Receptor
PDB id Resolution Class Description Source Keywords
1I72 2 Å EC: 4.1.1.50 HUMAN S-ADENOSYLMETHIONINE DECARBOXYLASE WITH COVALENTLY BOU PYRUVOYL GROUP AND COVALENTLY BOUND 5'-DEOXY-5'-[N-METHYL-NA MINOOXYETHYL) AMINO]ADENOSINE HOMO SAPIENS SPERMIDINE BIOSYNTHESIS LYASE DECARBOXYLASE PYRUVATE S- ADENOSYLMETHIONINE SANDWICH ALLOSTERIC ENZYME PYRUVOYL
Ref.: THE STRUCTURAL BASIS FOR SUBSTRATE SPECIFICITY AND INHIBITION OF HUMAN S-ADENOSYLMETHIONINE DECARBOXYL BIOCHEMISTRY V. 40 9484 2001
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MAO A:368;
Invalid;
none;
submit data
339.35 C13 H21 N7 O4 C[N@@...
PUT A:350;
Valid;
none;
submit data
88.151 C4 H12 N2 C(CCN...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3DZ6 1.83 Å EC: 4.1.1.50 HUMAN ADOMETDC WITH 5'-[(4-AMINOOXYBUTYL)METHYLAMINO]-5'DEOX ETHYLADENOSINE HOMO SAPIENS COMPLEXES OF ADOMETDC WITH 8-SUBSTITUTED LIGANDS DECARBOXYLLYASE PYRUVATE S-ADENOSYL-L-METHIONINE SPERMIDINE BIOSYNZYMOGEN
Ref.: NEW INSIGHTS INTO THE DESIGN OF INHIBITORS OF HUMAN S-ADENOSYLMETHIONINE DECARBOXYLASE: STUDIES OF ADEN SUBSTITUTION IN STRUCTURAL ANALOGUES OF S-ADENOSYLM J.MED.CHEM. V. 52 1388 2009
Members (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 1I7B - PUT C4 H12 N2 C(CCN)CN
2 3H0V ic50 = 15 uM M2T C12 H19 N5 O3 S CS(C)C[C@@....
3 3EPB Ka = 10000 M^-1 PUT C4 H12 N2 C(CCN)CN
4 1I72 - PUT C4 H12 N2 C(CCN)CN
5 3DZ4 ic50 = 400 nM C8M C15 H23 N7 O4 Cc1nc2c(nc....
6 3DZ5 - PUT C4 H12 N2 C(CCN)CN
7 1I7C ic50 = 0.4 uM MGB C5 H12 N8 [H]/N=C(N)....
8 3H0W ic50 = 600 nM N8M C13 H20 N6 O3 Cc1nc2c(nc....
9 3DZ6 ic50 = 15 nM M8E C17 H27 N7 O4 C[N@@](CCC....
10 3DZ7 - PUT C4 H12 N2 C(CCN)CN
11 1I79 - PUT C4 H12 N2 C(CCN)CN
12 3EPA Ka = 2000 M^-1 PUT C4 H12 N2 C(CCN)CN
13 3DZ2 ic50 = 70 uM A8M C15 H25 N7 O3 Cc1nc2c(nc....
70% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 1I7B - PUT C4 H12 N2 C(CCN)CN
2 3H0V ic50 = 15 uM M2T C12 H19 N5 O3 S CS(C)C[C@@....
3 3EPB Ka = 10000 M^-1 PUT C4 H12 N2 C(CCN)CN
4 1I72 - PUT C4 H12 N2 C(CCN)CN
5 3DZ4 ic50 = 400 nM C8M C15 H23 N7 O4 Cc1nc2c(nc....
6 3DZ5 - PUT C4 H12 N2 C(CCN)CN
7 1I7C ic50 = 0.4 uM MGB C5 H12 N8 [H]/N=C(N)....
8 3H0W ic50 = 600 nM N8M C13 H20 N6 O3 Cc1nc2c(nc....
9 3DZ6 ic50 = 15 nM M8E C17 H27 N7 O4 C[N@@](CCC....
10 3DZ7 - PUT C4 H12 N2 C(CCN)CN
11 1I79 - PUT C4 H12 N2 C(CCN)CN
12 3EPA Ka = 2000 M^-1 PUT C4 H12 N2 C(CCN)CN
13 3DZ2 ic50 = 70 uM A8M C15 H25 N7 O3 Cc1nc2c(nc....
50% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 1I7B - PUT C4 H12 N2 C(CCN)CN
2 3H0V ic50 = 15 uM M2T C12 H19 N5 O3 S CS(C)C[C@@....
3 3EPB Ka = 10000 M^-1 PUT C4 H12 N2 C(CCN)CN
4 1I72 - PUT C4 H12 N2 C(CCN)CN
5 3DZ4 ic50 = 400 nM C8M C15 H23 N7 O4 Cc1nc2c(nc....
6 3DZ5 - PUT C4 H12 N2 C(CCN)CN
7 1I7C ic50 = 0.4 uM MGB C5 H12 N8 [H]/N=C(N)....
