Receptor
PDB id Resolution Class Description Source Keywords
3G58 2.05 Å EC: 3.1.4.17 CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 4D WITH D155988/PMNPQ HOMO SAPIENS PHOSPHODIESTERASE PDE4D ALTERNATIVE SPLICING CAMP CYTOPLASM CYTOSKELETON HYDROLASE MEMBRANE METAL- BINDING PHOSPHOPROTEIN
Ref.: DESIGN OF PHOSPHODIESTERASE 4D (PDE4D) ALLOSTERIC MODULATORS FOR ENHANCING COGNITION WITH IMPROVED SAFETY. NAT.BIOTECHNOL. V. 28 63 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
988 A:901;
B:902;
C:903;
D:904;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
ic50 = 5 nM
341.363 C21 H15 N3 O2 c1cc(...
EDO A:12;
A:6;
A:7;
A:9;
B:10;
B:17;
B:3;
B:8;
C:13;
C:16;
C:18;
C:5;
D:11;
D:14;
D:15;
D:2;
D:4;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
MG A:625;
B:625;
C:625;
D:625;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
SO4 A:1;
Invalid;
none;
submit data
96.063 O4 S [O-]S...
ZN A:624;
B:624;
C:624;
D:624;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3G58 2.05 Å EC: 3.1.4.17 CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 4D WITH D155988/PMNPQ HOMO SAPIENS PHOSPHODIESTERASE PDE4D ALTERNATIVE SPLICING CAMP CYTOPLASM CYTOSKELETON HYDROLASE MEMBRANE METAL- BINDING PHOSPHOPROTEIN
Ref.: DESIGN OF PHOSPHODIESTERASE 4D (PDE4D) ALLOSTERIC MODULATORS FOR ENHANCING COGNITION WITH IMPROVED SAFETY. NAT.BIOTECHNOL. V. 28 63 2010
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 19 families.
1 3G58 ic50 = 5 nM 988 C21 H15 N3 O2 c1cc(cc(c1....
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: 988; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 988 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3G58; Ligand: 988; Similar sites found: 147
This union binding pocket(no: 1) in the query (biounit: 3g58.bio3) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1UO5 PIH 0.02716 0.40783 None
2 5AZC PGT 0.005579 0.47534 0.666667
3 2OBD PCW 0.004749 0.4435 1.04987
4 1GEG GLC 0.04934 0.40139 1.17188
5 4DSG UDP 0.02789 0.42804 1.31234
6 4DSG FAD 0.02789 0.42804 1.31234
7 5H94 LYS MET ASN THR GLN PHE THR ALA VAL 0.02703 0.42122 1.45455
8 2AX9 BHM 0.03281 0.4101 1.5625
9 1IID NHM 0.01822 0.42352 1.5748
10 4CL6 7SB 0.01188 0.41178 1.75439
11 1M7Y PPG 0.03214 0.40133 1.83727
12 5BYZ 4WE 0.004239 0.446 2.01149
13 2BIF BOG 0.008395 0.41915 2.09974
14 5F1R 42O 0.003523 0.44428 2.1097
15 4JZX 476 0.01344 0.4018 2.20994
16 4RC8 STE 0.01917 0.40317 2.25225
17 1SR7 MOF 0.01692 0.41675 2.3166
18 4OAR 2S0 0.0182 0.40101 2.32558
