Receptor
PDB id Resolution Class Description Source Keywords
3EPB 1.75 Å EC: 4.1.1.50 HUMAN ADOMETDC E256Q MUTANT COMPLEXED WITH PUTRESCINE HOMO SAPIENS ADOMETDC WITH MUTATION IN PUTRESCINE BINDING SITE DECARBOXYLASE LYASE PYRUVATE S-ADENOSYL-L-METHIONINE SPERMIDINE BIOSYNTHESIS ZYMOGEN
Ref.: STRUCTURAL BASIS FOR PUTRESCINE ACTIVATION OF HUMAN S-ADENOSYLMETHIONINE DECARBOXYLASE. BIOCHEMISTRY V. 47 13404 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PUT B:350;
Valid;
none;
Ka = 10000 M^-1
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: 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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