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Receptor
PDB id Resolution Class Description Source Keywords
4WDB 1.6 Å EC: 3.1.4.37 CATALYTIC DOMAIN OF MOUSE 2',3'-CYCLIC NUCLEOTIDE 3'- PHOSPHODIESTERASE, WITH MUTATION R307Q, COMPLEXED WITH 2'-A 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
2AM A:401;
Valid;
Atoms found LESS than expected: % Diff = 0;
submit data
347.221 C10 H14 N5 O7 P c1nc(...
CL A:402;
Invalid;
none;
submit data
35.453 Cl [Cl-]
View in 3D viewer
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
Ligand no: 1; Ligand: 2AM; Similar ligands found: 249
No: Ligand ECFP6 Tc MDL keys Tc
1 2AM 1 1
2 OVE 0.828125 0.957747
3 A2P 0.80597 0.956522
4 ATR 0.739726 0.971014
5 3AM 0.691176 0.956522
6 A2R 0.683544 0.930556
7 A22 0.675 0.930556
8 NA7 0.642857 0.905405
9 A3P 0.635135 0.942857
10 XYA 0.6 0.842857
11 ADN 0.6 0.842857
12 RAB 0.6 0.842857
13 7D5 0.591549 0.902778
14 A 0.589041 0.942857
15 AMP 0.589041 0.942857
16 25A 0.588235 0.916667
17 PAP 0.5875 0.957143
18 V3L 0.573171 0.916667
19 PPS 0.566265 0.848101
20 7D7 0.560606 0.763889
21 25L 0.549451 0.930556
22 ABM 0.545455 0.890411
23 A2D 0.545455 0.916667
24 ADP 0.544304 0.943662
25 101 0.539474 0.902778
26 SRA 0.539474 0.891892
27 7D3 0.538462 0.90411
28 AN2 0.5375 0.930556
29 2A5 0.536585 0.917808
30 5N5 0.536232 0.816901
31 PO4 PO4 A A A A PO4 0.533333 0.901408
32 AP2 0.531646 0.905405
33 BA3 0.531646 0.916667
34 A12 0.531646 0.905405
35 SAP 0.53012 0.893333
36 AGS 0.53012 0.893333
37 NPW 0.529412 0.8375
38 NDP 0.529412 0.87013
39 5CD 0.528571 0.777778
40 A4D 0.528571 0.816901
41 LMS 0.526316 0.780488
42 AP5 0.525 0.916667
43 B4P 0.525 0.916667
44 HEJ 0.52439 0.943662
45 ATP 0.52439 0.943662
46 TXP 0.524272 0.87013
47 NZQ 0.524272 0.858974
48 ODP 0.519231 0.858974
49 NJP 0.519231 0.893333
50 AT4 0.518519 0.905405
51 SON 0.518519 0.88
52 APC 0.518072 0.905405
53 AQP 0.518072 0.943662
54 5FA 0.518072 0.943662
55 XNP 0.514286 0.848101
56 M33 0.512195 0.90411
57 CA0 0.512195 0.891892
58 7D4 0.512195 0.90411
59 ADX 0.512195 0.825
60 AU1 0.512195 0.917808
61 EP4 0.506849 0.727273
62 50T 0.506024 0.930556
63 ACP 0.506024 0.917808
64 M2T 0.5 0.708861
65 AR6 0.5 0.916667
66 PRX 0.5 0.866667
67 DTA 0.5 0.76
68 TAT 0.5 0.905405
69 5AD 0.5 0.742857
70 T99 0.5 0.905405
71 APR 0.5 0.916667
72 ACQ 0.5 0.917808
73 ADQ 0.494505 0.917808
74 RBY 0.494118 0.88
75 ADV 0.494118 0.88
76 AD9 0.494118 0.917808
77 A3G 0.493671 0.797297
78 MTA 0.493333 0.746667
79 Y3J 0.492958 0.722222