19 1J78 VDY 0.00272 0.43271 2.3622
20 4QOM PYG 0.007596 0.4195 2.3622
21 1YKD CMP 0.01339 0.40385 2.3622
22 1YMT DR9 0.007345 0.43126 2.43902
23 3AQT RCO 0.01046 0.41644 2.44898
24 1UBY DMA 0.007768 0.41523 2.45232
25 3SVJ 4LI 0.005131 0.4296 2.46305
26 2AMT GPP 0.02464 0.40213 2.51572
27 4OMJ 2TX 0.01825 0.41623 2.51799
28 3KXC PLM 0.01852 0.40693 2.57732
29 3GKJ HC3 0.003519 0.43574 2.58621
30 1YOK P6L 0.0157 0.4229 2.62467
31 5UNJ RJW 0.005253 0.4213 2.62467
32 2E9L OLA 0.03509 0.40671 2.62467
33 2E9L PLM 0.03647 0.40487 2.62467
34 2E9L BGC 0.03803 0.40487 2.62467
35 1RX0 2MC 0.02586 0.40107 2.62467
36 2OKL BB2 0.006795 0.41803 2.7027
37 5V13 JH3 0.00918 0.41367 2.77778
38 3Q8G PEE 0.02746 0.42378 2.8125
39 3VRV YSD 0.01399 0.4357 2.95203
40 2A1L PCW 0.01262 0.43466 2.96296
41 5KAU RHQ 0.003141 0.43617 3.0303
42 4B7P 9UN 0.04104 0.40915 3.04348
43 3VHZ SOG 0.02094 0.42035 3.05344
44 3VHZ L2P GLC MAN SGA 0.02355 0.42035 3.05344
45 5HCN DAO 0.004616 0.40352 3.06513
46 4OIV XX9 0.02283 0.41745 3.09735
47 3R9V DXC 0.01045 0.42635 3.14685
48 5G3N X28 0.009467 0.4166 3.14961
49 3WCA FPS 0.01404 0.41577 3.14961
50 1OLM VTQ 0.01572 0.41329 3.14961
51 3HY9 098 0.005558 0.42421 3.16742
52 3E8T UQ8 0.04989 0.41034 3.18182
53 5GIC DLC 0.02496 0.40574 3.2
54 4DV8 0LX 0.03241 0.40554 3.23194
55 2E2R 2OH 0.008798 0.43475 3.27869
56 4RW3 TDA 0.03855 0.40824 3.31126
57 5EHR 5OD 0.00493 0.41806 3.41207
58 4POJ 2VP 0.02065 0.4031 3.4632
59 4P6X HCY 0.005511 0.44278 3.52941
60 5DY5 5GR 0.03462 0.42288 3.61842
61 4ORM FMN 0.03936 0.421 3.67454
62 4ORM ORO 0.03936 0.421 3.67454
63 4ORM 2V6 0.03936 0.421 3.67454
64 3W68 VIV 0.01056 0.41594 3.7594
65 2EVL GAL SPH EIC 0.04895 0.40944 3.82775
66 2VWA PTY 0.003173 0.44126 3.9604
67 5KBZ 3B2 0.02598 0.41052 3.97878
68 3I51 6PL 0.02555 0.40134 4.07407
69 2BW7 APC 0.04615 0.41084 4.10959
70 3ET1 ET1 0.0116 0.40685 4.12371
71 5DLY 5D7 0.02359 0.41764 4.13534
72 4IEH 1E9 0.01489 0.41015 4.14201
73 4OYA 1VE 0.03362 0.42419 4.19948
74 3SP6 IL2 0.01534 0.40286 4.21053
75 2FP2 TSA 0.007377 0.41826 4.21687
76 4G8R 96P 0.006655 0.42454 4.25532
77 3G5K BB2 0.002271 0.40707 4.37158
78 4ZOM 4Q3 0.02329 0.4376 4.44444
79 4NKW PLO 0.01293 0.40647 4.45344
80 1XW6 GSH 0.01097 0.43302 4.58716
81 2ZCQ B65 0.02764 0.41667 4.77816
82 1GQG DCD 0.01854 0.40389 4.85714
83 2XMY CDK 0.04819 0.41553 4.98688
84 4COL DTP 0.00843 0.41149 4.98688
85 4RHP PEF 0.001231 0.45134 5.10638
86 1WS1 BB2 0.003313 0.40083 5.12821
87 3ET3 ET1 0.002662 0.44162 5.13699
