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Receptor
PDB id Resolution Class Description Source Keywords
1XM4 2.31 Å EC: 3.1.4.17 CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4B IN COMPLEX WI PICLAMILAST HOMO SAPIENS PDE4B PICLAMILAST HYDROLASE
Ref.: STRUCTURAL BASIS FOR THE ACTIVITY OF DRUGS THAT INH PHOSPHODIESTERASES. STRUCTURE V. 12 2233 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:1002;
B:1002;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
PIL A:1003;
B:1003;
Valid;
Valid;
none;
none;
ic50 = 0.041 nM
381.253 C18 H18 Cl2 N2 O3 COc1c...
ZN A:1001;
B:1001;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1XM4 2.31 Å EC: 3.1.4.17 CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4B IN COMPLEX WI PICLAMILAST HOMO SAPIENS PDE4B PICLAMILAST HYDROLASE
Ref.: STRUCTURAL BASIS FOR THE ACTIVITY OF DRUGS THAT INH PHOSPHODIESTERASES. STRUCTURE V. 12 2233 2004
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 19 families.
1 1XM4 ic50 = 0.041 nM PIL C18 H18 Cl2 N2 O3 COc1ccc(cc....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 1XM4 ic50 = 0.041 nM PIL C18 H18 Cl2 N2 O3 COc1ccc(cc....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 1XM4 ic50 = 0.041 nM PIL C18 H18 Cl2 N2 O3 COc1ccc(cc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PIL; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 PIL 1 1
2 3GJ 0.505747 0.709677
3 ROF 0.476744 0.773585
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1XM4; Ligand: PIL; Similar sites found with APoc: 244
This union binding pocket(no: 1) in the query (biounit: 1xm4.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 1UO4 PIH None
3 1L0I PSR None
4 5Y02 HBX None
5 4F4S EFO None
6 5NNT DPV None
7 1ZEI CRS None
8 4V1F BQ1 None
9 4F06 PHB 1.07817
10 4LY9 1YY 1.25628
11 4LY9 S6P 1.25628
12 6C1R EFD 1.75879
13 2WR1 NAG 1.75879
14 1MT1 AG2 1.76991
15 4G8R 96P 1.8617
16 5IM3 DTP 2.01005
17 3E7O 35F 2.01005
18 4JE7 BB2 2.03046
19 3V66 D3A 2.05882
20 1BUC CAA 2.08877
21 2C9E PID 2.14067
22 3OKI OKI 2.14592
23 2PX6 DH9 2.21519
24 5NM7 GLY 2.25564
25 4OPC PGT 2.26131
26 5U97 PIT 2.26131
27 3HP9 CF1 2.26131
28 1YOK P6L 2.34375
29 5JF2 SF7 2.45098
30 3TDC 0EU 2.51256
31 3LDW ZOL 2.52525
32 5A8E XTK 2.53968
33 5N5U 7N8 2.54777
34 3FUR Z12 2.57353
35 4O4Z N2O 2.5974
36 4LPG 1MV 2.66667
37 2OKL BB2 2.7027
38 1LQY BB2 2.71739
39 4V3I ASP LEU THR ARG PRO 2.72374
40 2HZL PYR 2.73973
41 2XXP DSL 2.76382
42 3RS8 ALA TRP LEU PHE GLU ALA 2.76382
43 1OLM VTQ 2.76382
44 4TV1 36M 2.78884
45 1R6N 434 2.8436
