411765 0.738636
269 CAO 0.41129 0.761364
270 30N 0.41129 0.72043
271 COS 0.41129 0.770115
272 AMX 0.41129 0.797619
273 B1U 0.411215 0.722222
274 GJV 0.411111 0.734177
275 DND 0.410714 0.891892
276 128 0.410714 0.783133
277 SA8 0.410526 0.691358
278 A5D 0.410526 0.77027
279 PGS 0.408602 0.844156
280 2SA 0.408163 0.891892
281 CMX 0.408 0.788235
282 SCO 0.408 0.788235
283 NWQ 0.406977 0.722222
284 CA6 0.40625 0.697917
285 6C6 0.40625 0.866667
286 SAI 0.40625 0.717949
287 12D 0.405405 0.792683
288 AHZ 0.405405 0.802469
289 ADJ 0.405172 0.814815
290 FCX 0.404762 0.761364
291 ACO 0.404762 0.761364
292 FAM 0.404762 0.770115
293 N5O 0.404494 0.746667
294 S7M 0.40404 0.674699
295 GSU 0.403846 0.764706
296 KAA 0.403846 0.738636
297 7MC 0.403509 0.804878
298 L3W 0.403509 0.891892
299 YLB 0.403509 0.804878
300 YLC 0.403509 0.825
301 NIA 0.402299 0.807692
302 2GP 0.402174 0.891892
303 6IA 0.402062 0.822785
304 HAX 0.401575 0.770115
305 9K8 0.4 0.7
306 A4P 0.4 0.807229
307 80F 0.4 0.804878
Similar Ligands (3D)
Ligand no: 1; Ligand: A2P; Similar ligands found: 6
No: Ligand Similarity coefficient
1 IMP 0.8821
2 5GP 0.8752
3 G 0.8718
4 FMP 0.8702
5 XMP 0.8664
6 6CG 0.8597
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2XMI; Ligand: FLC; 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: 2xmi.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
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