Receptor
PDB id Resolution Class Description Source Keywords
2YP0 2.3 Å EC: 3.1.4.37 CATALYTIC DOMAIN OF MOUSE 2',3'-CYCLIC NUCLEOTIDE 3'- PHOSPHODIESTERASE, CRYSTALLIZED WITH 2'-AMPS MUS MUSCULUS HYDROLASE MYELIN NERVOUS SYSTEM
Ref.: CRYSTALLOGRAPHIC ANALYSIS OF THE REACTION CYCLE OF 2',3'-CYCLIC NUCLEOTIDE 3'-PHOSPHODIESTERASE, A UNI MEMBER OF THE 2H PHOSPHOESTERASE FAMILY J.MOL.BIOL. V. 425 4307 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
OVE A:401;
A:403;
Valid;
Valid;
none;
none;
submit data
363.287 C10 H14 N5 O6 P S c1nc(...
GOL A:402;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
1PE A:404;
Invalid;
none;
submit data
238.278 C10 H22 O6 C(COC...
ACY A:405;
Invalid;
none;
submit data
60.052 C2 H4 O2 CC(=O...
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 (2D)
Ligand no: 1; Ligand: OVE; Similar ligands found: 244
No: Ligand ECFP6 Tc MDL keys Tc
1 OVE 1 1
2 2AM 0.828125 0.957747
3 A2P 0.675676 0.916667
4 ATR 0.625 0.930556
5 3AM 0.616438 0.916667
6 A2R 0.581395 0.893333
7 A22 0.574713 0.893333
8 RAB 0.573529 0.808219
9 XYA 0.573529 0.808219
10 ADN 0.573529 0.808219
11 A3P 0.56962 0.90411
12 25A 0.568182 0.88
13 7D5 0.567568 0.866667
14 A 0.565789 0.90411
15 AMP 0.565789 0.90411
16 AT4 0.555556 0.945946
17 V3L 0.552941 0.88
18 NA7 0.549451 0.87013
19 7D7 0.536232 0.733333
20 25L 0.531915 0.893333
21 PAP 0.529412 0.917808
22 A4D 0.527778 0.808219
23 A2D 0.525 0.88
24 ABM 0.525 0.855263
25 45A 0.525 0.855263
26 ADP 0.52439 0.905405
27 SRA 0.518987 0.932432
28 AMP MG 0.518987 0.864865
29 7D3 0.518519 0.868421
30 AN2 0.518072 0.893333
31 2A5 0.517647 0.881579
32 TAT 0.517241 0.945946
33 T99 0.517241 0.945946
34 PO4 PO4 A A A A PO4 0.516129 0.864865
35 5N5 0.513889 0.783784
36 A12 0.512195 0.87013
37 BA3 0.512195 0.88
38 AP2 0.512195 0.87013
39 AGS 0.511628 0.933333
40 PPS 0.511364 0.8625
41 5CD 0.506849 0.746667
42 NWW 0.506849 0.726027
43 LMS 0.506329 0.795181
44 B4P 0.506024 0.88
45 AP5 0.506024 0.88
46 ATP 0.505882 0.905405
47 HEJ 0.505882 0.905405
48 5FA 0.5 0.905405
49 SON 0.5 0.846154
50 101 0.5 0.866667
51 APC 0.5 0.87013
52 AQP 0.5 0.905405
53 M33 0.494118 0.868421
54 ADX 0.494118 0.839506
55 7D4 0.494118 0.868421
56 AU1 0.494118 0.881579
57 CA0 0.494118 0.857143
58 A3G 0.493827 0.766234
59 50T 0.488372 0.893333
60 ACP 0.488372 0.881579
61 KG4 0.488372 0.857143
62 QQY 0.4875 0.90411
63 EP4 0.486842 0.7
64 ACQ 0.483146 0.881579
65 AR6 0.482759 0.88
66 APR 0.482759 0.88
67 PRX 0.482759 0.833333