46 6A5Y 9R0 2.94118
47 1PZO CBT 3.04183
48 4B7P 9UN 3.04348
49 3VHZ SOG 3.05344
50 1NU4 MLA 3.09278
51 1YUC EPH 3.13725
52 5TIV A3P 3.16206
53 6BR8 PGV 3.1746
54 6BR8 6OU 3.1746
55 1WS1 BB2 3.20513
56 1ZDU P3A 3.26531
57 5UNJ RJW 3.26531
58 5OSW DIU 3.26633
59 5EK3 5PK 3.26633
60 4DV8 0LX 3.26633
61 2A1L PCW 3.33333
62 3HB5 E2B 3.36391
63 3HB5 NAP 3.36391
64 5HCN DAO 3.44828
65 4EOX 0S5 3.44828
66 5M37 9SZ 3.47826
67 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 3.47826
68 5M36 9SZ 3.49345
69 1Q7E MET 3.51759
70 1ZED PNP 3.51759
71 1ZPD CIT 3.51759
72 2YOO K2B 3.51759
73 3O01 DXC 3.57143
74 2FP2 TSA 3.61446
75 5DCH 1YO 3.64583
76 2GWH PCI 3.69128
77 6CHP F0Y 3.72671
78 5LX9 OLB 3.76884
79 6CGN DA 3.76884
80 2FKW RG1 3.77358
81 1S17 GNR 3.88889
82 5G3N X28 3.93701
83 5ECP MET 4.0201
84 5ECP JAA 4.0201
85 5ECP ATP 4.0201
86 5CX6 CDP 4.0201
87 5B4B LP5 4.03226
88 6GL8 F3Q 4.06977
89 3AQT RCO 4.08163
90 2E2R 2OH 4.09836
91 5V13 JH3 4.16667
92 1I0B PEL 4.21687
93 5F1R 42O 4.21941
94 4QOM PYG 4.27136
95 1XQP 8HG 4.29688
96 3JRS A8S 4.32692
97 2CIX CEJ 4.34783
98 5H94 LYS MET ASN THR GLN PHE THR ALA VAL 4.36364
99 5N26 CPT 4.3956
100 5IF4 6AK 4.40252
101 5DLY 5D7 4.51128
102 4DJA DLZ 4.52261
103 4DJA FAD 4.52261
104 5OLK DTP 4.52261
105 5K52 OCD 4.5283
106 5K53 STE 4.58015
107 5G5W R8C 4.64286
108 2Z7I 742 4.70588
109 4DR9 BB2 4.77387
110 5W7D PX8 4.77387
111 4RFM 3P6 4.88722
112 2VWA PTY 4.9505
113 2C78 PUL 5.02513
114 4V1T ADP 5.02513
115 3KXC PLM 5.06329
116 4RHP PEF 5.10638
117 2ZCQ B65 5.11945
118 4UCC ZKW 5.15021
119 2BHW NEX 5.17241
120 5ERM 210 5.23416
121 3R9V DXC 5.24476
122 3VRV YSD 5.27638
123 4ZBR NPS 5.27638
124 4ZBR DIF 5.27638
125 2UW1 GVM 5.32544
126 4PGK Y69 5.32787
127 3G5K BB2 5.46448
128 1UVC STE 5.49451
129 5UR6 8KM 5.52486
130 2JC9 ADN 5.52764
131 5AAV GW5 5.55556
132 3F8C HT1 5.55556
133 5LWY OLA 5.60748
134 4OGQ 7PH 5.625
135 4OGQ 2WD 5.625
136 4OGQ 1O2 5.625
137 3TL1 JRO 5.66038
138 1G27 BB1 5.95238
139 5KD8 TNR 6.03015
140 3VPD CIT 6.04982
141 3N7S 3N7 6.25
142 1GNI OLA 6.28141
143 2E9L OLA 6.28141
144 2E9L BGC 6.28141
145 2E9L PLM 6.28141
146 5MUJ RAM ARA RAM 8OQ RAM GAL XXM 8PK 6.29921
147 3WCA FPS 6.30137
148 1DKF BMS 6.38298
149 4CL6 7SB 6.43275
150 3QLM PLM 6.45161
151 1R5L VIV 6.48855
152 4LH7 NMN 6.50155
153 1EM6 CP4 6.53266
154 2YI0 YI0 6.55022
155 3KP6 SAL 6.62252
156 5KAU RHQ 6.66667
157 4CVZ TYR GLU LEU ASP GLU LYS PHE ASP ARG LEU 6.68693
158 3W68 VIV 6.76692
159 4G31 0WH 6.78392
160 5V4R MGT 6.79012
161 4DXJ 0M9 6.90608
162 3KO0 TFP 6.93069
