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Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
M8E A:368;
Valid;
none;
ic50 = 15 nM
393.441 C17 H27 N7 O4 C[N@@...
PUT B: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
Ligand no: 1; Ligand: M8E; Similar ligands found: 9
No: Ligand ECFP6 Tc MDL keys Tc
1 M8E 1 1
2 M8M 0.595506 0.927711
3 A8M 0.538462 0.857143
4 C8M 0.489583 0.821429
5 N8M 0.47191 0.761905
6 O8M 0.46875 0.785714
7 MAO 0.463158 0.926829
8 MHZ 0.42 0.880952
9 5NB 0.41573 0.674157
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 N2P 0.636364 0.947368
4 16D 0.636364 0.9
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 with APoc: 132
This union binding pocket(no: 1) in the query (biounit: 3dz6.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 5XEG AKG 1.2987
2 3L5R 47X 1.63934
3 2VFT SOR 1.87266
4 4ZSI GLP 2.33918
5 4ZSI 4R1 2.33918
6 1KGI T4A 2.3622
7 3RGA LSB 2.62172
8 2OBD 2OB 2.62172
9 4KBS PX2 2.7907
10 3EM0 CHD 2.89855
11 4MNS 2AX 2.98507
12 4U03 TLL 2.98507
13 4EUE NAI 2.99625
14 2A1L PCW 2.99625
15 1T27 PCW 2.99625
16 2PD4 NAD 3.27273
17 2PD4 DCN 3.27273
18 1U3R 338 3.3195
19 4J26 EST 3.33333
20 4J24 EST 3.33333
21 6F6J SIN 3.37079
22 6F6J CUW 3.37079
23 6A63 LAT 3.62319
24 2C0U FAD NBT 3.87244
25 5CKW ANP 4.11985
26 3KJM 245 4.11985
27 6D6L FY4 4.47761
28 4GGL CJC 4.47761
29 4WB7 ATP 4.49438
30 1QIN GIP 4.49438
31 6FOF LAT 5.10204
32 1XKQ NDP 5.24345
33 1YYE 196 5.24345
34 1TT8 PHB 5.4878
35 1Y0G 8PP 5.97015
36 3U3U EAH 5.97015
37 4ZVI 4S4 5.97015
38 5NW7 9C2 5.97015
39 3B00 16A 5.99251
40 4NG2 OHN 6.19469
41 1WBI BTN 6.20155
42 4U0W 16G 6.50407
43 3WMX THR 6.74157
44 1KJM ALA GLN PHE SER ALA SER ALA SER ARG 7
45 2JFN GLU 7.11611
46 5XS3 VAL ARG SER ARG ARG CYS LEU ARG LEU 7.14286
47 3KPB SAM 7.37705
48 5DRB 5FJ 7.46269
49 6FUL E7Z 7.46269
50 2HJR APR 7.46269
51 5U98 VAL THR THR ASP ILE GLN VAL LYS VAL 7.46269
52 5NBP BGC BGC BGC 7.46269
53 2RFX LEU SER SER PRO VAL THR LYS SER PHE 7.46269
54 4KCF AKM 7.49064
55 4EVQ PHB 7.49064
56 1OPK P16 7.49064
57 4RFR RHN 7.88177
58 3STD MQ0 8.48485
59 5NIU 8YZ 8.59375
60 4WN5 MVC 8.69565
61 5N2F 8HW 8.87097
62 2HXT EHM 8.95522
63 3GXO MQA 8.95522
64 6G0X RAM GLC GLA NAG NDG NAG 8.95522
65 3SXS PP2 8.95522
