Receptor
PDB id Resolution Class Description Source Keywords
2QYN 1.57 Å EC: 3.1.4.17 CRYSTAL STRUCTURE OF PDE4D2 IN COMPLEX WITH INHIBITOR NPV HOMO SAPIENS PDE4D SELECTIVE INHIBITOR NVP ALTERNATIVE SPLICING CAMP CYTOPLASM CYTOSKELETON HYDROLASE MEMBRANE METAL-BINDINGPHOSPHORYLATION
Ref.: STRUCTURES OF THE FOUR SUBFAMILIES OF PHOSPHODIESTERASE-4 PROVIDE INSIGHT INTO THE SELECTIVITY OF THEIR INHIBITORS. BIOCHEM.J. V. 408 193 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:502;
B:502;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
24.305 Mg [Mg+2...
NPV A:1;
B:1;
 Valid;
Valid;
 none;
none;
 ic50 = 0.57 uM
371.346 C21 H13 N3 O4 c1cc(...
ZN A:501;
B:501;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1XON 1.72 Å EC: 3.1.4.17 CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4D IN COMPLEX WI PICLAMILAST HOMO SAPIENS PHOSPHODIESTERASE PDE PDE4D PICLAMILAST HYDROLASE
Ref.: STRUCTURAL BASIS FOR THE ACTIVITY OF DRUGS THAT INH PHOSPHODIESTERASES. STRUCTURE V. 12 2233 2004
Members (57)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 19 families.
1 2QYN ic50 = 0.57 uM NPV C21 H13 N3 O4 c1cc(cc(c1....
2 6F8R ic50 = 20 uM CZK C22 H31 N3 O4 COc1ccc(cc....
3 6NJI - KR4 C19 H19 Cl N4 O CCc1nc(nc(....
4 3G58 ic50 = 5 nM 988 C21 H15 N3 O2 c1cc(cc(c1....
5 6BOJ - E31 C21 H20 Cl N3 O CCc1cc(nc(....
6 3SL6 ic50 = 0.29 uM JN8 C22 H27 N3 O4 S2 CCNC(=O)N1....
7 1OYN ic50 = 0.55 uM ROL C16 H21 N O3 COc1ccc(cc....
8 6F8X ic50 = 17 uM D08 C21 H30 N2 O6 COc1ccc(cc....
9 1Y2B ic50 = 82 uM DEE C8 H12 N2 O2 CCOC(=O)c1....
10 6IMD ic50 = 58.5 uM AH9 C12 H15 N O3 COc1cc2c(c....
11 1TBB - ROL C16 H21 N O3 COc1ccc(cc....
12 4W1O - 3GJ C19 H17 Cl2 N3 O4 CCc1cc(on1....
13 5LBO - 6M5 C33 H40 N6 O4 COc1ccc(cc....
14 6IMT ic50 = 0.25 uM AK0 C22 H23 F N2 O3 COc1cc2c(c....
15 6RCW - JX2 C30 H33 N3 O4 COc1ccc(cc....
16 6HWO Ki = 0.00000079 M FFZ C28 H29 N3 O3 CC(C)N1C(=....
17 6IMI ic50 = 26.1 uM AH6 C13 H17 N O3 CCOc1cc2c(....
18 6IMB ic50 = 58.5 uM AH9 C12 H15 N O3 COc1cc2c(c....
19 1ZKN - IBM C10 H14 N4 O2 CC(C)CN1c2....
20 6NJJ - KR7 C21 H15 Cl F3 N O2 c1cc(cc(c1....
21 3SL4 ic50 = 0.027 uM JN4 C21 H21 N3 O4 S C=CNC(=O)N....
22 1XOQ ic50 = 0.68 nM ROF C17 H14 Cl2 F2 N2 O3 c1cc(c(cc1....
23 1Y2E ic50 = 0.16 uM 5DE C14 H17 N3 O2 CCOC(=O)c1....
24 1PTW - AMP C10 H14 N5 O7 P c1nc(c2c(n....
25 6FTW - E6Z C25 H29 N3 O3 COc1ccc(cc....
26 5WQA ic50 = 0.011 uM J20 C36 H26 O5 COc1ccc(cc....
27 1Y2D ic50 = 2 uM 4DE C15 H18 N2 O3 CCOC(=O)c1....
28 6F8W ic50 = 23 uM D0E C22 H29 N3 O4 COc1ccc(cc....
29 6AKR - A0O C15 H16 O3 CC(=CCc1c(....
30 1XON ic50 = 0.021 nM PIL C18 H18 Cl2 N2 O3 COc1ccc(cc....
31 6NJH - KRD C19 H18 Cl N5 O CCc1nc(nc(....
32 1TB7 - AMP C10 H14 N5 O7 P c1nc(c2c(n....
