Receptor
PDB id Resolution Class Description Source Keywords
5WQA 2.3 Å EC: 3.1.4.17 CRYSTAL STRUCTURE OF PDE4D CATALYTIC DOMAIN COMPLEXED WITH SELAGINPULVILINS K HOMO SAPIENS NATURAL PDE4 INHIBTOR HYDROLASE-INHIBITOR COMPLEX
Ref.: THE DISCOVERY, COMPLEX CRYSTAL STRUCTURE, AND RECOG MECHANISM OF A NOVEL NATURAL PDE4 INHIBITOR FROM SE PULVINATA BIOCHEM. PHARMACOL. V. 130 51 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN A:502;
B:503;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
J20 A:501;
B:501;
Valid;
Valid;
none;
none;
ic50 = 0.011 uM
538.589 C36 H26 O5 COc1c...
MG A:503;
B:502;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+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 (27)
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 3SL6 ic50 = 0.29 uM JN8 C22 H27 N3 O4 S2 CCNC(=O)N1....
3 1OYN ic50 = 0.55 uM ROL C16 H21 N O3 COc1ccc(cc....
4 1Y2B ic50 = 82 uM DEE C8 H12 N2 O2 CCOC(=O)c1....
5 1TBB - ROL C16 H21 N O3 COc1ccc(cc....
6 4W1O - 3GJ C19 H17 Cl2 N3 O4 CCc1cc(on1....
7 1ZKN - IBM C10 H14 N4 O2 CC(C)CN1c2....
8 3SL4 ic50 = 0.027 uM JN4 C21 H21 N3 O4 S C=CNC(=O)N....
9 1XOQ ic50 = 0.68 nM ROF C17 H14 Cl2 F2 N2 O3 c1cc(c(cc1....
10 1Y2E ic50 = 0.16 uM 5DE C14 H17 N3 O2 CCOC(=O)c1....
11 1PTW - AMP C10 H14 N5 O7 P c1nc(c2c(n....
12 5WQA ic50 = 0.011 uM J20 C36 H26 O5 COc1ccc(cc....
13 1Y2D ic50 = 2 uM 4DE C15 H18 N2 O3 CCOC(=O)c1....
14 1XON ic50 = 0.021 nM PIL C18 H18 Cl2 N2 O3 COc1ccc(cc....
15 1TB7 - AMP C10 H14 N5 O7 P c1nc(c2c(n....
16 1XOR ic50 = 0.39 uM ZAR C12 H10 F2 N2 O3 COc1cc(ccc....
17 3G4K ic50 = 288 nM ROL C16 H21 N O3 COc1ccc(cc....
18 1Y2C ic50 = 0.27 uM 3DE C14 H17 N2 O2 CCOC(=O)c1....
19 2FM0 ic50 = 0.4 nM M98 C23 H18 F8 N2 O4 S c1cc(c[n+]....
20 1Y2K ic50 = 0.021 uM 7DE C14 H15 N3 O4 CCOC(=O)c1....
21 1XOM ic50 = 0.011 uM CIO C20 H25 N O4 COc1ccc(cc....
22 2PW3 - CMP C10 H12 N5 O6 P c1nc(c2c(n....
23 1Q9M ic50 = 0.33 uM ROL C16 H21 N O3 COc1ccc(cc....
24 4WCU ic50 = 3 nM 3KQ C24 H22 Cl2 N2 O5 COc1ccc(c(....
25 2FM5 ic50 = 43 nM M99 C23 H18 F8 N2 O4 S c1cc(c[n+]....
26 3G4I - D71 C19 H13 N5 O4 c1cc(cc(c1....
27 3G4L ic50 = 5.8 nM ROF C17 H14 Cl2 F2 N2 O3 c1cc(c(cc1....
70% Homology Family (53)
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 3SL6 ic50 = 0.29 uM JN8 C22 H27 N3 O4 S2 CCNC(=O)N1....
3 1OYN ic50 = 0.55 uM ROL C16 H21 N O3 COc1ccc(cc....
4 1Y2B ic50 = 82 uM DEE C8 H12 N2 O2 CCOC(=O)c1....
5 1TBB - ROL C16 H21 N O3 COc1ccc(cc....
6 4W1O - 3GJ C19 H17 Cl2 N3 O4 CCc1cc(on1....