80 ATF 0.488636 0.905405
81 AV2 0.488636 0.916667
82 2VA 0.488095 0.797297
83 2GP 0.487805 0.905405
84 QQY 0.487179 0.863014
85 ACK 0.487179 0.913043
86 103 0.487179 0.835616
87 3AD 0.486111 0.828571
88 OAD 0.483871 0.891892
89 9X8 0.483871 0.868421
90 6YZ 0.483146 0.917808
91 ANP 0.482759 0.917808
92 6RE 0.481013 0.75641
93 3DH 0.480519 0.746667
94 NAP 0.477876 0.891892
95 5AL 0.477273 0.878378
96 ADP PO3 0.476744 0.888889
97 NVA 2AD 0.476744 0.75641
98 NEC 0.475 0.767123
99 D5M 0.475 0.902778
100 DA 0.475 0.902778
101 AOC 0.475 0.794521
102 QQX 0.474359 0.851351
103 DG1 0.473684 0.87013
104 TAP 0.473684 0.857143
105 1DG 0.473684 0.87013
106 CC5 0.471429 0.788732
107 SO8 0.471264 0.786667
108 VRT 0.471264 0.766234
109 5X8 0.470588 0.736842
110 5AS 0.46988 0.755814
111 7L1 0.469565 0.772727
112 NA0 0.469565 0.88
113 ZAS 0.468354 0.74026
114 ADP BMA 0.468085 0.891892
115 9ZA 0.467391 0.857143
116 5SV 0.467391 0.822785
117 9ZD 0.467391 0.857143
118 SRP 0.466667 0.88
119 GAP 0.465909 0.866667
120 3AT 0.465909 0.943662
121 3D1 0.465753 0.794521
122 3L1 0.465753 0.794521
123 A3S 0.464286 0.808219
124 S4M 0.463415 0.662791
125 MAO 0.457831 0.73494
126 00A 0.457447 0.833333
127 DSH 0.45679 0.721519
128 MAP 0.456522 0.893333
129 ADP ALF 0.455556 0.820513
130 ALF ADP 0.455556 0.820513
131 A3T 0.453488 0.819444
132 SFG 0.453488 0.723684
133 DAT 0.453488 0.90411
134 APU 0.45283 0.893333
135 A A A 0.452632 0.853333
136 8QN 0.451613 0.878378
137 OOB 0.451613 0.878378
138 J7C 0.451219 0.766234
139 A3N 0.451219 0.783784
140 ADP VO4 0.450549 0.878378
141 VO4 ADP 0.450549 0.878378
142 A A 0.447917 0.916667
143 PR8 0.447917 0.825
144 4AD 0.446809 0.868421
145 A3R 0.446809 0.881579
146 A1R 0.446809 0.881579
147 AMO 0.446809 0.88
148 PAJ 0.446809 0.858974
149 GJV 0.445783 0.746835
150 0WD 0.445455 0.87013
151 NMN AMP PO4 0.445455 0.820513
152 UPA 0.443396 0.881579
153 BIS 0.443299 0.881579
154 FYA 0.443299 0.878378
155 3OD 0.443299 0.891892
156 PTJ 0.443299 0.846154
157 1ZZ 0.443299 0.792683
158 A5D 0.443182 0.76
159 SA8 0.443182 0.682927
160 DLL 0.442105 0.878378
161 AHX 0.442105 0.87013
162 AR6 AR6 0.441176 0.864865
163 DAL AMP 0.44086 0.853333
164 GGZ 0.44086 0.822785
165 CO7 0.439024 0.781609
166 TM1 0.438776 0.771084
167 G5A 0.438202 0.755814
168 SAH 0.438202 0.717949
169 SAI 0.438202 0.708861
170 3UK 0.4375 0.866667
171 SMM 0.434783 0.662791
172 S7M 0.434783 0.666667
173 9SN 0.434343 0.822785
174 5F1 0.434211 0.72973
175 OMR 0.433962 0.804878
176 AS 0.433735 0.855263