33 6FDC ic50 = 2.3 uM DD5 C22 H29 F2 N3 O4 c1cc(c(cc1....
34 6IND ic50 = 0.24 uM AKO C23 H26 N2 O3 Cc1ccc2c(c....
35 6INK ic50 = 0.27 uM AKU C22 H24 N2 O3 COc1cc2c(c....
36 6IMR ic50 = 4.3 uM AJX C23 H26 N2 O3 COc1cc2c(c....
37 1XOR ic50 = 0.39 uM ZAR C12 H10 F2 N2 O3 COc1cc(ccc....
38 3G4K ic50 = 288 nM ROL C16 H21 N O3 COc1ccc(cc....
39 1Y2C ic50 = 0.27 uM 3DE C14 H17 N2 O2 CCOC(=O)c1....
40 2FM0 ic50 = 0.4 nM M98 C23 H18 F8 N2 O4 S c1cc(c[n+]....
41 6KJZ ic50 = 420 nM MKU C24 H26 O6 CC(=CCc1c2....
42 6F8T ic50 = 7 uM CZT C22 H34 N2 O5 C[C@@H]1CN....
43 1Y2K ic50 = 0.021 uM 7DE C14 H15 N3 O4 CCOC(=O)c1....
44 1XOM ic50 = 0.011 uM CIO C20 H25 N O4 COc1ccc(cc....
45 6KK0 ic50 = 17 nM M36 C31 H36 O8 CC(=CCc1c2....
46 2PW3 - CMP C10 H12 N5 O6 P c1nc(c2c(n....
47 6IM6 ic50 = 20.7 uM AH3 C13 H17 N O3 CCOc1cc2c(....
48 1Q9M ic50 = 0.33 uM ROL C16 H21 N O3 COc1ccc(cc....
49 4WCU ic50 = 3 nM 3KQ C24 H22 Cl2 N2 O5 COc1ccc(c(....
50 6F8U ic50 = 0.8 uM CZQ C21 H28 F2 N2 O5 C[C@@H]1CN....
51 6INM ic50 = 0.51 uM AKU C22 H24 N2 O3 COc1cc2c(c....
52 2FM5 ic50 = 43 nM M99 C23 H18 F8 N2 O4 S c1cc(c[n+]....
53 3G4I - D71 C19 H13 N5 O4 c1cc(cc(c1....
54 6F6U ic50 = 16 uM CV8 C21 H30 N2 O5 C[C@@H]1CN....
55 6F8V ic50 = 16 uM D0B C24 H33 N3 O4 C[C@@H]1CN....
56 6IMO ic50 = 0.65 uM AJL C21 H22 N2 O3 COc1cc2c(c....
57 3G4L ic50 = 5.8 nM ROF C17 H14 Cl2 F2 N2 O3 c1cc(c(cc1....
70% Homology Family (84)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 15 families.
1 2QYN ic50 = 0.57 uM NPV C21 H13 N3 O4 c1cc(cc(c1....
2 6F8R ic50 = 20 uM CZK C22 H31 N3 O4 COc1ccc(cc....
3 6NJI - KR4 C19 H19 Cl N4 O CCc1nc(nc(....
4 3G58 ic50 = 5 nM 988 C21 H15 N3 O2 c1cc(cc(c1....
5 6BOJ - E31 C21 H20 Cl N3 O CCc1cc(nc(....
6 3SL6 ic50 = 0.29 uM JN8 C22 H27 N3 O4 S2 CCNC(=O)N1....
7 1OYN ic50 = 0.55 uM ROL C16 H21 N O3 COc1ccc(cc....
8 6F8X ic50 = 17 uM D08 C21 H30 N2 O6 COc1ccc(cc....
9 1Y2B ic50 = 82 uM DEE C8 H12 N2 O2 CCOC(=O)c1....
10 6IMD ic50 = 58.5 uM AH9 C12 H15 N O3 COc1cc2c(c....
11 1TBB - ROL C16 H21 N O3 COc1ccc(cc....
12 4W1O - 3GJ C19 H17 Cl2 N3 O4 CCc1cc(on1....
13 5LBO - 6M5 C33 H40 N6 O4 COc1ccc(cc....
14 6IMT ic50 = 0.25 uM AK0 C22 H23 F N2 O3 COc1cc2c(c....
15 6RCW - JX2 C30 H33 N3 O4 COc1ccc(cc....
16 6HWO Ki = 0.00000079 M FFZ C28 H29 N3 O3 CC(C)N1C(=....
17 6IMI ic50 = 26.1 uM AH6 C13 H17 N O3 CCOc1cc2c(....
18 6IMB ic50 = 58.5 uM AH9 C12 H15 N O3 COc1cc2c(c....