7 1ZKN - IBM C10 H14 N4 O2 CC(C)CN1c2....
8 3SL4 ic50 = 0.027 uM JN4 C21 H21 N3 O4 S C=CNC(=O)N....
9 1XOQ ic50 = 0.68 nM ROF C17 H14 Cl2 F2 N2 O3 c1cc(c(cc1....
10 1Y2E ic50 = 0.16 uM 5DE C14 H17 N3 O2 CCOC(=O)c1....
11 1PTW - AMP C10 H14 N5 O7 P c1nc(c2c(n....
12 5WQA ic50 = 0.011 uM J20 C36 H26 O5 COc1ccc(cc....
13 1Y2D ic50 = 2 uM 4DE C15 H18 N2 O3 CCOC(=O)c1....
14 1XON ic50 = 0.021 nM PIL C18 H18 Cl2 N2 O3 COc1ccc(cc....
15 1TB7 - AMP C10 H14 N5 O7 P c1nc(c2c(n....
16 1XOR ic50 = 0.39 uM ZAR C12 H10 F2 N2 O3 COc1cc(ccc....
17 3G4K ic50 = 288 nM ROL C16 H21 N O3 COc1ccc(cc....
18 1Y2C ic50 = 0.27 uM 3DE C14 H17 N2 O2 CCOC(=O)c1....
19 2FM0 ic50 = 0.4 nM M98 C23 H18 F8 N2 O4 S c1cc(c[n+]....
20 1Y2K ic50 = 0.021 uM 7DE C14 H15 N3 O4 CCOC(=O)c1....
21 1XOM ic50 = 0.011 uM CIO C20 H25 N O4 COc1ccc(cc....
22 2PW3 - CMP C10 H12 N5 O6 P c1nc(c2c(n....
23 1Q9M ic50 = 0.33 uM ROL C16 H21 N O3 COc1ccc(cc....
24 4WCU ic50 = 3 nM 3KQ C24 H22 Cl2 N2 O5 COc1ccc(c(....
25 2FM5 ic50 = 43 nM M99 C23 H18 F8 N2 O4 S c1cc(c[n+]....
26 3G4I - D71 C19 H13 N5 O4 c1cc(cc(c1....
27 3G4L ic50 = 5.8 nM ROF C17 H14 Cl2 F2 N2 O3 c1cc(c(cc1....
28 3G58 ic50 = 5 nM 988 C21 H15 N3 O2 c1cc(cc(c1....
29 2QYK ic50 = 3.3 uM NPV C21 H13 N3 O4 c1cc(cc(c1....
30 3GWT ic50 = 7.94 pM 066 C27 H26 N4 O5 S Cc1cc(cc2c....
31 3WD9 ic50 = 8.3 nM QPC C24 H27 N5 O2 CC(C)(C)CN....
32 4KP6 ic50 = 0.87 nM 1S1 C12 H17 N9 CCC(CC)(C#....
33 4NW7 ic50 = 237 nM 2O5 C20 H17 Cl N4 O2 c1cc(cc(c1....
34 3FRG ic50 = 4 nM SK4 C18 H17 N3 O4 S COc1cccc(c....
35 1RO9 - 8BR C10 H13 Br N5 O7 P c1nc(c2c(n....
36 1XOT ic50 = 3.8 uM VDN C23 H32 N6 O4 S CCCc1nc(c2....
37 1XLX ic50 = 0.025 uM CIO C20 H25 N O4 COc1ccc(cc....
38 3O57 ic50 = 79.4 pM ZG2 C29 H34 N6 O3 CCn1c2c(cn....
39 3HMV - HBT C17 H17 N3 O4 S C[C@H]1CCc....
40 3O56 ic50 = 794 pM ZG1 C21 H27 N7 O3 CCn1c2c(cn....
41 1XLZ ic50 = 0.96 uM FIL C15 H20 N2 O4 C/C(=NOC(=....
42 1XN0 ic50 = 0.57 uM ROL C16 H21 N O3 COc1ccc(cc....
43 1TB5 - AMP C10 H14 N5 O7 P c1nc(c2c(n....
44 3D3P ic50 = 3.1 nM 20A C21 H25 N5 O2 CCn1c2c(cn....
45 3W5E ic50 = 11 nM NVW C25 H28 N4 O3 S CC(C)(C)NC....