68 ADP BEF 0.482353 0.853333
69 ADP MG 0.482353 0.853333
70 M2T 0.480519 0.703704
71 DTA 0.480519 0.776316
72 J4G 0.479167 0.835443
73 5AD 0.478873 0.712329
74 ADQ 0.478723 0.881579
75 HQG 0.478261 0.893333
76 AD9 0.477273 0.881579
77 RBY 0.477273 0.846154
78 ADV 0.477273 0.846154
79 9BG 0.477064 0.860759
80 N5O 0.47561 0.753247
81 NEC 0.47561 0.736842
82 MTA 0.474359 0.74026
83 KL2 0.474359 0.851351
84 ATF 0.472527 0.87013
85 CUU 0.471264 0.905405
86 ACK 0.469136 0.875
87 9X8 0.46875 0.883117
88 OAD 0.46875 0.857143
89 ADP BMA 0.46875 0.857143
90 6YZ 0.467391 0.881579
91 ANP 0.466667 0.881579
92 3AD 0.466667 0.794521
93 A3S 0.465116 0.776316
94 N5A 0.464286 0.727273
95 6RE 0.463415 0.728395
96 NWQ 0.4625 0.706667
97 3DH 0.4625 0.74026
98 5AL 0.461538 0.844156
99 V2G 0.461538 0.8375
100 8LE 0.461538 0.8125
101 ATP MG 0.460674 0.853333
102 ADP PO3 0.460674 0.853333
103 APC MG 0.460674 0.831169
104 KMQ 0.46 0.846154
105 NPW 0.458716 0.807229
106 NDP 0.458716 0.8375
107 DA 0.457831 0.866667
108 D5M 0.457831 0.866667
109 AOC 0.457831 0.763158
110 QQX 0.45679 0.891892
111 AV2 0.456522 0.88
112 ANP MG 0.456522 0.844156
113 BEF ADP 0.455556 0.831169
114 5X8 0.454545 0.730769
115 2VA 0.454545 0.766234
116 TXP 0.454545 0.8375
117 A3T 0.454545 0.786667
118 NZQ 0.454545 0.82716
119 5AS 0.453488 0.770115
120 Y3J 0.453333 0.693333
121 9ZA 0.452632 0.825
122 5SV 0.452632 0.792683
123 OZV 0.452632 0.88
124 9ZD 0.452632 0.825
125 J7C 0.452381 0.7375
126 CC5 0.452055 0.756757
127 8LH 0.451613 0.846154
128 SRP 0.451613 0.846154
129 ZAS 0.451219 0.7125
130 103 0.451219 0.802632
131 GAP 0.450549 0.833333
132 3AT 0.450549 0.905405
133 NJP 0.45045 0.858974
134 ODP 0.45045 0.82716
135 3D1 0.447368 0.763158
136 3L1 0.447368 0.763158
137 S4M 0.447059 0.659091
138 GJV 0.447059 0.719512
139 XNP 0.446429 0.817073
140 NVA 2AD 0.444444 0.728395
141 FYA 0.444444 0.844156
142 JB6 0.444444 0.871795
143 MAP 0.442105 0.858974
144 QA7 0.442105 0.8125
145 8LQ 0.442105 0.822785
146 MAO 0.44186 0.709302
147 LQJ 0.441176 0.88
148 VO4 ADP 0.44086 0.857143
149 ALF ADP 0.44086 0.790123
150 DSH 0.440476 0.716049
151 SO8 0.43956 0.75641
152 VRT 0.43956 0.7375
153 DAT 0.438202 0.868421
154 OOB 0.4375 0.844156
155 8QN 0.4375 0.844156
156 5F1 0.435897 0.701299
157 A3N 0.435294 0.753247
158 PR8 0.434343 0.795181
159 AMO 0.43299 0.846154
160 A1R 0.43299 0.848101
161 4AD 0.43299 0.835443
162 A3R 0.43299 0.848101
163 PAJ 0.43299 0.82716
164 1ZZ 0.43 0.764706
165 BIS 0.43 0.848101
