Receptor
PDB id Resolution Class Description Source Keywords
3H0V 2.24 Å EC: 4.1.1.50 HUMAN ADOMETDC WITH 5'-DEOXY-5'-(DIMETHYLSULFONIO) ADENOSINE HOMO SAPIENS ADOMETDC WITH COMPETITIVE SUBSTRATE ANALOGS AUTOCATALYTIC CLEAVAGE DECARBOXYLASE LYASE PHOSPHOPROTEIN POLYAMINE BIOSYNTHESIS PYRUVATE S-ADENOSYL-L-METHIONINE SCHIFF BASE SPERMIDINE BIOSYNTHESIS ZYMOGEN
Ref.: ROLE OF THE SULFONIUM CENTER IN DETERMINING THE LIGAND SPECIFICITY OF HUMAN S-ADENOSYLMETHIONINE DECARBOXYLASE. BIOCHEMISTRY V. 48 6423 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
M2T A:368;
Valid;
none;
ic50 = 15 uM
313.376 C12 H19 N5 O3 S CS(C)...
PUT B:350;
Valid;
none;
submit data
88.151 C4 H12 N2 C(CCN...
PYR A:68;
Invalid;
none;
submit data
88.062 C3 H4 O3 CC(=O...
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'DEOXY-8-ETHYLADENOSINE HOMO SAPIENS COMPLEXES OF ADOMETDC WITH 8-SUBSTITUTED LIGANDS DECARBOXYLASE LYASE PYRUVATE S-ADENOSYL-L-METHIONINE SPERMIDINE BIOSYNTHESIS ZYMOGEN
Ref.: NEW INSIGHTS INTO THE DESIGN OF INHIBITORS OF HUMAN S-ADENOSYLMETHIONINE DECARBOXYLASE: STUDIES OF ADENINE C8 SUBSTITUTION IN STRUCTURAL ANALOGUES OF S-ADENOSYLMETHIONINE 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
Ligand no: 1; Ligand: M2T; Similar ligands found: 247
No: Ligand ECFP6 Tc MDL keys Tc
1 M2T 1 1
2 XYA 0.741379 0.828571
3 ADN 0.741379 0.828571
4 RAB 0.741379 0.828571
5 S4M 0.720588 0.844156
6 5N5 0.716667 0.828571
7 A4D 0.704918 0.855072
8 5CD 0.704918 0.84058
9 EP4 0.698413 0.941176
10 MTA 0.676923 0.940298
11 DTA 0.661538 0.819444
12 3DH 0.656716 0.884058
13 SAM 0.636364 0.878378
14 5AD 0.622951 0.80597
15 MAO 0.616438 0.765432
16 ZAS 0.614286 0.797297
17 AMP 0.614286 0.753247
18 A 0.614286 0.753247
19 S7M 0.6125 0.828947
20 SMM 0.6125 0.868421
21 ABM 0.611111 0.779221
22 6RE 0.605634 0.766234
23 SRA 0.605634 0.7375
24 AMP MG 0.597222 0.75641
25 DSH 0.597222 0.8
26 AOC 0.597222 0.830986
27 A12 0.594595 0.707317
28 AP2 0.594595 0.707317
29 A3N 0.589041 0.819444
30 J7C 0.589041 0.753247
31 A2D 0.589041 0.734177
32 5AS 0.586667 0.685393
33 GJV 0.581081 0.75641
34 BA3 0.573333 0.734177
35 MHZ 0.571429 0.765432
36 M33 0.571429 0.769231
37 GEK 0.571429 0.837838
38 ADP 0.565789 0.734177
39 AP5 0.565789 0.734177
40 B4P 0.565789 0.734177
41 ACP 0.564103 0.716049
42 5X8 0.564103 0.84507
43 7D7 0.5625 0.75
44 Y3J 0.560606 0.757143
45 AN2 0.558442 0.725
46 A7D 0.558442 0.833333
47 SON 0.558442 0.707317
48 APC 0.556962 0.707317
49 PRX 0.556962 0.759494
50 CA0 0.551282 0.716049
51 ADP MG 0.551282 0.746835
52 ADX 0.551282 0.705882
53 AU1 0.551282 0.716049
54 ADV 0.55 0.707317
55 RBY 0.55 0.707317
56 SA8 0.55 0.826667
57 EEM 0.548781 0.828947
58 SFG 0.544304 0.780822
59 ADP BEF 0.544304 0.728395
60 BEF ADP 0.544304 0.728395
61 ATP 0.544304 0.734177
62 50T 0.544304 0.725
