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Receptor
PDB id Resolution Class Description Source Keywords
2YOZ 2.1 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
CL A:1385;
Invalid;
none;
submit data
35.453 Cl [Cl-]
ACT A:1386;
A:1384;
A:1383;
A:1382;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
59.044 C2 H3 O2 CC(=O...
GOL A:1380;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
OVE A:1379;
Valid;
none;
submit data
363.287 C10 H14 N5 O6 P S c1nc(...
1PE A:1381;
Invalid;
none;
submit data
238.278 C10 H22 O6 C(COC...
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: OVE; Similar ligands found: 218
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 ADN 0.573529 0.808219
9 RAB 0.573529 0.808219
10 XYA 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 ABM 0.525 0.855263
24 A2D 0.525 0.88
25 ADP 0.52439 0.905405
26 SRA 0.518987 0.932432
27 7D3 0.518519 0.868421
28 AN2 0.518072 0.893333
29 2A5 0.517647 0.881579
30 TAT 0.517241 0.945946
31 T99 0.517241 0.945946
32 PO4 PO4 A A A A PO4 0.516129 0.864865
33 5N5 0.513889 0.783784
34 AP2 0.512195 0.87013
35 A12 0.512195 0.87013
36 BA3 0.512195 0.88
37 SAP 0.511628 0.933333
38 AGS 0.511628 0.933333
39 PPS 0.511364 0.8625
40 5CD 0.506849 0.746667
41 LMS 0.506329 0.795181
42 B4P 0.506024 0.88
43 AP5 0.506024 0.88
44 ATP 0.505882 0.905405
45 HEJ 0.505882 0.905405
46 5FA 0.5 0.905405
47 101 0.5 0.866667
48 SON 0.5 0.846154
49 APC 0.5 0.87013
50 AQP 0.5 0.905405
51 7D4 0.494118 0.868421
52 M33 0.494118 0.868421
53 ADX 0.494118 0.839506
54 CA0 0.494118 0.857143
55 AU1 0.494118 0.881579
56 A3G 0.493827 0.766234
57 50T 0.488372 0.893333
58 ACP 0.488372 0.881579
59 QQY 0.4875 0.90411
60 EP4 0.486842 0.7
61 ACQ 0.483146 0.881579
62 PRX 0.482759 0.833333
63 APR 0.482759 0.88
64 AR6 0.482759 0.88
65 DTA 0.480519 0.776316
66 M2T 0.480519 0.703704
67 5AD 0.478873 0.712329
68 ADQ 0.478723 0.881579
69 ADV 0.477273 0.846154
70 AD9 0.477273 0.881579
71 RBY 0.477273 0.846154
72 NEC 0.47561 0.736842
73 MTA 0.474359 0.74026
74 ATF 0.472527 0.87013
75 ACK 0.469136 0.875
76 OAD 0.46875 0.857143
77 9X8 0.46875 0.883117
78 ADP BMA 0.46875 0.857143
79 6YZ 0.467391 0.881579
80 3AD 0.466667 0.794521
81 ANP 0.466667 0.881579
82 A3S 0.465116 0.776316
83 6RE 0.463415 0.728395
84 3DH 0.4625 0.74026
85 5AL 0.461538 0.844156
86 ADP PO3 0.460674 0.853333
87 NPW 0.458716 0.807229
88 NDP 0.458716 0.8375
89 DA 0.457831 0.866667
90 AOC 0.457831 0.763158
91 D5M 0.457831 0.866667
92 QQX 0.45679 0.891892
93 AV2 0.456522 0.88
94 NZQ 0.454545 0.82716
95 TXP 0.454545 0.8375
96 5X8 0.454545 0.730769
97 A3T 0.454545 0.786667
98 2VA 0.454545 0.766234
99 5AS 0.453488 0.770115
100 Y3J 0.453333 0.693333
101 9ZA 0.452632 0.825
102 9ZD 0.452632 0.825
103 5SV 0.452632 0.792683
104 J7C 0.452381 0.7375
105 CC5 0.452055 0.756757
106 SRP 0.451613 0.846154
107 103 0.451219 0.802632
108 ZAS 0.451219 0.7125
109 3AT 0.450549 0.905405