166 3OD 0.43 0.857143
167 PTJ 0.43 0.814815
168 AHX 0.428571 0.8375
169 AR6 AR6 0.428571 0.831169
170 A5D 0.428571 0.776316
171 00A 0.428571 0.802469
172 DLL 0.428571 0.844156
173 JNT 0.428571 0.881579
174 GGZ 0.427083 0.8375
175 DAL AMP 0.427083 0.820513
176 MHZ 0.426966 0.670455
177 TM1 0.425743 0.744186
178 3UK 0.424242 0.833333
179 G5A 0.423913 0.770115
180 H1Q 0.422222 0.842105
181 SFG 0.422222 0.696203
182 OMR 0.422018 0.776471
183 7L1 0.421488 0.786517
184 SMM 0.421053 0.659091
185 NMN AMP PO4 0.421053 0.790123
186 NOC 0.421053 0.72973
187 2GP 0.420455 0.87013
188 LAD 0.42 0.804878
189 B5V 0.42 0.822785
190 WAQ 0.42 0.802469
191 DDS 0.419355 0.842105
192 DTP 0.419355 0.868421
193 AS 0.418605 0.894737
194 UPA 0.418182 0.848101
195 ATP A A A 0.417476 0.842105
196 ATP A 0.417476 0.842105
197 NAP 0.416667 0.857143
198 SP1 0.416667 0.88
199 RP1 0.416667 0.88
200 ME8 0.415842 0.785714
201 NB8 0.415842 0.814815
202 TXA 0.415842 0.846154
203 A7D 0.41573 0.766234
204 AFH 0.415094 0.82716
205 TAP 0.413223 0.871795
206 DG1 0.413223 0.8375
207 1DG 0.413223 0.8375
208 SA8 0.413043 0.658824
209 D3Y 0.412371 0.75641
210 TSB 0.412371 0.788235
211 5CA 0.412371 0.790698
212 5J9 0.411765 0.702381
213 MYR AMP 0.411765 0.744186
214 A5A 0.410526 0.776471
215 N01 0.410256 0.820513
216 NA0 0.409836 0.846154
217 2BA 0.409091 0.851351
218 CMP 0.409091 0.863014
219 SAH 0.408602 0.7125
220 SAI 0.408602 0.682927
221 GEK 0.408163 0.686747
222 9SN 0.407767 0.792683
223 S7M 0.40625 0.662791
224 SSA 0.40625 0.790698
225 P5A 0.405941 0.736264
226 3NZ 0.405941 0.75
227 G3A 0.40566 0.8375
228 ARJ 0.405063 0.716216
229 NX8 0.404255 0.686747
230 SAM 0.404255 0.662791
231 B5M 0.403846 0.8125
232 FA5 0.403846 0.822785
233 B5Y 0.403846 0.8125
234 NWZ 0.402174 0.674699
235 VMS 0.402062 0.758621
236 52H 0.402062 0.75
237 54H 0.402062 0.758621
238 G5P 0.401869 0.8375
239 ARG AMP 0.401869 0.776471
240 APU 0.401786 0.858974
241 AAT 0.4 0.719512
242 XAH 0.4 0.785714
243 DZ4 0.4 0.846154
244 EEM 0.4 0.643678
Similar Ligands (3D)
Ligand no: 1; Ligand: OVE; Similar ligands found: 19
No: Ligand Similarity coefficient
1 U2P 0.9328
2 SGP 0.9156
3 C2P 0.8982
4 C3P 0.8916
5 T3P 0.8883
6 GMP 0.8838
7 FMC 0.8811
8 NOS 0.8775
9 AD3 0.8733
10 U3P 0.8664
11 6MD 0.8661
12 UM3 0.8656
13 TMP 0.8654
14 5NB 0.8646
15 1DA 0.8624
16 PRH 0.8595
17 BRY 0.8567
18 HPR 0.8566
19 5ID 0.8541
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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