63 5FA 0.5375 0.734177
64 APR 0.5375 0.734177
65 AQP 0.5375 0.734177
66 AR6 0.5375 0.734177
67 ACQ 0.536585 0.716049
68 3AM 0.534247 0.717949
69 A3G 0.533333 0.783784
70 NEC 0.533333 0.777778
71 A5D 0.530864 0.819444
72 SAP 0.530864 0.719512
73 ADP PO3 0.530864 0.776316
74 AD9 0.530864 0.716049
75 AGS 0.530864 0.719512
76 5AL 0.53012 0.746835
77 3AD 0.529412 0.814286
78 SAI 0.52439 0.786667
79 SAH 0.52439 0.821918
80 ATP MG 0.52439 0.746835
81 G5A 0.52439 0.666667
82 A5A 0.52381 0.709302
83 GAP 0.518072 0.7375
84 TAT 0.518072 0.728395
85 ANP 0.518072 0.716049
86 AAT 0.511905 0.75641
87 54H 0.511628 0.732558
88 52H 0.511628 0.724138
89 VMS 0.511628 0.732558
90 ADP ALF 0.505882 0.719512
91 ATF 0.505882 0.707317
92 ALF ADP 0.505882 0.719512
93 TSB 0.505747 0.701149
94 DAL AMP 0.505747 0.769231
95 53H 0.505747 0.724138
96 A3S 0.5 0.794521
97 5SV 0.5 0.722892
98 VO4 ADP 0.5 0.746835
99 SSA 0.5 0.666667
100 SRP 0.5 0.707317
101 8QN 0.5 0.746835
102 ADP VO4 0.5 0.746835
103 2AM 0.5 0.708861
104 ANP MG 0.5 0.719512
105 LSS 0.494382 0.727273
106 4AD 0.494382 0.719512
107 PAJ 0.494382 0.756098
108 0UM 0.494382 0.769231
109 A3P 0.493671 0.730769
110 QQX 0.493333 0.679012
111 CC5 0.492537 0.826087
112 62X 0.488889 0.820513
113 NVA LMS 0.488889 0.707865
114 A22 0.488636 0.725
115 5CA 0.488636 0.666667
116 MAP 0.488636 0.698795
117 A3T 0.487805 0.830986
118 QQY 0.486842 0.6875
119 ACK 0.486842 0.701299
120 7D5 0.486486 0.679012
121 K15 0.483516 0.772152
122 LEU LMS 0.483516 0.747126
123 OAD 0.483516 0.7375
124 S8M 0.483146 0.789474
125 25A 0.483146 0.734177
126 OOB 0.483146 0.725
127 OVE 0.480519 0.703704
128 26A 0.478873 0.871429
129 PR8 0.478261 0.666667
130 AMO 0.477778 0.707317
131 NSS 0.477778 0.685393
132 A1R 0.477778 0.690476
133 DSZ 0.477778 0.666667
134 ADQ 0.477778 0.716049
135 CMP 0.475 0.736842
136 2BA 0.475 0.727273
137 1ZZ 0.473118 0.697674
138 NB8 0.473118 0.682353
139 SXZ 0.473118 0.853333
140 3OD 0.473118 0.7375
141 TXA 0.473118 0.728395
142 ME8 0.473118 0.759036
143 PTJ 0.473118 0.765432
144 AHX 0.472527 0.682353
145 00A 0.472527 0.690476
146 DLL 0.472527 0.725
147 MYR AMP 0.468085 0.717647
148 SP1 0.467532 0.7125
149 RP1 0.467532 0.7125
150 A6D 0.467391 0.75
151 3UK 0.467391 0.716049
152 ADP BMA 0.467391 0.7375
153 3L1 0.464789 0.756757
154 3D1 0.464789 0.756757
155 MTP 0.464789 0.783784
156 LAD 0.462366 0.674419
157 P5A 0.462366 0.638298
158 A A 0.462366 0.75641
159 KAA 0.462366 0.645161
160 WAQ 0.462366 0.690476
161 GSU 0.462366 0.666667
162 PAP 0.458824 0.721519
163 2FA 0.458333 0.773333
164 YAP 0.458333 0.698795
165 6MD 0.458333 0.842857
166 FYA 0.457447 0.725
167 BIS 0.457447 0.690476
168 JB6 0.457447 0.710843
169 A2P 0.45679 0.717949
170 7MC 0.456311 0.662921
171 D3Y 0.455556 0.773333
172 TYR AMP 0.453608 0.728395
173 YSA 0.453608 0.666667
