Receptor
PDB id Resolution Class Description Source Keywords
2YPE 1.9 Å EC: 3.1.4.37 CATALYTIC DOMAIN OF MOUSE 2',3'-CYCLIC NUCLEOTIDE 3'- PHOSPHODIESTERASE, WITH MUTATION H309S, CRYSTALLIZED WITH 2C YCLIC AMP 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
ACY A:1381;
A:1379;
 Invalid;
Invalid;
 none;
none;
 submit data
60.052 C2 H4 O2 CC(=O...
ACK A:1382;
 Valid;
 none;
 submit data
329.206 C10 H12 N5 O6 P c1nc(...
CL A:1380;
 Invalid;
 none;
 submit data
35.453 Cl [Cl-]
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: ACK; Similar ligands found: 130
No: Ligand ECFP6 Tc MDL keys Tc
1 ACK 1 1
2 QQY 0.735294 0.941176
3 QQX 0.720588 0.927536
4 GGZ 0.658537 0.818182
5 LQJ 0.604396 0.914286
6 KL2 0.583333 0.940298
7 7D7 0.567164 0.782609
8 ADN 0.536232 0.811594
9 XYA 0.536232 0.811594
10 RAB 0.536232 0.811594
11 CMP 0.5 0.897059
12 2BA 0.5 0.884058
13 5N5 0.5 0.785714
14 7D5 0.493506 0.847222
15 5CD 0.493151 0.771429
16 A4D 0.493151 0.785714
17 2AM 0.487179 0.913043
18 M2T 0.486842 0.701299
19 3AM 0.481013 0.926471
20 A 0.475 0.885714
21 AMP 0.475 0.885714
22 EP4 0.473684 0.72
23 NWW 0.472973 0.75
24 3AD 0.472973 0.823529
25 OVE 0.469136 0.875
26 DTA 0.467532 0.753425
27 5AD 0.464789 0.761194
28 A3G 0.463415 0.767123
29 MTA 0.461538 0.739726
30 AV2 0.461538 0.887324
31 Y3J 0.459459 0.73913
32 CC5 0.458333 0.782609
33 J7C 0.457831 0.736842
34 LMS 0.45679 0.753086
35 RP1 0.45679 0.835616
36 SP1 0.45679 0.835616
37 A3S 0.453488 0.777778
38 3L1 0.453333 0.763889
39 3D1 0.453333 0.763889
40 7D3 0.452381 0.824324
41 AMP MG 0.451219 0.871429
42 6RE 0.451219 0.727273
43 3DH 0.45 0.739726
44 A2P 0.447059 0.898551
45 A3P 0.447059 0.885714
46 NEC 0.445783 0.760563
47 ADP 0.44186 0.861111
48 45A 0.440476 0.861111
49 ABM 0.440476 0.861111
50 A2D 0.440476 0.861111
51 ZAS 0.439024 0.733333
52 GJV 0.435294 0.717949
53 S4M 0.435294 0.654762
54 SRA 0.433735 0.837838
55 7D4 0.431818 0.824324
56 MAO 0.430233 0.707317
57 BA3 0.430233 0.861111
58 AP2 0.430233 0.826667
59 A12 0.430233 0.826667
60 DSH 0.428571 0.714286
61 SO8 0.428571 0.756757
62 AOC 0.428571 0.763889
63 OZV 0.427083 0.887324
64 2VA 0.426966 0.767123
65 A3T 0.426966 0.788732
66 ATP 0.426966 0.861111
67 HEJ 0.426966 0.861111
68 5X8 0.426966 0.72973
69 5AS 0.425287 0.729412
70 AF2 AF2 AF2 AF2 AF2 AF2 0.425287 0.805556
71 B4P 0.425287 0.861111
72 AP5 0.425287 0.861111
73 A3N 0.423529 0.753425
74 1YC 0.423077 0.835616
75 AQP 0.422222 0.861111
76 5FA 0.422222 0.861111
77 APC 0.422222 0.826667
78 2A5 0.422222 0.837838
79 ADP BEF 0.420455 0.859155
80 SON 0.420455 0.826667
81 AN2 0.420455 0.849315