110 GAP 0.450549 0.833333
111 NJP 0.45045 0.858974
112 ODP 0.45045 0.82716
113 3D1 0.447368 0.763158
114 3L1 0.447368 0.763158
115 S4M 0.447059 0.659091
116 GJV 0.447059 0.719512
117 XNP 0.446429 0.817073
118 NVA 2AD 0.444444 0.728395
119 JB6 0.444444 0.871795
120 FYA 0.444444 0.844156
121 MAP 0.442105 0.858974
122 MAO 0.44186 0.709302
123 ALF ADP 0.44086 0.790123
124 ADP ALF 0.44086 0.790123
125 DSH 0.440476 0.716049
126 SO8 0.43956 0.75641
127 VRT 0.43956 0.7375
128 A A A 0.438776 0.820513
129 DAT 0.438202 0.868421
130 8QN 0.4375 0.844156
131 OOB 0.4375 0.844156
132 ADP VO4 0.43617 0.844156
133 VO4 ADP 0.43617 0.844156
134 5F1 0.435897 0.701299
135 A3N 0.435294 0.753247
136 A A 0.434343 0.88
137 PR8 0.434343 0.795181
138 A1R 0.43299 0.848101
139 PAJ 0.43299 0.82716
140 AMO 0.43299 0.846154
141 A3R 0.43299 0.848101
142 4AD 0.43299 0.835443
143 BIS 0.43 0.848101
144 1ZZ 0.43 0.764706
145 3OD 0.43 0.857143
146 PTJ 0.43 0.814815
147 AR6 AR6 0.428571 0.831169
148 DLL 0.428571 0.844156
149 AHX 0.428571 0.8375
150 A5D 0.428571 0.776316
151 00A 0.428571 0.802469
152 GGZ 0.427083 0.8375
153 DAL AMP 0.427083 0.820513
154 MHZ 0.426966 0.670455
155 TM1 0.425743 0.744186
156 3UK 0.424242 0.833333
157 G5A 0.423913 0.770115
158 SFG 0.422222 0.696203
159 OMR 0.422018 0.776471
160 7L1 0.421488 0.786517
161 SMM 0.421053 0.659091
162 NMN AMP PO4 0.421053 0.790123
163 NOC 0.421053 0.72973
164 2GP 0.420455 0.87013
165 LAD 0.42 0.804878
166 WAQ 0.42 0.802469
167 B5V 0.42 0.822785
168 DTP 0.419355 0.868421
169 DDS 0.419355 0.842105
170 AS 0.418605 0.894737
171 UPA 0.418182 0.848101
172 ATP A A A 0.417476 0.842105
173 NAP 0.416667 0.857143
174 RP1 0.416667 0.88
175 SP1 0.416667 0.88
176 TXA 0.415842 0.846154
177 NB8 0.415842 0.814815
178 ME8 0.415842 0.785714
179 A7D 0.41573 0.766234
180 AFH 0.415094 0.82716
181 DG1 0.413223 0.8375
182 1DG 0.413223 0.8375
183 TAP 0.413223 0.871795
184 SA8 0.413043 0.658824
185 D3Y 0.412371 0.75641
186 TSB 0.412371 0.788235
187 5CA 0.412371 0.790698
188 5J9 0.411765 0.702381
189 MYR AMP 0.411765 0.744186
190 A5A 0.410526 0.776471
191 N01 0.410256 0.820513
192 NA0 0.409836 0.846154
193 CMP 0.409091 0.863014
194 2BA 0.409091 0.851351
195 SAH 0.408602 0.7125
196 SAI 0.408602 0.682927
197 GEK 0.408163 0.686747
198 9SN 0.407767 0.792683
199 SSA 0.40625 0.790698
200 S7M 0.40625 0.662791
201 P5A 0.405941 0.736264
202 3NZ 0.405941 0.75
203 G3A 0.40566 0.8375
204 ARJ 0.405063 0.716216
205 SAM 0.404255 0.662791
206 YAP 0.403846 0.8125
207 FA5 0.403846 0.822785
208 B5Y 0.403846 0.8125
209 B5M 0.403846 0.8125
210 54H 0.402062 0.758621
211 52H 0.402062 0.75
212 VMS 0.402062 0.758621
213 G5P 0.401869 0.8375
214 ARG AMP 0.401869 0.776471
215 APU 0.401786 0.858974
216 XAH 0.4 0.785714
217 EEM 0.4 0.643678
218 AAT 0.4 0.719512
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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