174 KB1 0.452632 0.746835
175 25L 0.452632 0.725
176 2VA 0.452381 0.859155
177 5F1 0.452055 0.739726
178 PLP AAD 0.449541 0.767442
179 9SN 0.447917 0.682353
180 7D3 0.444444 0.662651
181 ATP A A A 0.443299 0.766234
182 FA5 0.443299 0.707317
183 PPS 0.443182 0.686047
184 NVA 2AD 0.44186 0.797297
185 7MD 0.44 0.659091
186 XAH 0.438776 0.659091
187 1DA 0.438356 0.828571
188 VRT 0.436782 0.8
189 SO8 0.436782 0.847222
190 NOC 0.43662 0.746479
191 KH3 0.435644 0.7625
192 TAD 0.435644 0.694118
193 GTA 0.435644 0.717647
194 4UV 0.434343 0.698795
195 AMP DBH 0.434343 0.7375
196 V3L 0.431818 0.734177
197 3NZ 0.431579 0.789474
198 AHZ 0.431373 0.717647
199 2A5 0.430233 0.674699
200 7C5 0.43 0.734177
201 G3A 0.43 0.682353
202 YLB 0.428571 0.681818
203 48N 0.427184 0.702381
204 YLP 0.427184 0.662921
205 AFH 0.425743 0.674419
206 4UU 0.425743 0.698795
207 G5P 0.425743 0.682353
208 AR6 AR6 0.425743 0.75641
209 ATR 0.425287 0.708861
210 7D4 0.423529 0.662651
211 UP5 0.423077 0.698795
212 4UW 0.423077 0.714286
213 AV2 0.422222 0.670732
214 4YB 0.421569 0.652174
215 OMR 0.419048 0.689655
216 WSA 0.419048 0.674157
217 ARJ 0.418919 0.732394
218 COD 0.418182 0.715909
219 LAQ 0.417476 0.678161
220 ARG AMP 0.417476 0.670455
221 AP0 0.415094 0.702381
222 4TC 0.415094 0.682353
223 YLC 0.415094 0.678161
224 LPA AMP 0.413462 0.697674
225 A2R 0.413043 0.725
226 DND 0.409524 0.728395
227 NXX 0.409524 0.728395
228 TXD 0.409524 0.710843
229 NAI 0.409524 0.690476
230 NAX 0.409524 0.666667
231 6V0 0.409524 0.682353
232 101 0.407407 0.679012
233 A A A 0.40625 0.746835
234 V1N 0.405941 0.734177
235 AF3 ADP 3PG 0.40566 0.694118
236 ALF ADP 3PG 0.40566 0.694118
237 TYM 0.40566 0.707317
238 649 0.40566 0.638298
239 TXE 0.40566 0.690476
240 LA8 ALF 3PG 0.40566 0.694118
241 T5A 0.40367 0.662921
242 UPA 0.401869 0.690476
243 AFX 0.4 0.662338
244 IVH 0.4 0.772152
245 AYB 0.4 0.674157
246 3AT 0.4 0.7125
247 CNA 0.4 0.728395
Ligand no: 2; 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 Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3DZ6; Ligand: PUT; Similar sites found: 33
This union binding pocket(no: 1) in the query (biounit: 3dz6.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5A65 TPP 0.005875 0.43736 1.1236
2 3TYZ PAB 0.01857 0.42786 2.99625
3 4EUE NAI 0.01713 0.41595 2.99625
4 4M82 NGB 0.02426 0.40607 2.99625
5 2XMY CDK 0.01783 0.4382 3.74532
6 3WCA FPS 0.01141 0.42261 4.49438
7 1Y0G 8PP 0.02993 0.41395 5.97015
8 4NG2 OHN 0.004147 0.45841 6.19469
9 3WMX THR 0.008323 0.41233 6.74157
10 2JFN GLU 0.01363 0.40234 7.11611
11 5U98 1KX 0.01593 0.43921 7.46269
12 4KCF AKM 0.01075 0.42569 7.49064
13 5J8O 6GZ 0.009998 0.41704 8.87097
14 3GD9 GLC BGC BGC BGC 0.00566 0.43788 8.95522
15 4CLI 5P8 0.04047 0.40123 8.95522
16 3G08 FEE 0.04436 0.41877 9.09091
17 4BAE RWX 0.01746 0.40655 9.26829