163 1M2Z BOG 7.00389
164 3E70 GDP 7.0122
165 2XSU PIE 7.05128
166 5OCA 9QZ 7.14286
167 4F7E 0SH 7.14286
168 1HG4 LPP 7.16846
169 3ET3 ET1 7.19178
170 1XVB BHL 7.19794
171 5C1M OLC 7.2
172 5C1M CLR 7.2
173 3ET1 ET1 7.2165
174 3TJH SER PRO LEU ASP SER LEU TRP TRP ILE 7.22222
175 3W5N RAM 7.28643
176 2BIF BOG 7.28643
177 1KPG 16A 7.31707
178 4NAT ADP 7.5
179 4NAT 2W5 7.5
180 6CB2 OLC 7.50853
181 2BCG GER 7.53769
182 5TVI MYR 7.6087
183 5AZC PGT 7.66667
184 1SR7 MOF 7.72201
185 1U25 IHS 7.78894
186 2HKJ RDC 7.78894
187 3KMZ EQO 7.89474
188 1P1M MET 8.0402
189 4ZGM 32M 8.19672
190 2BJ4 OHT 8.33333
191 2ALG DAO 8.69565
192 6CAY ERG 8.87574
193 5MTE BB2 9.48905
194 2X5W K2B 9.54774
195 2BW7 APC 9.58904
196 3ZCB ATP 9.59596
197 3SFI 3SF 9.74576
198 1NTV ASN PHE ASP ASN PRO VAL TYR ARG LYS THR 9.86842
199 6GMN F4E 9.87654
200 1BWO LPC 10
201 5CHR 4NC 10.219
202 3RUG DB6 10.9272
203 3SCM LGN 10.9272
204 4WO4 JLS 11
205 5C9J DAO 11.1111
206 5WL1 CUY 11.1111
207 5WL1 D3D 11.1111
208 3HUJ AGH 11.1111
209 5T70 THR SER ASN LEU GLN GLU GLN ILE GLY TRP 11.1111
210 5U98 1KX 11.1111
211 3IIS PID 11.2583
212 3G08 FEE 11.5789
213 3QUZ QUV 11.5789
214 3SQP 3J8 12.0603
215 5W7B MYR 12.766
216 1JGS SAL 13.0435
217 4WVO 3UZ 13.2597
218 1N8V BDD 13.3929
219 2Y69 CHD 13.8158
220 3D04 SAK 15.0943
221 1DTL BEP 16.7702
222 1HBK MYR 16.8539
223 4WGF HX2 17.0732
224 5UGW GSH 17.7143
225 2WOR 2AN 18
226 5Z84 CHD 19.2661
227 5W97 CHD 19.2661
228 5ZCO CHD 19.2661
229 5ZCO PEK 19.2661
230 2DYR PEK 19.2661
231 2DYS PEK 19.2661
232 2DYS PGV 19.2661
233 5ZCO TGL 19.2661
234 5Z84 PGV 19.2661
235 5Z84 TGL 19.2661
236 3E3U NVC 20.3046
237 5MWE TCE 24.6914
238 1T0S BML 34.8837
239 3BJC WAN 36.4322
240 5G57 6M5 42.7778
241 5EDE 5M6 43.8095
242 3HR1 PF9 44.2105
243 4QGE 35O 45.7286
244 3TGE TGE 47.8528
Pocket No.: 2; Query (leader) PDB : 1XM4; Ligand: PIL; Similar sites found with APoc: 22
This union binding pocket(no: 2) in the query (biounit: 1xm4.bio2) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 2AMT GPP None
2 3DZT EAH 0.990099
3 1JQI CAA 1.80412
4 6A0S NDP 1.80723
5 4H6Q TFB 2.24359
6 1YMT DR9 2.43902
7 2YPO PHE 3.26633
8 3GZ9 D32 3.51759
9 4URX FK1 3.78378
10 4RC8 STE 4.05405
11 1W3R PYR 4.16667
12 1K7L 544 4.27136
13 2WZG UPG 4.77387
14 5LWY OLB 5.60748
15 2QE4 JJ3 5.64516
16 4RW3 TDA 6.95364
17 4RYV ZEA 7.74194
18 5IKH 6BW 10.804
19 6GH1 ARG LEU PRO ALA LYS ALA PRO LEU LEU 11
20 3RMK BML 12.0482
21 5XS3 VAL ARG SER ARG ARG CYS LEU ARG LEU 12.2449
22 2DYR TGL 19.2661
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