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: 213
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 XYA 0.573529 0.808219
9 ADN 0.573529 0.808219
10 RAB 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 V3L 0.552941 0.88
17 NA7 0.549451 0.87013
18 7D7 0.536232 0.733333
19 25L 0.531915 0.893333
20 PAP 0.529412 0.917808
21 A4D 0.527778 0.808219
22 ABM 0.525 0.855263
23 A2D 0.525 0.88
24 ADP 0.52439 0.905405
25 SRA 0.518987 0.932432
26 7D3 0.518519 0.868421
27 AN2 0.518072 0.893333
28 2A5 0.517647 0.881579
29 TAT 0.517241 0.945946
30 PO4 PO4 A A A A PO4 0.516129 0.864865
31 5N5 0.513889 0.783784
32 AMP MG 0.5125 0.831169
33 A12 0.512195 0.87013
34 AP2 0.512195 0.87013
35 BA3 0.512195 0.88
36 AGS 0.511628 0.933333
37 SAP 0.511628 0.933333
38 PPS 0.511364 0.8625
39 5CD 0.506849 0.746667
40 AP5 0.506024 0.88
41 B4P 0.506024 0.88
42 ATP 0.505882 0.905405
43 101 0.5 0.866667
44 5FA 0.5 0.905405
45 AQP 0.5 0.905405
46 APC 0.5 0.87013
47 SON 0.5 0.846154
48 7D4 0.494118 0.868421
49 CA0 0.494118 0.857143
50 M33 0.494118 0.868421
51 ADX 0.494118 0.839506
52 AU1 0.494118 0.881579
53 A3G 0.493827 0.766234
54 ACP 0.488372 0.881579
55 50T 0.488372 0.893333
56 QQY 0.4875 0.90411
57 EP4 0.486842 0.7
58 ACQ 0.483146 0.881579
59 AR6 0.482759 0.88
60 APR 0.482759 0.88
61 PRX 0.482759 0.833333
62 M2T 0.480519 0.703704
63 DTA 0.480519 0.776316
64 5AD 0.478873 0.712329
65 ADQ 0.478723 0.881579
66 RBY 0.477273 0.846154
67 ADV 0.477273 0.846154
68 AD9 0.477273 0.881579
69 ADP MG 0.476744 0.820513
70 NEC 0.47561 0.736842
71 MTA 0.474359 0.74026
72 ATF 0.472527 0.87013
73 ADP BEF 0.471264 0.8
74 BEF ADP 0.471264 0.8
75 ACK 0.469136 0.875
76 ADP BMA 0.46875 0.857143
77 OAD 0.46875 0.857143
78 ANP 0.466667 0.881579
79 3AD 0.466667 0.794521
80 A3S 0.465116 0.776316
81 6RE 0.463415 0.728395
82 3DH 0.4625 0.74026
83 5AL 0.461538 0.844156
84 ADP PO3 0.460674 0.853333
85 NVA 2AD 0.460674 0.75641
86 NDP 0.458716 0.8375
87 NPW 0.458716 0.807229
88 AOC 0.457831 0.763158
89 DA 0.457831 0.866667
90 D5M 0.457831 0.866667
91 QQX 0.45679 0.891892
92 AV2 0.456522 0.88
93 ATP MG 0.455556 0.820513
94 A3T 0.454545 0.786667
95 NZQ 0.454545 0.82716
96 5X8 0.454545 0.730769
97 2VA 0.454545 0.766234
98 TXP 0.454545 0.8375
99 5AS 0.453488 0.770115
100 Y3J 0.453333 0.693333
101 5SV 0.452632 0.792683
102 J7C 0.452381 0.7375
103 CC5 0.452055 0.756757
104 SRP 0.451613 0.846154
105 ANP MG 0.451613 0.8125
106 ZAS 0.451219 0.7125
107 103 0.451219 0.802632
108 3AT 0.450549 0.905405
109 GAP 0.450549 0.833333
110 NJP 0.45045 0.858974
111 ODP 0.45045 0.82716
112 3L1 0.447368 0.763158
113 3D1 0.447368 0.763158
114 GJV 0.447059 0.719512