18 2DDQ HRB 0.006323 0.40645 10.3286
19 1KQW RTL 0.01193 0.41049 10.4478
20 1QKQ MAN 0.00378 0.45214 11.9403
21 3BXO UPP 0.02618 0.40411 13.4328
22 4PSB GA3 0.03164 0.40082 13.4328
23 3ZW2 GLA NAG GAL FUC 0.0178 0.40266 13.7931
24 1LSH PLD 0.02347 0.42377 14.9254
25 5H2D ERG 0.01574 0.4009 14.9254
26 4USI ATP 0.007694 0.42342 15.5844
27 2QCD U5P 0.02919 0.40372 16.4179
28 2P1M IHP 0.03605 0.40295 16.4179
29 3EW2 BTN 0.003857 0.42915 17.9104
30 4QYN RTL 0.02356 0.40231 20.8955
31 1NYW DAU 0.009848 0.42658 23.8806
32 2XK9 XK9 0.01743 0.42531 23.8806
33 4YRD 3IT 0.003003 0.41196 25.3731
Pocket No.: 2; Query (leader) PDB : 3DZ6; Ligand: M8E; Similar sites found: 54
This union binding pocket(no: 2) in the query (biounit: 3dz6.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1J2Z SOG 0.0205 0.40761 2.24719
2 3A4T SFG 0.002669 0.40121 2.99625
3 3JQ3 ADP 0.0163 0.40158 3.74532
4 5DYO FLU 0.02725 0.40099 4.24528
5 5V1B 8UY 0.01422 0.41309 5.41667
6 1N07 FMN 0.0169 0.40075 5.52147
7 5FUI APY 0.0000284 0.52524 5.61798
8 2BJK NAD 0.008475 0.41681 5.97015
9 5THZ SAH 0.008406 0.40364 5.97015
10 2PWY SAH 0.009469 0.40136 6.20155
11 3QDY CBS 0.01434 0.41742 6.29371
12 3QDW NDG 0.02125 0.40646 6.29371
13 4DSU BZI 0.01915 0.4103 6.34921
14 4I8P NAD 0.01106 0.41036 7.46269
15 4GLW NMN 0.01509 0.40967 7.46269
16 5U98 1KX 0.04035 0.40218 7.46269
17 4B9E FAH 0.02132 0.4022 7.49064
18 1UYY BGC BGC 0.0004311 0.49031 7.63359
19 2OFD NGA 0.009034 0.42212 7.74648
20 4Z2S NDG 0.01135 0.41737 7.74648
21 4Z2S NAG 0.01135 0.41737 7.74648
22 2OFE NAG 0.01362 0.41307 7.74648
23 5TVA COA 0.003612 0.42014 7.91667
24 5LRT ADP 0.01079 0.40038 8.2397
25 5OFW 9TW 0.01344 0.41424 8.95522
26 5N53 8NB 0.01901 0.40755 8.95522
27 4L2I NAD 0.01768 0.41156 8.98876
28 3IES M24 0.01632 0.40368 8.98876
29 4N9Z V3L 0.004918 0.42634 9.3633
30 3H0L ADP 0.0002786 0.49319 9.57447
31 4XMF HSM 0.002598 0.42931 10.4478
32 1OFL NGK GCD 0.02049 0.4104 10.4478
33 2CJU PHX 0.0003044 0.51204 10.7438
34 1DCP HBI 0.01532 0.41098 11.5385
35 3HVJ 705 0.01012 0.41648 11.7647
36 4YWV SSN 0.002731 0.43561 11.9403
37 1T90 NAD 0.004108 0.42757 11.9403
38 1JQN DCO 0.004912 0.42233 13.4328
39 1GQ2 OXL 0.00901 0.41878 13.4328
40 4B0T ADP 0.005765 0.41245 13.4328
41 3ACL 3F1 0.007718 0.40531 13.4328
42 2XVD AS6 0.01124 0.40384 13.4328
43 4WOE ADP 0.009824 0.42244 14.9254
44 3I9U DTU 0.01071 0.41447 14.9254
45 2UUU FAD 0.03923 0.40082 14.9254
46 2UUU PL3 0.03923 0.40082 14.9254
47 5KJW 53C 0.001461 0.47032 16.4179
48 4WCX MET 0.0119 0.40983 16.4179
49 5JJU AMP 0.0119 0.40419 16.4179
50 3M6W SAM 0.009631 0.40098 17.9104
51 5XDT MB3 0.01568 0.40338 19.403
52 2GN3 MMA 0.02208 0.41278 26.8657
53 2GNM MAN 0.03193 0.40232 26.8657
54 4FZV SAM 0.00378 0.41546 31.3433
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