19 1ZKN - IBM C10 H14 N4 O2 CC(C)CN1c2....
20 6NJJ - KR7 C21 H15 Cl F3 N O2 c1cc(cc(c1....
21 3SL4 ic50 = 0.027 uM JN4 C21 H21 N3 O4 S C=CNC(=O)N....
22 1XOQ ic50 = 0.68 nM ROF C17 H14 Cl2 F2 N2 O3 c1cc(c(cc1....
23 1Y2E ic50 = 0.16 uM 5DE C14 H17 N3 O2 CCOC(=O)c1....
24 1PTW - AMP C10 H14 N5 O7 P c1nc(c2c(n....
25 6FTW - E6Z C25 H29 N3 O3 COc1ccc(cc....
26 5WQA ic50 = 0.011 uM J20 C36 H26 O5 COc1ccc(cc....
27 1Y2D ic50 = 2 uM 4DE C15 H18 N2 O3 CCOC(=O)c1....
28 6F8W ic50 = 23 uM D0E C22 H29 N3 O4 COc1ccc(cc....
29 6AKR - A0O C15 H16 O3 CC(=CCc1c(....
30 1XON ic50 = 0.021 nM PIL C18 H18 Cl2 N2 O3 COc1ccc(cc....
31 6NJH - KRD C19 H18 Cl N5 O CCc1nc(nc(....
32 1TB7 - AMP C10 H14 N5 O7 P c1nc(c2c(n....
33 6FDC ic50 = 2.3 uM DD5 C22 H29 F2 N3 O4 c1cc(c(cc1....
34 6IND ic50 = 0.24 uM AKO C23 H26 N2 O3 Cc1ccc2c(c....
35 6INK ic50 = 0.27 uM AKU C22 H24 N2 O3 COc1cc2c(c....
36 6IMR ic50 = 4.3 uM AJX C23 H26 N2 O3 COc1cc2c(c....
37 1XOR ic50 = 0.39 uM ZAR C12 H10 F2 N2 O3 COc1cc(ccc....
38 3G4K ic50 = 288 nM ROL C16 H21 N O3 COc1ccc(cc....
39 1Y2C ic50 = 0.27 uM 3DE C14 H17 N2 O2 CCOC(=O)c1....
40 2FM0 ic50 = 0.4 nM M98 C23 H18 F8 N2 O4 S c1cc(c[n+]....
41 6KJZ ic50 = 420 nM MKU C24 H26 O6 CC(=CCc1c2....
42 6F8T ic50 = 7 uM CZT C22 H34 N2 O5 C[C@@H]1CN....
43 1Y2K ic50 = 0.021 uM 7DE C14 H15 N3 O4 CCOC(=O)c1....
44 1XOM ic50 = 0.011 uM CIO C20 H25 N O4 COc1ccc(cc....
45 6KK0 ic50 = 17 nM M36 C31 H36 O8 CC(=CCc1c2....
46 2PW3 - CMP C10 H12 N5 O6 P c1nc(c2c(n....
47 6IM6 ic50 = 20.7 uM AH3 C13 H17 N O3 CCOc1cc2c(....
48 1Q9M ic50 = 0.33 uM ROL C16 H21 N O3 COc1ccc(cc....
49 4WCU ic50 = 3 nM 3KQ C24 H22 Cl2 N2 O5 COc1ccc(c(....
50 6F8U ic50 = 0.8 uM CZQ C21 H28 F2 N2 O5 C[C@@H]1CN....
51 6INM ic50 = 0.51 uM AKU C22 H24 N2 O3 COc1cc2c(c....
52 2FM5 ic50 = 43 nM M99 C23 H18 F8 N2 O4 S c1cc(c[n+]....
53 3G4I - D71 C19 H13 N5 O4 c1cc(cc(c1....
54 6F6U ic50 = 16 uM CV8 C21 H30 N2 O5 C[C@@H]1CN....
55 6F8V ic50 = 16 uM D0B C24 H33 N3 O4 C[C@@H]1CN....
56 6IMO ic50 = 0.65 uM AJL C21 H22 N2 O3 COc1cc2c(c....
57 3G4L ic50 = 5.8 nM ROF C17 H14 Cl2 F2 N2 O3 c1cc(c(cc1....
58 5OHJ ic50 = 0.0378 nM 9VE C32 H34 Cl2 F2 N3 O8 S CN(C)C(=O)....
59 5LAQ Ki = 0.63 nM 6M5 C33 H40 N6 O4 COc1ccc(cc....
60 2QYK ic50 = 3.3 uM NPV C21 H13 N3 O4 c1cc(cc(c1....
61 3GWT ic50 = 7.94 pM 066 C27 H26 N4 O5 S Cc1cc(cc2c....
