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 MORE than expected: % Diff = 2;
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: 237
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 ADN 0.6 0.842857
11 RAB 0.6 0.842857
12 XYA 0.6 0.842857
13 7D5 0.591549 0.902778
14 AMP 0.589041 0.942857
15 A 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 AMP MG 0.532468 0.864865
33 AP2 0.531646 0.905405
34 A12 0.531646 0.905405
35 BA3 0.531646 0.916667
36 SAP 0.53012 0.893333
37 AGS 0.53012 0.893333
38 NDP 0.529412 0.87013
39 NPW 0.529412 0.8375
40 5CD 0.528571 0.777778
41 A4D 0.528571 0.816901
42 B4P 0.525 0.916667
43 AP5 0.525 0.916667
44 ATP 0.52439 0.943662
45 TXP 0.524272 0.87013
46 NZQ 0.524272 0.858974
47 ODP 0.519231 0.858974
48 NJP 0.519231 0.893333
49 SON 0.518519 0.88
50 5FA 0.518072 0.943662
51 AQP 0.518072 0.943662
52 APC 0.518072 0.905405
53 XNP 0.514286 0.848101
54 7D4 0.512195 0.90411
55 CA0 0.512195 0.891892
56 ADX 0.512195 0.825
57 M33 0.512195 0.90411
58 AU1 0.512195 0.917808
59 EP4 0.506849 0.727273
60 ACP 0.506024 0.917808
61 50T 0.506024 0.930556
62 AR6 0.5 0.916667
63 TAT 0.5 0.905405
64 M2T 0.5 0.708861
65 ACQ 0.5 0.917808
66 APR 0.5 0.916667
67 5AD 0.5 0.742857
68 PRX 0.5 0.866667
69 DTA 0.5 0.76
70 ADQ 0.494505 0.917808
71 ADV 0.494118 0.88
72 RBY 0.494118 0.88
73 AD9 0.494118 0.917808
74 ADP MG 0.493976 0.853333
75 A3G 0.493671 0.797297
76 MTA 0.493333 0.746667
77 Y3J 0.492958 0.722222
78 ATF 0.488636 0.905405
79 AV2 0.488636 0.916667
80 2VA 0.488095 0.797297
81 ADP BEF 0.488095 0.831169
82 BEF ADP 0.488095 0.831169
83 2GP 0.487805 0.905405
84 103 0.487179 0.835616
85 ACK 0.487179 0.913043
86 QQY 0.487179 0.863014
87 3AD 0.486111 0.828571
88 OAD 0.483871 0.891892
89 ANP 0.482759 0.917808
90 6RE 0.481013 0.75641
91 3DH 0.480519 0.746667
92 NAP 0.477876 0.891892
93 5AL 0.477273 0.878378
94 ADP PO3 0.476744 0.888889
95 DA 0.475 0.902778
96 D5M 0.475 0.902778
97 NEC 0.475 0.767123
98 AOC 0.475 0.794521
99 QQX 0.474359 0.851351
100 1DG 0.473684 0.87013
101 TAP 0.473684 0.857143
102 DG1 0.473684 0.87013
103 CC5 0.471429 0.788732
104 SO8 0.471264 0.786667
105 VRT 0.471264 0.766234
106 ATP MG 0.471264 0.853333
107 5X8 0.470588 0.736842
108 5AS 0.46988 0.755814
109 NA0 0.469565 0.88
110 ZAS 0.468354 0.74026
111 ADP BMA 0.468085 0.891892
112 5SV 0.467391 0.822785
113 SRP 0.466667 0.88
114 GAP 0.465909 0.866667
115 3AT 0.465909 0.943662
116 3L1 0.465753 0.794521
117 3D1 0.465753 0.794521
118 A3S 0.464286 0.808219
119 S4M 0.463415 0.662791
120 NVA 2AD 0.45977 0.786667
121 MAO 0.457831 0.73494
122 00A 0.457447 0.833333
123 DSH 0.45679 0.721519
124 MAP 0.456522 0.893333
125 ALF ADP 0.455556 0.820513
126 ADP ALF 0.455556 0.820513
127 DAT 0.453488 0.90411
128 SFG 0.453488 0.723684
129 A3T 0.453488 0.819444
130 APU 0.45283 0.893333
131 A A A 0.452632 0.853333
132 OOB 0.451613 0.878378
133 8QN 0.451613 0.878378
134 J7C 0.451219 0.766234
135 A3N 0.451219 0.783784
136 ANP MG 0.450549 0.844156
137 VO4 ADP 0.450549 0.878378
138 ADP VO4 0.450549 0.878378
139 A A 0.447917 0.916667
140 PR8 0.447917 0.825
141 A1R 0.446809 0.881579
142 4AD 0.446809 0.868421
143 AMO 0.446809 0.88
