Receptor
PDB id Resolution Class Description Source Keywords
2YPH 2.1 Å EC: 3.1.4.37 CATALYTIC DOMAIN OF MOUSE 2',3'-CYCLIC NUCLEOTIDE 3'- PHOSPHODIESTERASE, WITH MUTATION H230S, CRYSTALLIZED WITH 2 ',3-(RP)-CYCLIC-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
ACT A:1379;
Invalid;
none;
submit data
59.044 C2 H3 O2 CC(=O...
CL A:1380;
Invalid;
none;
submit data
35.453 Cl [Cl-]
QQY A:1381;
Valid;
none;
submit data
345.272 C10 H12 N5 O5 P S c1nc(...
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: QQY; Similar ligands found: 113
No: Ligand ECFP6 Tc MDL keys Tc
1 QQY 1 1
2 ACK 0.735294 0.941176
3 QQX 0.695652 0.985507
4 7D7 0.567164 0.739726
5 XYA 0.536232 0.767123
6 RAB 0.536232 0.767123
7 ADN 0.536232 0.767123
8 5N5 0.521127 0.743243
9 A4D 0.513889 0.767123
10 GGZ 0.511111 0.822785
11 7D5 0.493506 0.802632
12 5CD 0.493151 0.72973
13 OVE 0.4875 0.90411
14 2AM 0.487179 0.863014
15 M2T 0.486842 0.6875
16 3AM 0.481013 0.875
17 AMP 0.475 0.837838
18 A 0.475 0.837838
19 EP4 0.473684 0.683544
20 3AD 0.472973 0.777778
21 A3S 0.470588 0.736842
22 DTA 0.467532 0.76
23 5AD 0.464789 0.71831
24 A3G 0.463415 0.727273
25 MTA 0.461538 0.723684
26 AV2 0.461538 0.84
27 J7C 0.457831 0.7
28 ZAS 0.45679 0.696203
29 3L1 0.453333 0.723684
30 3D1 0.453333 0.723684
31 7D3 0.452381 0.782051
32 6RE 0.451219 0.691358
33 3DH 0.45 0.723684
34 2BA 0.447059 0.835616
35 CMP 0.447059 0.847222
36 A3P 0.447059 0.837838
37 A2P 0.447059 0.849315
38 AMP MG 0.445783 0.792208
39 DSH 0.445783 0.7
40 AOC 0.445783 0.723684
41 ADP 0.44186 0.815789
42 A2D 0.440476 0.815789
43 ABM 0.440476 0.815789
44 Y3J 0.44 0.69863
45 RP1 0.439024 0.890411
46 SP1 0.439024 0.890411
47 CC5 0.438356 0.739726
48 S4M 0.435294 0.643678
49 SRA 0.433735 0.866667
50 7D4 0.431818 0.782051
51 AU1 0.431818 0.794872
52 BA3 0.430233 0.815789
53 MAO 0.430233 0.674419
54 AP2 0.430233 0.78481
55 A12 0.430233 0.78481
56 SO8 0.428571 0.717949
57 NEC 0.428571 0.72
58 5X8 0.426966 0.714286
59 ATP 0.426966 0.815789
60 2VA 0.426966 0.727273
61 A3T 0.426966 0.746667
62 B4P 0.425287 0.815789
63 5AS 0.425287 0.735632
64 AP5 0.425287 0.815789
65 TAT 0.423913 0.855263
66 A3N 0.423529 0.714286
67 0UM 0.42268 0.654762
68 5FA 0.422222 0.815789
69 2A5 0.422222 0.794872
70 AQP 0.422222 0.815789
71 APC 0.422222 0.78481
72 A7D 0.420455 0.75
73 AN2 0.420455 0.805195
74 SON 0.420455 0.78481
75 GJV 0.418605 0.682927
76 NVA 2AD 0.417582 0.717949
77 PAP 0.417582 0.826667
78 ATR 0.417582 0.837838
79 101 0.416667 0.826667
80 MHZ 0.41573 0.655172
81 M33 0.41573 0.805195
82 ADX 0.41573 0.780488
83 ADP MG 0.41573 0.782051
84 CA0 0.41573 0.794872
85 VRT 0.413043 0.7
86 SAH 0.413043 0.696203
87 DA 0.411765 0.802632
88 D5M 0.411765 0.802632
89 SFG 0.411111 0.679487
90 BEF ADP 0.411111 0.7625
91 50T 0.411111 0.805195
92 ADP BEF 0.411111 0.7625
93 ACP 0.411111 0.794872
94 AFX 0.410256 0.653846
95 ARJ 0.410256 0.69863
96 V3L 0.408602 0.815789
97 ACQ 0.408602 0.794872
98 APR 0.406593 0.815789
99 PRX 0.406593 0.794872
100 AR6 0.406593 0.815789
101 5F1 0.405063 0.684211
102 EEM 0.404255 0.627907
103 PPS 0.404255 0.780488
104 AGS 0.402174 0.844156
105 ADP PO3 0.402174 0.813333
106 RBY 0.402174 0.78481
107 ADV 0.402174 0.78481
108 SA8 0.402174 0.642857
109 A5D 0.402174 0.76
110 SAP 0.402174 0.844156
111 AD9 0.402174 0.794872
112 D3Y 0.402062 0.717949
113 TM1 0.401961 0.729412
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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