66 3KFF ZBT 8.95522
67 3KFF XBT 8.95522
68 3GD9 GLC BGC BGC BGC 8.95522
69 5Y80 IRE 8.98876
70 3RUG DB6 9.09091
71 4BAE RWX 9.26829
72 5K4W THR 9.73783
73 2DDQ HRB 10.3286
74 5IXG OTP 10.4478
75 3DLG GWE 10.4478
76 2OFV 242 10.4478
77 5N0L ILE 10.4478
78 2X32 OTP 10.4478
79 2X34 UQ8 10.4478
80 2HZQ STR 10.4478
81 1SJD NPG 11.9403
82 4HKP 16B 11.9403
83 4LOO SB4 11.9403
84 5FP4 YC8 11.9403
85 5LGD PLM 11.9403
86 4IGQ THR M3L GLN 11.9403
87 4K3H 1OM 12.7119
88 6HDT BTN 12.782
89 1NWW HPN 13.4228
90 2QA8 GEN 13.4328
91 4B2Z P5S 13.4328
92 3BXO UPP 13.4328
93 1F52 ADP 13.4328
94 5TDF ADP 13.4328
95 5MJA 7O3 13.4328
96 5DXG EST 13.4328
97 4V24 GYR 13.4328
98 5DXE EST 13.4328
99 4PSB GA3 13.4328
100 5VNF VAL THR SER VAL VAL 13.4328
101 1SWG BTN 13.4328
102 5Y1G AKB 13.4831
103 3ZW2 NAG GAL FUC 13.7931
104 1LSH PLD 14.9254
105 4YBN FAD 14.9254
106 4F7E 0SH 14.9254
107 3SCM LGN 14.9254
108 2RDQ AKG 14.9254
109 2QCD U5P 16.4179
110 1LFO OLA 16.4179
111 2P1M IHP 16.4179
112 2P1O NLA 16.4179
113 2P1O IHP 16.4179
114 2FTB OLA 16.8
115 4D52 GXL 17.2285
116 5AIG VPR 17.9104
117 3EW2 BTN 17.9104
118 1K0E TRP 19.403
119 4DXD 9PC 19.403
120 4EMV 0R9 19.403
121 4QRH 0O2 19.403
122 3L9R L9R 20.8955
123 5IXH OTP 20.8955
124 4QYN RTL 20.8955
125 3L9R L9Q 20.8955
126 4P7X YCP 20.8955
127 4P7X AKG 20.8955
128 5KD6 6C7 20.8955
129 3HQP OXL 20.8955
130 1NYW DAU 23.8806
131 3STK PLM 29.8507
132 3ZXE PGZ 30.0752
Pocket No.: 2; Query (leader) PDB : 3DZ6; Ligand: M8E; Similar sites found with APoc: 136
This union binding pocket(no: 2) in the query (biounit: 3dz6.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 6B79 ORA None
2 6BVE PGA 1.22449
3 1Y7P RIP 1.34529
4 5OM2 DXT 2.24719
5 1J2Z SOG 2.24719
6 2HRL SIA GAL SIA BGC NGA CEQ 2.3622
7 3EFV NAD 2.99625
8 3A4T SFG 2.99625
9 4GN8 ASO 3.37079
10 5EJL C2E 3.62903
11 3JQ3 ADP 3.74532
12 3WLE NAD 3.74532
13 1RJW ETF 4.11985
14 2IMP NAI 4.11985
15 5DYO FLU 4.24528
16 6GNO XDI 4.44444
17 4PXL NAD 4.47761
18 5HSA FAS 4.47761
19 5L13 6ZE 4.47761
20 1M5B BN1 4.47761
21 1NAA 6FA 4.49438
22 6BR7 BEF 4.51128
23 3KIF GDL 4.71698
24 1Z0N BCD 5.20833
25 5V1B 8UY 5.41667
26 1SQL GUN 5.47945
27 1N07 FMN 5.52147
28 2RDE C2E 5.57769
29 5FUI APY 5.61798
30 1F9V ADP 5.97015
31 3PE2 E1B 5.97015