8 3H0W ic50 = 600 nM N8M C13 H20 N6 O3 Cc1nc2c(nc....
9 3DZ6 ic50 = 15 nM M8E C17 H27 N7 O4 C[N@@](CCC....
10 3DZ7 - PUT C4 H12 N2 C(CCN)CN
11 1I79 - PUT C4 H12 N2 C(CCN)CN
12 3EPA Ka = 2000 M^-1 PUT C4 H12 N2 C(CCN)CN
13 3DZ2 ic50 = 70 uM A8M C15 H25 N7 O3 Cc1nc2c(nc....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: PUT; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 PUT 1 1
2 13D 0.666667 0.8
3 16D 0.636364 0.9
4 N2P 0.636364 0.947368
5 DIA 0.583333 0.9
6 AML 0.5 0.652174
Similar Ligands (3D)
Ligand no: 1; Ligand: PUT; Similar ligands found: 323
No: Ligand Similarity coefficient
1 7CL 1.0000
2 BXO 1.0000
3 ETX 1.0000
4 4HA 1.0000
5 XAP 1.0000
6 PE9 1.0000
7 5BR 0.9969
8 NBN 0.9919
9 9A7 0.9851
10 BUB 0.9821
11 O8Y 0.9809
12 HE2 0.9795
13 BAL 0.9759
14 HP6 0.9754
15 BBU 0.9718
16 3CL 0.9716
17 1KA 0.9706
18 1SP 0.9702
19 BMD 0.9690
20 BUQ 0.9689
21 YIV 0.9687
22 CRD 0.9686
23 PXO 0.9685
24 EGD 0.9663
25 0CL 0.9644
26 BUA 0.9644
27 SGL 0.9642
28 3OH 0.9641
29 9A4 0.9618
30 ABU 0.9613
31 266 0.9606
32 3BB 0.9592
33 3GR 0.9591
34 BU4 0.9590
35 SSN 0.9589
36 FW5 0.9581
37 ITU 0.9568
38 25T 0.9540
39 LEA 0.9539
40 GOL 0.9521
41 SLP 0.9519
42 GXV 0.9513
43 MMU 0.9509
44 SAR 0.9505
45 A8C 0.9489
46 SIN 0.9484
47 MTG 0.9461
48 1DH 0.9452
49 2HA 0.9450
50 MEU 0.9428
51 MSF 0.9427
52 2RA 0.9425
53 MLA 0.9395
54 PG3 0.9371
55 DAV 0.9368
56 2KT 0.9366
57 AOA 0.9364
58 DSS 0.9338
59 DGY 0.9338
60 CYS 0.9336
61 IVA 0.9320
62 ABA 0.9317
63 AAE 0.9314
64 P2D 0.9306
65 C2N 0.9303
66 DCY 0.9299
67 PG0 0.9292
68 MLI 0.9291
69 FUM 0.9285
70 HIU 0.9274
71 DSN 0.9272
72 MLM 0.9271
73 A3B 0.9271
74 SER 0.9267
75 3SS 0.9266
76 D2P 0.9261
77 VKC 0.9259
78 DE2 0.9257
79 MAE 0.9252
80 24T 0.9250
81 MTD 0.9247
82 NMG 0.9241
83 C5J 0.9236
84 PRI 0.9234
85 3PY 0.9233
86 DMG 0.9229
87 NVI 0.9223
88 HE4 0.9220
89 ISU 0.9216
90 HX2 0.9215
91 03W 0.9212
92 DBB 0.9211
93 HTX 0.9211
94 H95 0.9208
95 CHT 0.9206
96 MRY 0.9206
97 4MV 0.9205
98 E60 0.9204
99 SHF 0.9197
100 FJO 0.9195
101 GLY 0.9192
102 OCT 0.9188
103 2HE 0.9187
104 LER 0.9177
105 HYN 0.9172
106 23W 0.9171
107 6NA 0.9168
108 3HR 0.9161
109 HSE 0.9158
110 SHO 0.9155
111 CEJ 0.9155
112 IPU 0.9149
113 HV2 0.9143
114 MZW 0.9141
115 HUI 0.9141
116 BP9 0.9141
117 ETM 0.9139
118 HVQ 0.9133
119 OPE 0.9132
120 HDA 0.9131
121 SMB 0.9122
122 BVC 0.9121
123 TAU 0.9120
124 3HL 0.9120
125 COM 0.9114
126 9X7 0.9110
127 XPO 0.9097
128 BHL 0.9092
129 BHL BHL 0.9092
130 4SD 0.9088
131 EFS 0.9088
132 IHG 0.9086
133 THR 0.9078
134 9YL 0.9074
135 HSM 0.9073
136 VX 0.9069
137 69O 0.9062
138 F3V 0.9060
139 JZ5 0.9058
140 MZ0 0.9053
141 ATO 0.9048
142 DTU 0.9048
143 DTL 0.9044
144 POA 0.9042
145 KG7 0.9042
146 DXX 0.9040
147 DQY 0.9035
148 NVA 0.9031
149 IQ0 0.9030
150 OHG 0.9023
151 8X3 0.9016
152 OSM 0.9011
153 39J 0.9011
154 BVG 0.9009
155 HCS 0.9007
156 OXL 0.9007
157 PPI 0.9002