46 4MYQ ic50 = 32 nM 19T C19 H18 Cl N3 O2 S CCc1c(nc(n....
47 2QYL ic50 = 0.65 uM NPV C21 H13 N3 O4 c1cc(cc(c1....
48 1XOS ic50 = 20 uM VIA C22 H30 N6 O4 S CCCc1c2c(n....
49 1XM6 ic50 = 0.42 uM 5RM C14 H19 N O4 CCCOc1cc(c....
50 1RO6 Ki ~ 375 nM ROL C16 H21 N O3 COc1ccc(cc....
51 1Y2H ic50 = 0.056 uM 6DE C14 H15 Cl N2 O2 CCOC(=O)c1....
52 1ROR - AMP C10 H14 N5 O7 P c1nc(c2c(n....
53 3G4G ic50 = 19 nM D71 C19 H13 N5 O4 c1cc(cc(c1....
50% Homology Family (6)
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 5WQA ic50 = 0.011 uM J20 C36 H26 O5 COc1ccc(cc....
3 1Y2D ic50 = 2 uM 4DE C15 H18 N2 O3 CCOC(=O)c1....
4 2HD1 ic50 ~ 500 uM IBM C10 H14 N4 O2 CC(C)CN1c2....
5 3G58 ic50 = 5 nM 988 C21 H15 N3 O2 c1cc(cc(c1....
6 3O56 ic50 = 794 pM ZG1 C21 H27 N7 O3 CCn1c2c(cn....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: J20; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 J20 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1XON; Ligand: PIL; Similar sites found: 36
This union binding pocket(no: 1) in the query (biounit: 1xon.bio2) has 32 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1GEG GLC 0.03412 0.40347 1.17188
2 3KP6 SAL 0.04439 0.40409 1.98676
3 4N6W FLC 0.0158 0.41065 2.19298
4 2WR1 NAG 0.01392 0.44548 2.29226
5 2XMY CDK 0.01586 0.40419 2.34899
6 2CIR BG6 0.0346 0.40566 2.3569
7 5JF2 SF7 0.01149 0.40342 2.45098
8 3LGG CFE 0.01213 0.41254 2.5788
9 2OKL BB2 0.009246 0.41099 2.7027
10 1W2D ADP 0.02795 0.40199 3.01887
11 3VSV XYP 0.03008 0.40414 3.15186
12 5GWE GWM 0.0327 0.40225 3.15186
13 5M77 7K2 7K3 0.02496 0.40085 3.15186
14 1DKF OLA 0.01185 0.41301 3.43348
15 2F5X ASP 0.0386 0.40236 3.4384
16 3G5K BB2 0.01047 0.41196 4.37158
17 5HSS 64Z 0.02277 0.41042 4.58221
18 5BU2 RIB 0.003816 0.46158 4.87106
19 3P9T TCL 0.01087 0.4227 5.02283
20 1WS1 BB2 0.007381 0.41909 5.12821
21 5UC9 MYR 0.0485 0.40016 5.44413
22 3N7S 3N7 0.01403 0.43926 6.25
23 3ZCB ATP 0.01041 0.41572 6.56566
24 4V3I ASP LEU THR ARG PRO 0.02575 0.41722 6.61479
25 5EW9 5VC 0.02979 0.40714 7.01107
26 5OCA 9QZ 0.0005967 0.50997 7.14286
27 5V4R MGT 0.0006396 0.51211 7.40741
28 3R9V DXC 0.03454 0.40724 7.69231
29 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 0.02105 0.40823 8.57143
30 4MGA 27L 0.01515 0.43472 10.1961
31 4UCC ZKW 0.02414 0.42158 10.7296
32 5DCH 1YO 0.007746 0.44276 13.5417
33 1O4T OXL 0.004053 0.45851 14.0401
34 1T0S BML 0.005739 0.43438 16.2791
35 3BJC WAN 0.0000007863 0.43111 42.1203
36 5EDE 5M6 0.0000008209 0.46137 43.8095
Pocket No.: 2; Query (leader) PDB : 1XON; Ligand: PIL; Similar sites found: 3
This union binding pocket(no: 2) in the query (biounit: 1xon.bio1) has 33 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3RV5 DXC 0.02858 0.40221 None
2 4LH7 NMN 0.04847 0.40037 7.12074
3 2QJY UQ2 0.0264 0.41497 9.09091
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