32 1KY8 NAP 5.97015
33 2BJK NAD 5.97015
34 5THZ SAH 5.97015
35 2PWY SAH 6.20155
36 3QDY CBS 6.29371
37 3QDW NDG 6.29371
38 5HV0 AKG 6.91244
39 5TZO 7V7 6.91489
40 5L2M 6ZY 7.11611
41 3JZ4 NAP 7.46269
42 6F97 FAD 7.46269
43 5VCM UDP 7.46269
44 4XPQ FUL 7.46269
45 4I8P NAD 7.46269
46 4GLW NMN 7.46269
47 4A0M NAD 7.46269
48 5U98 1KX 7.46269
49 4B9E FAH 7.49064
50 1UYY BGC BGC 7.63359
51 5N2D 8J8 7.63889
52 2OFD NGA 7.74648
53 4Z2S NAG 7.74648
54 4Z2S NDG 7.74648
55 2OFE NAG 7.74648
56 4RDN 6MD 7.78443
57 3RHJ NAP 7.86517
58 5TVA COA 7.91667
59 5LRT ADP 8.2397
60 5NIU 8YZ 8.59375
61 6B5G CQY 8.95522
62 5JFL NAD 8.95522
63 6B5G NAD 8.95522
64 5OFW 9TW 8.95522
65 5N53 8NB 8.95522
66 1SDW IYT 8.95522
67 4L2I NAD 8.98876
68 3A7R LAQ 8.98876
69 3IES M24 8.98876
70 2AG4 LP3 9.14634
71 2AG4 OLA 9.14634
72 3H0L ADP 9.57447
73 4XMF HSM 10.4478
74 2Z3U CRR 10.4478
75 1OFL NGK GCD 10.4478
76 4PZ2 NAD 10.4478
77 5KWW 6YA 10.4478
78 4ZUL UN1 10.4478
79 1NE7 16G 10.4478
80 6C0B PAM 10.4478
81 2CJU PHX 10.7438
82 1Y2W NAG 11.2676
83 1DCP HBI 11.5385
84 3HVJ 705 11.7647
85 4YWV SSN 11.9403
86 2EV9 SKM 11.9403
87 4RF7 ARG 11.9403
88 5WL1 CUY 11.9403
89 5WL1 D3D 11.9403
90 1T90 NAD 11.9403
91 2IU8 PLM 11.9403
92 1VA6 P2S 11.9403
93 1VA6 ADP 11.9403
94 1TL2 NDG 11.9403
95 2B56 U5P 13.1086
96 2QE0 NAP 13.4328
97 3VZ3 NAP 13.4328
98 4OE4 NAD 13.4328
99 1JQN DCO 13.4328
100 1GQ2 OXL 13.4328
101 4B0T ADP 13.4328
102 3ACL 3F1 13.4328
103 2XVD AS6 13.4328
104 1LSH PLD 14.9254
105 4WOE ADP 14.9254
106 5BVE 4VG 14.9254
107 2G50 PYR 14.9254
108 3I9U DTU 14.9254
109 3FPF TNA 14.9254
110 3FPF MTA 14.9254
111 5Y4R C2E 14.9254
112 2UUU FAD 14.9254
113 2UUU PL3 14.9254
114 3CBC DBS 14.9254
115 5FLJ QUE 15.5914
116 2VL1 GLY GLY 16.4179
117 5KJW 53C 16.4179
118 6E1Q CFA 16.4179
119 5WXU FLC 16.4179
120 4WCX MET 16.4179
121 5JJU AMP 16.4179
122 1W0O SIA 17.9104
123 3M6W SAM 17.9104
124 5HWV MBN 18.4615
125 1ZEA DVA DPR GLY DSN DGN DHI DTY DAS DSN 19.403
126 5XDT MB3 19.403
127 1GPM AMP 19.403
128 2WOX NDP 20.8955
129 5L2R MLA 23.8806
130 6H3O FAD 25.3731
131 2GN3 MMA 26.8657
132 2GNM MAN 26.8657
133 5LXT GTP 28.3582
134 4FZV SAM 31.3433
135 5AE2 FAD 37.3134
136 3HSS MLA 41.791
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