82 ADP MG 0.420455 0.859155
83 AT4 0.420455 0.826667
84 AD9 0.417582 0.837838
85 ATR 0.417582 0.885714
86 NVA 2AD 0.417582 0.727273
87 PAP 0.417582 0.873239
88 101 0.416667 0.873239
89 AU1 0.41573 0.837838
90 M33 0.41573 0.849315
91 ADX 0.41573 0.775
92 MHZ 0.41573 0.686747
93 CA0 0.41573 0.837838
94 NWQ 0.414634 0.728571
95 VRT 0.413043 0.736842
96 SAH 0.413043 0.710526
97 DA 0.411765 0.847222
98 D5M 0.411765 0.847222
99 N5O 0.411765 0.777778
100 KG4 0.411111 0.837838
101 SFG 0.411111 0.716216
102 ACP 0.411111 0.837838
103 50T 0.411111 0.849315
104 CUU 0.411111 0.861111
105 ARJ 0.410256 0.73913
106 AFX 0.410256 0.689189
107 ACQ 0.408602 0.837838
108 T99 0.408602 0.826667
109 V3L 0.408602 0.861111
110 TAT 0.408602 0.826667
111 AR6 0.406593 0.861111
112 PRX 0.406593 0.837838
113 APR 0.406593 0.861111
114 5F1 0.405063 0.722222
115 A7D 0.404494 0.767123
116 PPS 0.404255 0.775
117 N5A 0.402299 0.75
118 ADP PO3 0.402174 0.859155
119 SA8 0.402174 0.675
120 RBY 0.402174 0.826667
121 ATP MG 0.402174 0.859155
122 APC MG 0.402174 0.835616
123 ADV 0.402174 0.826667
124 AGS 0.402174 0.815789
125 D3Y 0.402062 0.756757
126 TM1 0.401961 0.765432
127 1YD 0.4 0.813333
128 ALF ADP 0.4 0.792208
129 ANP MG 0.4 0.849315
130 4BW 0.4 0.813333
Similar Ligands (3D)
Ligand no: 1; Ligand: ACK; Similar ligands found: 83
No: Ligand Similarity coefficient
1 SGP 0.9755
2 2GP 0.9133
3 P2G 0.9106
4 T3P 0.9095
5 103 0.9045
6 FMC 0.9041
7 FMB 0.9032
8 5FD 0.9022
9 9DI 0.9010
10 AD3 0.8993
11 NOS 0.8978
12 TAL 0.8968
13 1DA 0.8954
14 TBN 0.8948
15 UA2 0.8936
16 XTS 0.8926
17 IMH 0.8920
18 DBM 0.8911
19 3GP 0.8900
20 3BH 0.8890
21 6MD 0.8888
22 2FA 0.8885
23 MDR 0.8885
24 5ID 0.8883
25 UM3 0.8882
26 8OX 0.8873
27 FTU 0.8871
28 EKH 0.8865
29 3Q0 0.8857
30 MTP 0.8856
31 BGC GAL 0.8846
32 GMP 0.8842
33 RPP 0.8831
34 HPR 0.8829
35 PRH 0.8829
36 NOC 0.8829
37 26A 0.8822
38 RVD 0.8818
39 GP0 0.8816
40 5NB 0.8803
41 MBY 0.8797
42 JMQ 0.8793
43 AGV 0.8790
44 GNG 0.8787
45 AZZ 0.8782
46 GPK 0.8773
47 PUR 0.8772
48 CFE 0.8770
49 38B 0.8769
50 THM 0.8767
51 MTH 0.8758
52 CL9 0.8755
53 MTI 0.8741
54 MG7 0.8736
55 DK4 0.8725
56 6J3 0.8722
57 URI 0.8721
58 EZB 0.8719
59 MCF 0.8714
60 4UO 0.8713
61 5UD 0.8707
62 581 0.8707
63 5P7 0.8705
64 KS5 0.8700
65 6EN 0.8689
66 5I5 0.8687
67 5BX 0.8687
68 BNY 0.8685
69 F01 0.8681
70 DCF 0.8665
71 53X 0.8655
72 5MD 0.8644
73 Z57 0.8644
74 HO4 0.8627
75 AQ1 0.8622
76 TO1 0.8618
77 RFZ 0.8617
78 Z15 0.8617
79 MTM 0.8616
80 CJZ 0.8598
81 2HN 0.8583
82 13A 0.8545
83 UUA 0.8534
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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