62 3WD9 ic50 = 8.3 nM QPC C24 H27 N5 O2 CC(C)(C)CN....
63 4KP6 ic50 = 0.87 nM 1S1 C12 H17 N9 CCC(CC)(C#....
64 4NW7 ic50 = 237 nM 2O5 C20 H17 Cl N4 O2 c1cc(cc(c1....
65 3FRG ic50 = 3.98 nM SK4 C18 H17 N3 O4 S COc1cccc(c....
66 1RO9 - 8BR C10 H13 Br N5 O7 P c1nc(c2c(n....
67 1XOT ic50 = 3.8 uM VDN C23 H32 N6 O4 S CCCc1nc(c2....
68 1XLX ic50 = 0.025 uM CIO C20 H25 N O4 COc1ccc(cc....
69 3O57 ic50 = 79.4 pM ZG2 C29 H34 N6 O3 CCn1c2c(cn....
70 3HMV - HBT C17 H17 N3 O4 S C[C@H]1CCc....
71 3O56 ic50 = 794 pM ZG1 C21 H27 N7 O3 CCn1c2c(cn....
72 1XLZ ic50 = 0.96 uM FIL C15 H20 N2 O4 C/C(=NOC(=....
73 1XN0 ic50 = 0.57 uM ROL C16 H21 N O3 COc1ccc(cc....
74 1TB5 - AMP C10 H14 N5 O7 P c1nc(c2c(n....
75 3D3P ic50 = 3.1 nM 20A C21 H25 N5 O2 CCn1c2c(cn....
76 3W5E ic50 = 11 nM NVW C25 H28 N4 O3 S CC(C)(C)NC....
77 4MYQ ic50 = 32 nM 19T C19 H18 Cl N3 O2 S CCc1c(nc(n....
78 2QYL ic50 = 0.65 uM NPV C21 H13 N3 O4 c1cc(cc(c1....
79 1XOS ic50 = 20 uM VIA C22 H30 N6 O4 S CCCc1c2c(n....
80 1XM6 ic50 = 0.42 uM 5RM C14 H19 N O4 CCCOc1cc(c....
81 1RO6 Ki ~ 375 nM ROL C16 H21 N O3 COc1ccc(cc....
82 1Y2H ic50 = 0.056 uM 6DE C14 H15 Cl N2 O2 CCOC(=O)c1....
83 1ROR - AMP C10 H14 N5 O7 P c1nc(c2c(n....
84 3G4G ic50 = 19 nM D71 C19 H13 N5 O4 c1cc(cc(c1....
50% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 2QYN ic50 = 0.57 uM NPV C21 H13 N3 O4 c1cc(cc(c1....
2 6F8R ic50 = 20 uM CZK C22 H31 N3 O4 COc1ccc(cc....
3 6NJI - KR4 C19 H19 Cl N4 O CCc1nc(nc(....
4 3G58 ic50 = 5 nM 988 C21 H15 N3 O2 c1cc(cc(c1....
5 6BOJ - E31 C21 H20 Cl N3 O CCc1cc(nc(....
6 3SL6 ic50 = 0.29 uM JN8 C22 H27 N3 O4 S2 CCNC(=O)N1....
7 1OYN ic50 = 0.55 uM ROL C16 H21 N O3 COc1ccc(cc....
8 6F8X ic50 = 17 uM D08 C21 H30 N2 O6 COc1ccc(cc....
9 2HD1 ic50 ~ 500 uM IBM C10 H14 N4 O2 CC(C)CN1c2....
10 5OHJ ic50 = 0.0378 nM 9VE C32 H34 Cl2 F2 N3 O8 S CN(C)C(=O)....
11 3G3N ic50 = 0.51 uM TC8 C15 H10 F2 N2 O S CSC1=Nc2cc....
12 4Y2B ic50 = 4.4 nM EPK C16 H18 N4 O S CCN1C(=O)c....
13 1ZKL ic50 = 8.1 uM IBM C10 H14 N4 O2 CC(C)CN1c2....
14 4PM0 ic50 = 45 nM 32V C15 H17 N3 O S CCN1C(=O)c....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: NPV; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 NPV 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: NPV; Similar ligands found: 3
No: Ligand Similarity coefficient
1 AVM 0.8805
2 O32 0.8801
3 6ZF 0.8789
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1XON; Ligand: PIL; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 1xon.bio2) has 46 residues
No: Leader PDB Ligand Sequence Similarity
1 4Y2B EPK 47.851
Pocket No.: 2; Query (leader) PDB : 1XON; Ligand: PIL; Similar sites found with APoc: 2
This union binding pocket(no: 2) in the query (biounit: 1xon.bio1) has 47 residues
No: Leader PDB Ligand Sequence Similarity
1 6CPT IBM 41.5473
2 4Y2B EPK 47.851
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