88 3KMZ EQO 0.0006694 0.48176 5.26316
89 2QZT PLM 0.02796 0.40198 5.40541
90 5MES 7LT 0.0104 0.40278 5.55556
91 3JRS A8S 0.002988 0.43299 5.76923
92 4OIC A8S 0.01301 0.40248 5.77428
93 3E7O 35F 0.01166 0.42499 5.83333
94 1D5Z ACE ALC ARG ALA ODA SER LEU NH2 0.02542 0.41101 5.85774
95 4UCC ZKW 0.01294 0.41446 6.03675
96 2Q8H TF4 0.0205 0.40366 6.03675
97 4DR9 BB2 0.00354 0.40612 6.25
98 4DXJ 0M9 0.01179 0.42224 6.35359
99 4V3I ASP LEU THR ARG PRO 0.009115 0.41961 6.61479
100 5K52 OCD 0.00535 0.42872 6.79245
101 4INB 1F6 0.01449 0.40584 6.84932
102 5V3Y 5V8 0.006829 0.40896 6.99301
103 5IVX ARG GLY PRO GLY ARG ALA PHE VAL THR ILE 0.03516 0.41027 7
104 3G08 FEE 0.003679 0.47067 7.07071
105 5OCA 9QZ 0.002304 0.46244 7.14286
106 4CVZ TYR GLU LEU ASP GLU LYS PHE ASP ARG LEU 0.02844 0.40951 7.14286
107 5MBC FMN 0.01301 0.40248 7.36544
108 4EN4 GT0 0.02129 0.41806 7.37179
109 4EN4 GT1 0.02129 0.41806 7.37179
110 4EN4 ATP 0.02129 0.41806 7.37179
111 5V4R MGT 0.0002017 0.51476 7.40741
112 1L0I PSR 0.005361 0.42951 7.69231
113 5CHR 4NC 0.0002186 0.44709 8.75912
114 2EW5 Y12 0.01341 0.4057 8.83978
115 1NTV ASN PHE ASP ASN PRO VAL TYR ARG LYS THR 0.01042 0.41622 9.21053
116 1Q1Y BB2 0.00601 0.41632 9.42408
117 2BJ4 OHT 0.01055 0.41256 9.52381
118 4ZB6 GDS 0.02011 0.40215 9.86547
119 3KO0 TFP 0.003633 0.42953 9.90099
120 2PX6 DH9 0.007098 0.41506 10.7595
121 3QFJ LEU LEU PHE GLY PHE PRO VAL TYR VAL 0.01923 0.425 11
122 5L2J 70E 0.01785 0.44113 11.2245
123 3KP6 SAL 0.002849 0.45536 11.2583
124 2D5Z L35 0.04662 0.42277 11.6438
125 5IKH 6BW 0.02424 0.4099 11.811
126 2Y69 CHD 0.01158 0.41167 12.1622
127 1BWO LPC 0.007411 0.41817 12.2222
128 2DYR PGV 0.02434 0.41404 12.3288
129 1N8V BDD 0.01471 0.42103 12.5
130 1I0B PEL 0.006702 0.42672 12.6506
131 5TO8 7FM 0.03713 0.40542 12.766
132 1FP1 HCC 0.006781 0.42003 13.9785
133 5LWY OLA 0.007556 0.41776 14.0187
134 4H07 IPH 0.02249 0.40804 14.2857
135 2WCJ M21 0.01938 0.40294 14.8936
136 1IDA 0PO 0.02643 0.41117 15.1515
137 5U98 VAL THR THR ASP ILE GLN VAL LYS VAL 0.0299 0.40294 16.2455
138 5CSD ACD 0.03104 0.40754 16.3522
139 3E3U NVC 0.003568 0.40618 17.7665
140 5MWE TCE 0.002998 0.41044 25.9259
141 4V1T ADP 0.006804 0.418 26.5625
142 3HR1 PF9 0.0000008265 0.50965 36.0526
143 3BJC WAN 0.0000003829 0.58002 38.5827
144 3SHZ 5CO 0.0000000425 0.65167 42.3631
145 5EDE 5M6 0.00007465 0.50045 43.8095
146 3TGE TGE 0.0000001566 0.7041 48.1595
147 4QGE 35O 0.0000004605 0.60733 49.3438
Pocket No.: 2; Query (leader) PDB : 3G58; Ligand: 988; Similar sites found: 28