144 PAJ 0.446809 0.858974
145 GJV 0.445783 0.746835
146 0WD 0.445455 0.87013
147 NMN AMP PO4 0.445455 0.820513
148 UPA 0.443396 0.881579
149 PTJ 0.443299 0.846154
150 1ZZ 0.443299 0.792683
151 3OD 0.443299 0.891892
152 BIS 0.443299 0.881579
153 FYA 0.443299 0.878378
154 A5D 0.443182 0.76
155 SA8 0.443182 0.682927
156 DLL 0.442105 0.878378
157 AHX 0.442105 0.87013
158 AR6 AR6 0.441176 0.864865
159 DAL AMP 0.44086 0.853333
160 GGZ 0.44086 0.822785
161 CO7 0.439024 0.781609
162 TM1 0.438776 0.771084
163 SAH 0.438202 0.717949
164 SAI 0.438202 0.708861
165 G5A 0.438202 0.755814
166 3UK 0.4375 0.866667
167 S7M 0.434783 0.666667
168 SMM 0.434783 0.662791
169 9SN 0.434343 0.822785
170 5F1 0.434211 0.72973
171 OMR 0.433962 0.804878
172 AS 0.433735 0.855263
173 DTP 0.433333 0.90411
174 LAD 0.43299 0.835443
175 WAQ 0.43299 0.833333
176 SP1 0.432099 0.84
177 RP1 0.432099 0.84
178 A7D 0.430233 0.773333
179 ATP A A A 0.43 0.876712
180 NB8 0.428571 0.846154
181 TXA 0.428571 0.88
182 EEM 0.428571 0.666667
183 JB6 0.428571 0.833333
184 ME8 0.428571 0.792683
185 TSB 0.425532 0.77381
186 MHZ 0.425287 0.694118
187 MYR AMP 0.424242 0.771084
188 A5A 0.423913 0.761905
189 2BA 0.423529 0.887324
190 CMP 0.423529 0.9
191 ENP 0.42268 0.866667
192 ARJ 0.421053 0.746479
193 N01 0.421053 0.853333
194 GEK 0.421053 0.691358
195 SSA 0.419355 0.776471
196 NOC 0.418919 0.760563
197 P5A 0.418367 0.722222
198 SAM 0.417582 0.666667
199 DDS 0.417582 0.876712
200 YAP 0.415842 0.844156
201 FA5 0.415842 0.855263
202 52H 0.414894 0.735632
203 54H 0.414894 0.744186
204 VMS 0.414894 0.744186
205 AFH 0.413462 0.858974
206 ANZ 0.413462 0.820513
207 AAT 0.413043 0.703704
208 A U 0.412844 0.844156
209 XAH 0.411765 0.814815
210 NAI 0.411215 0.857143
211 ZDA 0.411111 0.837838
212 53H 0.410526 0.735632
213 5CA 0.410526 0.776471
214 D3Y 0.410526 0.786667
215 5J9 0.41 0.728395
216 K15 0.408163 0.658824
217 A6D 0.408163 0.698795
218 4UV 0.407767 0.844156
219 V1N 0.407767 0.890411
220 LAQ 0.40566 0.792683
221 ETB 0.405172 0.809524
222 DCA 0.405172 0.8
223 3NZ 0.40404 0.779221
224 G3A 0.403846 0.87013
225 AP0 0.40367 0.846154
226 5HG 0.402597 0.723684
227 AFX 0.402597 0.675325
228 NSS 0.402062 0.755814
229 0UM 0.402062 0.695122
230 LSS 0.402062 0.719101
231 DSZ 0.402062 0.755814
232 48N 0.401869 0.846154
233 PUA 0.401709 0.858974
234 7MD 0.4 0.8375
235 4UU 0.4 0.844156
236 G5P 0.4 0.87013
237 0XU 0.4 0.701299
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2XMI; Ligand: FLC; Similar sites found: 14
This union binding pocket(no: 1) in the query (biounit: 2xmi.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1EYN 2AN 0.02352 0.41214 2.71493
2 5LDQ NAP 0.00002838 0.55318 3.9548
3 4USI AKG 0.01423 0.41094 4.54545
4 3N0S ACO 0.02226 0.41527 4.97738
5 5JCM ISD 0.04619 0.41497 4.97738
6 5JCM FAD 0.0451 0.41497 4.97738
7 5JCM NAD 0.04619 0.41497 4.97738
8 5JJ2 MLI 0.000004922 0.5667 5.21327
9 4X5S AZM 0.01165 0.41571 6.33484
10 3KDU NKS 0.03377 0.41179 9.04977
11 4RJD TFP 0.02127 0.40081 9.09091
12 2VFK AMP 0.00003107 0.55108 10.7317
13 4HIA FMN 0.01006 0.42766 13.0682
14 1JH7 UVC 0.002748 0.44696 15.873
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