158 P7I 0.9000
159 BTL 0.8992
160 PGA 0.8989
161 OXD 0.8982
162 2EZ 0.8981
163 GOA 0.8973
164 FAH 0.8966
165 A20 0.8965
166 AKR 0.8965
167 CSS 0.8965
168 1BP 0.8964
169 OKG 0.8961
170 TZC 0.8957
171 R3W 0.8955
172 GLV 0.8950
173 XIX 0.8948
174 PRO 0.8945
175 SMV 0.8944
176 CP 0.8943
177 F50 0.8940
178 NIE 0.8940
179 TFB 0.8940
180 HBR 0.8939
181 1DU 0.8934
182 ORN 0.8932
183 HVB 0.8925
184 BRP 0.8925
185 AMC 0.8924
186 DCL 0.8918
187 PYR 0.8917
188 JBN 0.8915
189 9SB 0.8910
190 C21 0.8908
191 ALO 0.8908
192 2A1 0.8906
193 HAE 0.8905
194 PYC 0.8897
195 MZY 0.8896
196 LAC 0.8896
197 BRJ 0.8894
198 EDO 0.8888
199 COI 0.8885
200 HBS 0.8882
201 FCN 0.8882
202 DAL 0.8874
203 MLT 0.8874
204 2OP 0.8866
205 KIV 0.8860
206 ALA 0.8855
207 VAL 0.8853
208 BAE 0.8852
209 ODV 0.8846
210 PRS 0.8844
211 IOM 0.8843
212 CRN 0.8843
213 CMS 0.8839
214 TEO 0.8838
215 273 0.8836
216 BUO 0.8834
217 CP2 0.8833
218 XRG 0.8830
219 2PC 0.8829
220 TB6 0.8826
221 DTT 0.8824
222 LMR 0.8823
223 NMU 0.8822
224 SAT 0.8822
225 TP5 0.8816
226 DAS 0.8814
227 ASP 0.8812
228 ALQ 0.8807
229 ATQ 0.8804
230 265 0.8801
231 AKB 0.8801
232 FOA 0.8799
233 OAA 0.8798
234 NOE 0.8797
235 1CB 0.8796
236 2MH 0.8796
237 PAE 0.8793
238 7VD 0.8790
239 MPD 0.8789
240 OXM 0.8788
241 PCT 0.8787
242 UGC 0.8785
243 S0H 0.8783
244 ETF 0.8780
245 HBX 0.8775
246 PYF 0.8771
247 DPR 0.8771
248 DCE 0.8769
249 2RH 0.8767
250 SYN 0.8762
251 ASN 0.8761
252 PY7 0.8760
253 BXA 0.8757
254 BML 0.8752
255 DYA 0.8748
256 GUA 0.8748
257 7WG 0.8744
258 TSZ 0.8744
259 HAI 0.8741
260 GXE 0.8740
261 CXL 0.8736
262 ABN 0.8733
263 FPI 0.8732
264 TAN 0.8726
265 MET 0.8722
266 3MT 0.8721
267 HGY 0.8721
268 NAK 0.8713
269 NLE 0.8708
270 6SP 0.8708
271 2A3 0.8708
272 BYZ 0.8707
273 IPH 0.8705
274 1MR 0.8704
275 THE 0.8701
276 LEU 0.8700
277 CNH 0.8700
278 GLY GLY 0.8699
279 MGX 0.8699
280 V1L 0.8693
281 J3K 0.8689
282 UY7 0.8686
283 4CH 0.8684
284 CYH 0.8682
285 PYZ 0.8680
286 TB0 0.8678
287 4MZ 0.8676
288 QPT 0.8670
289 PCA 0.8669
290 282 0.8668
291 2IM 0.8667
292 B24 0.8667
293 3BR 0.8667
294 JYD 0.8667
295 GBL 0.8657
296 NHY 0.8655
297 ES3 0.8652
298 HYP 0.8649
299 PYJ 0.8645
300 VSO 0.8641
301 HZP 0.8633
302 T2C 0.8631
303 PPF 0.8619
304 XBT 0.8619
305 BAQ 0.8617
306 URP 0.8616
307 ICN 0.8606
308 FQI 0.8601
309 1AC 0.8596
310 CB0 0.8596
311 NBE 0.8590
312 ZBT 0.8585
313 PAH 0.8578
314 BHH 0.8573
315 APY 0.8569
316 HPY 0.8565
317 OK7 0.8564
318 CXF 0.8559
319 MMQ 0.8554
320 192 0.8550
321 RSO 0.8546
322 14J 0.8540
323 IZC 0.8513
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3DZ6; Ligand: PUT; 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: 3dz6.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3DZ6; Ligand: M8E; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3dz6.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
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