This union binding pocket(no: 2) in the query (biounit: 3g58.bio4) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2Q2Y ADP 0.02311 0.40365 1.90736
2 2Q2Y MKR 0.02206 0.40365 1.90736
3 3WYJ H78 0.02499 0.41852 1.97628
4 3TDC 0EU 0.00303 0.46572 2.62467
5 4L4J NAG NAG BMA MAN NAG 0.02666 0.4112 2.71493
6 5GWE GWM 0.01487 0.40581 2.88714
7 4AQ0 DMJ 0.006569 0.42824 3.14961
8 5ECP MET 0.02165 0.40501 3.14961
9 5ECP JAA 0.02165 0.40501 3.14961
10 5ECP ATP 0.02265 0.40501 3.14961
11 2HFU MEV 0.02342 0.40275 3.31325
12 1M2Z BOG 0.04797 0.40024 3.89105
13 5E58 CPZ 0.009871 0.41448 3.93701
14 3KDU NKS 0.0221 0.40362 4.33213
15 4XBT FLC 0.001662 0.42891 4.51613
16 4XBT 3ZQ 0.003714 0.41367 4.51613
17 3TL1 JRO 0.01584 0.40884 5.03145
18 5ML3 DL3 0.02331 0.40152 5.36913
19 3KYQ DPV 0.01614 0.40843 5.52764
20 2WH8 II2 0.01867 0.4009 6.05327
21 1G27 BB1 0.006345 0.40351 6.54762
22 3B2Q ATP 0.002613 0.42983 6.56168
23 4LH7 NMN 0.01876 0.40783 7.12074
24 3KRO IPE 0.007069 0.41348 8.13648
25 3KRO DST 0.007069 0.41348 8.13648
26 4TO8 FLC 0.02882 0.40441 8.90411
27 2V57 PRL 0.01961 0.40906 16.8421
28 3D78 NBB 0.04347 0.40451 29.4118
Pocket No.: 3; Query (leader) PDB : 3G58; Ligand: 988; Similar sites found: 12
This union binding pocket(no: 3) in the query (biounit: 3g58.bio2) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3GDN FAD 0.03755 0.41042 2.09974
2 4ZBR DIF 0.01937 0.4149 2.88714
3 4ZBR NPS 0.01839 0.4149 2.88714
4 4TWP AXI 0.0301 0.4147 2.95203
5 1EM6 CP4 0.008271 0.47271 3.14961
6 4ZW3 4S9 0.02052 0.41582 3.41207
7 4NAT 2W5 0.04536 0.40084 3.75
8 3H0A D30 0.02781 0.40082 5.51471
9 1A27 EST 0.006 0.41855 6.03675
10 2I0G I0G 0.04541 0.4098 6.22568
11 3L0E G58 0.02746 0.4011 6.71937
12 5L2J 6UL 0.03815 0.42175 11.2245
Pocket No.: 4; Query (leader) PDB : 3G58; Ligand: 988; Similar sites found: 12
This union binding pocket(no: 4) in the query (biounit: 3g58.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5A8E XTK 0.01072 0.41721 1.90476
2 2WR1 NAG 0.01003 0.4009 2.09974
3 3LDW ZOL 0.01161 0.42509 2.62467
4 3QP8 HL0 0.01432 0.40048 2.71739
5 3FUR Z12 0.009289 0.44344 5.51471
6 4DXJ IPE 0.01165 0.42501 6.35359
7 1WUB OTP 0.04798 0.40307 6.74157
8 1FO0 ILE ASN PHE ASP PHE ASN THR ILE 0.02782 0.41387 7.07071
9 1T27 PCW 0.01171 0.43545 7.38007
10 5C0C ARG GLN PHE GLY PRO ASP TRP ILE VAL ALA 0.03262 0.4145 11
11 5SVV FMN 0.01826 0.40094 17.5182
12 4RKK GLC GLC GLC GLC GLC GLC 0.01307 0.4003 17.7711
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