115 S4M 0.447059 0.659091
116 XNP 0.446429 0.817073
117 FYA 0.444444 0.844156
118 JB6 0.444444 0.871795
119 DAL AMP 0.442105 0.820513
120 MAP 0.442105 0.858974
121 MAO 0.44186 0.709302
122 ADP ALF 0.44086 0.790123
123 ALF ADP 0.44086 0.790123
124 DSH 0.440476 0.716049
125 SO8 0.43956 0.75641
126 VRT 0.43956 0.7375
127 A A A 0.438776 0.820513
128 DAT 0.438202 0.868421
129 OOB 0.4375 0.844156
130 8QN 0.4375 0.844156
131 VO4 ADP 0.43617 0.844156
132 ADP VO4 0.43617 0.844156
133 5F1 0.435897 0.701299
134 A3N 0.435294 0.753247
135 A A 0.434343 0.88
136 PR8 0.434343 0.795181
137 A1R 0.43299 0.848101
138 AMO 0.43299 0.846154
139 4AD 0.43299 0.835443
140 PAJ 0.43299 0.82716
141 BIS 0.43 0.848101
142 1ZZ 0.43 0.764706
143 PTJ 0.43 0.814815
144 3OD 0.43 0.857143
145 AR6 AR6 0.428571 0.831169
146 DLL 0.428571 0.844156
147 AHX 0.428571 0.8375
148 00A 0.428571 0.802469
149 A5D 0.428571 0.776316
150 GGZ 0.427083 0.8375
151 MHZ 0.426966 0.670455
152 TM1 0.425743 0.744186
153 3UK 0.424242 0.833333
154 G5A 0.423913 0.770115
155 SFG 0.422222 0.696203
156 OMR 0.422018 0.776471
157 NMN AMP PO4 0.421053 0.790123
158 NOC 0.421053 0.72973
159 SMM 0.421053 0.659091
160 2GP 0.420455 0.87013
161 LAD 0.42 0.804878
162 WAQ 0.42 0.802469
163 DTP 0.419355 0.868421
164 DDS 0.419355 0.842105
165 AS 0.418605 0.894737
166 UPA 0.418182 0.848101
167 ATP A A A 0.417476 0.842105
168 SP1 0.416667 0.88
169 NAP 0.416667 0.857143
170 RP1 0.416667 0.88
171 NB8 0.415842 0.814815
172 TXA 0.415842 0.846154
173 ME8 0.415842 0.785714
174 A7D 0.41573 0.766234
175 AFH 0.415094 0.82716
176 DG1 0.413223 0.8375
177 TAP 0.413223 0.871795
178 1DG 0.413223 0.8375
179 SA8 0.413043 0.658824
180 TSB 0.412371 0.788235
181 5CA 0.412371 0.790698
182 D3Y 0.412371 0.75641
183 5J9 0.411765 0.702381
184 MYR AMP 0.411765 0.744186
185 A5A 0.410526 0.776471
186 N01 0.410256 0.820513
187 LEU LMS 0.41 0.733333
188 NA0 0.409836 0.846154
189 2BA 0.409091 0.851351
190 CMP 0.409091 0.863014
191 SAI 0.408602 0.682927
192 SAH 0.408602 0.7125
193 GEK 0.408163 0.686747
194 9SN 0.407767 0.792683
195 S7M 0.40625 0.662791
196 SSA 0.40625 0.790698
197 3NZ 0.405941 0.75
198 P5A 0.405941 0.736264
199 G3A 0.40566 0.8375
200 ARJ 0.405063 0.716216
201 SAM 0.404255 0.662791
202 FA5 0.403846 0.822785
203 YAP 0.403846 0.8125
204 54H 0.402062 0.758621
205 VMS 0.402062 0.758621
206 52H 0.402062 0.75
207 G5P 0.401869 0.8375
208 APU 0.401786 0.858974
209 NVA LMS 0.4 0.733333
210 XAH 0.4 0.785714
211 AAT 0.4 0.719512
212 TYR AMP 0.4 0.8
213 EEM 0.4 0.643678
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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