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 2C YCLIC-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 (2D)
Ligand no: 1; Ligand: QQY; Similar ligands found: 128
No: Ligand ECFP6 Tc MDL keys Tc
1 QQY 1 1
2 ACK 0.735294 0.941176
3 QQX 0.695652 0.985507
4 KL2 0.583333 0.887324
5 7D7 0.567164 0.739726
6 RAB 0.536232 0.767123
7 ADN 0.536232 0.767123
8 XYA 0.536232 0.767123
9 5N5 0.521127 0.743243
10 A4D 0.513889 0.767123
11 GGZ 0.511111 0.822785
12 7D5 0.493506 0.802632
13 5CD 0.493151 0.72973
14 OVE 0.4875 0.90411
15 2AM 0.487179 0.863014
16 M2T 0.486842 0.6875
17 3AM 0.481013 0.875
18 A 0.475 0.837838
19 AMP 0.475 0.837838
20 LQJ 0.474747 0.864865
21 EP4 0.473684 0.683544
22 NWW 0.472973 0.708333
23 3AD 0.472973 0.777778
24 A3S 0.470588 0.736842
25 DTA 0.467532 0.76
26 5AD 0.464789 0.71831
27 A3G 0.463415 0.727273
28 MTA 0.461538 0.723684
29 AV2 0.461538 0.84
30 J7C 0.457831 0.7
31 LMS 0.45679 0.759036
32 ZAS 0.45679 0.696203
33 3L1 0.453333 0.723684
34 3D1 0.453333 0.723684
35 7D3 0.452381 0.782051
36 AMP MG 0.451219 0.824324
37 6RE 0.451219 0.691358
38 3DH 0.45 0.723684
39 A2P 0.447059 0.849315
40 CMP 0.447059 0.847222
41 2BA 0.447059 0.835616
42 A3P 0.447059 0.837838
43 DSH 0.445783 0.7
44 AOC 0.445783 0.723684
45 ADP 0.44186 0.815789
46 45A 0.440476 0.815789
47 ABM 0.440476 0.815789
48 A2D 0.440476 0.815789
49 Y3J 0.44 0.69863
50 RP1 0.439024 0.890411
51 SP1 0.439024 0.890411
52 CC5 0.438356 0.739726
53 AT4 0.436782 0.855263
54 S4M 0.435294 0.643678
55 SRA 0.433735 0.866667
56 7D4 0.431818 0.782051
57 AU1 0.431818 0.794872
58 MAO 0.430233 0.674419
59 BA3 0.430233 0.815789
60 A12 0.430233 0.78481
61 AP2 0.430233 0.78481
62 SO8 0.428571 0.717949
63 NEC 0.428571 0.72
64 A3T 0.426966 0.746667
65 ATP 0.426966 0.815789
66 5X8 0.426966 0.714286
67 HEJ 0.426966 0.815789
68 2VA 0.426966 0.727273
69 AP5 0.425287 0.815789
70 AF2 AF2 AF2 AF2 AF2 AF2 0.425287 0.763158
71 B4P 0.425287 0.815789
72 5AS 0.425287 0.735632
73 T99 0.423913 0.855263
74 TAT 0.423913 0.855263
75 A3N 0.423529 0.714286
76 0UM 0.42268 0.654762
77 APC 0.422222 0.78481
78 5FA 0.422222 0.815789
79 2A5 0.422222 0.794872
80 AQP 0.422222 0.815789
81 ADP BEF 0.420455 0.813333
82 ADP MG 0.420455 0.813333
83 SON 0.420455 0.78481
84 AN2 0.420455 0.805195
85 A7D 0.420455 0.75
86 GJV 0.418605 0.682927
87 NVA 2AD 0.417582 0.691358
88 ATR 0.417582 0.837838
89 PAP 0.417582 0.826667
90 101 0.416667 0.826667
91 MHZ 0.41573 0.655172
92 ADX 0.41573 0.780488
93 M33 0.41573 0.805195
94 CA0 0.41573 0.794872
95 NWQ 0.414634 0.689189
96 SAH 0.413043 0.696203
97 VRT 0.413043 0.7
98 D5M 0.411765 0.802632
99 N5O 0.411765 0.736842
100 DA 0.411765 0.802632
101 CUU 0.411111 0.815789
102 ACP 0.411111 0.794872
103 SFG 0.411111 0.679487
104 KG4 0.411111 0.794872
105 50T 0.411111 0.805195
106 ARJ 0.410256 0.69863
107 AFX 0.410256 0.653846
108 V3L 0.408602 0.815789
109 ACQ 0.408602 0.794872
110 AR6 0.406593 0.815789
111 PRX 0.406593 0.794872
112 APR 0.406593 0.815789
113 5F1 0.405063 0.684211
114 EEM 0.404255 0.627907
115 PPS 0.404255 0.780488
116 N5A 0.402299 0.710526
117 ATP MG 0.402174 0.813333
118 A5D 0.402174 0.76
119 ADP PO3 0.402174 0.813333
120 AD9 0.402174 0.794872
121 APC MG 0.402174 0.792208
122 RBY 0.402174 0.78481
123 ADV 0.402174 0.78481
124 AGS 0.402174 0.844156
125 SA8 0.402174 0.642857
126 D3Y 0.402062 0.717949
127 TM1 0.401961 0.729412
128 ANP MG 0.4 0.805195
Similar Ligands (3D)
Ligand no: 1; Ligand: QQY; Similar ligands found: 62
No: Ligand Similarity coefficient
1 SGP 0.9694
2 9DI 0.9147
3 FMC 0.9144
4 FMB 0.9142
5 5FD 0.9064
6 2GP 0.9043
7 TBN 0.9029
8 AD3 0.9011
9 NOS 0.8982
10 FM1 0.8978
11 DBM 0.8964
12 P2G 0.8950
13 3BH 0.8946
14 MDR 0.8946
15 TAL 0.8931
16 XTS 0.8926
17 PRH 0.8923
18 6MD 0.8918
19 GMP 0.8910
20 IMH 0.8902
21 4UO 0.8896
22 5ID 0.8886
23 UA2 0.8885
24 MTP 0.8884
25 1DA 0.8883
26 HPR 0.8880
27 FTU 0.8855
28 5NB 0.8847
29 CFE 0.8843
30 8OX 0.8817
31 26A 0.8804
32 EKH 0.8789
33 GP0 0.8759
34 MBY 0.8754
35 GNG 0.8750
36 JMQ 0.8750
37 RFZ 0.8743
38 AZZ 0.8741
39 2FA 0.8724
40 PUR 0.8715
41 5I5 0.8714
42 DCF 0.8713
43 RPP 0.8705
44 MTH 0.8702
45 MTM 0.8697
46 URI 0.8695
47 F01 0.8688
48 MG7 0.8681
49 5MD 0.8672
50 CL9 0.8668
51 6J3 0.8662
52 13A 0.8657
53 EZB 0.8657
54 GPK 0.8654
55 DK4 0.8654
56 5UD 0.8653
57 MTI 0.8649
58 THM 0.8628
59 NOC 0.8627
60 AGV 0.8614
61 GPU 0.8567
62 MCF 0.8566
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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