177 DTP 0.433333 0.90411
178 LAD 0.43299 0.835443
179 WAQ 0.43299 0.833333
180 B5V 0.43299 0.855263
181 RP1 0.432099 0.84
182 SP1 0.432099 0.84
183 A7D 0.430233 0.773333
184 ATP A A A 0.43 0.876712
185 TXA 0.428571 0.88
186 NB8 0.428571 0.846154
187 ME8 0.428571 0.792683
188 JB6 0.428571 0.833333
189 EEM 0.428571 0.666667
190 TSB 0.425532 0.77381
191 MHZ 0.425287 0.694118
192 MYR AMP 0.424242 0.771084
193 A5A 0.423913 0.761905
194 CMP 0.423529 0.9
195 2BA 0.423529 0.887324
196 ENP 0.42268 0.866667
197 ARJ 0.421053 0.746479
198 GEK 0.421053 0.691358
199 N01 0.421053 0.853333
200 SSA 0.419355 0.776471
201 NOC 0.418919 0.760563
202 P5A 0.418367 0.722222
203 SAM 0.417582 0.666667
204 DDS 0.417582 0.876712
205 FA5 0.415842 0.855263
206 YAP 0.415842 0.844156
207 B5M 0.415842 0.844156
208 B5Y 0.415842 0.844156
209 54H 0.414894 0.744186
210 52H 0.414894 0.735632
211 VMS 0.414894 0.744186
212 AFH 0.413462 0.858974
213 ANZ 0.413462 0.820513
214 AAT 0.413043 0.703704
215 A U 0.412844 0.844156
216 XAH 0.411765 0.814815
217 NAI 0.411215 0.857143
218 ZDA 0.411111 0.837838
219 8X1 0.410526 0.730337
220 D3Y 0.410526 0.786667
221 53H 0.410526 0.735632
222 5CA 0.410526 0.776471
223 5J9 0.41 0.728395
224 A6D 0.408163 0.698795
225 K15 0.408163 0.658824
226 TYR AMP 0.407767 0.820513
227 4UV 0.407767 0.844156
228 V1N 0.407767 0.890411
229 LAQ 0.40566 0.792683
230 DCA 0.405172 0.8
231 ETB 0.405172 0.809524
232 3NZ 0.40404 0.779221
233 G3A 0.403846 0.87013
234 AP0 0.40367 0.846154
235 5HG 0.402597 0.723684
236 AFX 0.402597 0.675325
237 NSS 0.402062 0.755814
238 0UM 0.402062 0.695122
239 DSZ 0.402062 0.755814
240 LSS 0.402062 0.719101
241 48N 0.401869 0.846154
242 PUA 0.401709 0.858974
243 0XU 0.4 0.701299
244 7MD 0.4 0.8375
245 9K8 0.4 0.673913
246 G5P 0.4 0.87013
247 ARG AMP 0.4 0.804878
248 GA7 0.4 0.905405
249 4UU 0.4 0.844156
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: 23
This union binding pocket(no: 1) in the query (biounit: 2xmi.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 6CS9 PIO None
2 4C8E C5P None
3 1EYN 2AN 2.71493
4 4COQ SAN 2.71493
5 4OHU 2TK 3.16742
6 4OHU NAD 3.16742
7 4DOO DAO 3.41463
8 5LDQ NAP 3.9548
9 4X7R NTO 4.0724
10 4USI AKG 4.54545
11 5JCM NAD 4.97738
12 5JCM FAD 4.97738
13 5JCM ISD 4.97738
14 5JJ2 MLI 5.21327
15 4U8P UDP 5.42986
16 5XVG 8FX 5.42986
17 2P4Y C03 5.88235
18 4X5S AZM 6.33484
19 3KDU NKS 9.04977
20 4RJD TFP 9.09091
21 6C0B PAM 10.4072
22 2VFK AMP 10.7317
23 1JH7 UVC 15.873
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