-->
Receptor
PDB id Resolution Class Description Source Keywords
3DCM 2 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE THERMOTOGA MARITIMA SPOUT FAMILY RN METHYLTRANSFERASE PROTEIN TM1570 IN COMPLEX WITH S-ADENOSYLM ETHIONINE THERMOTOGA MARITIMA TREFOIL KNOT SPOUT MTASE ADOMET BINDING TRANSFERASE
Ref.: CRYSTAL STRUCTURE OF THERMOTOGA MARITIMA SPOUT SUPE RNA METHYLTRANSFERASE TM1570 IN COMPLEX WITH S-ADENOSYL-L-METHIONINE PROTEINS V. 74 245 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SAM X:5452;
Valid;
none;
submit data
398.437 C15 H22 N6 O5 S C[S@@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3DCM 2 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE THERMOTOGA MARITIMA SPOUT FAMILY RN METHYLTRANSFERASE PROTEIN TM1570 IN COMPLEX WITH S-ADENOSYLM ETHIONINE THERMOTOGA MARITIMA TREFOIL KNOT SPOUT MTASE ADOMET BINDING TRANSFERASE
Ref.: CRYSTAL STRUCTURE OF THERMOTOGA MARITIMA SPOUT SUPE RNA METHYLTRANSFERASE TM1570 IN COMPLEX WITH S-ADENOSYL-L-METHIONINE PROTEINS V. 74 245 2009
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 3DCM - SAM C15 H22 N6 O5 S C[S@@+](CC....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 3DCM - SAM C15 H22 N6 O5 S C[S@@+](CC....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 3DCM - SAM C15 H22 N6 O5 S C[S@@+](CC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SAM; Similar ligands found: 202
No: Ligand ECFP6 Tc MDL keys Tc
1 SAM 1 1
2 SMM 0.792683 0.96
3 S4M 0.6875 0.909091
4 S7M 0.670455 0.945946
5 M2T 0.636364 0.878378
6 GEK 0.612903 0.931507
7 SAI 0.571429 0.878378
8 ADN 0.565789 0.773333
9 RAB 0.565789 0.773333
10 XYA 0.565789 0.773333
11 5CD 0.564103 0.783784
12 EP4 0.5625 0.826667
13 SA8 0.56044 0.945205
14 SFG 0.555556 0.875
15 5X8 0.555556 0.888889
16 5N5 0.551282 0.773333
17 A4D 0.544304 0.797297
18 EEM 0.542553 0.945946
19 SAH 0.537634 0.916667
20 DTA 0.536585 0.789474
21 62X 0.535354 0.884615
22 MTA 0.53012 0.875
23 3DH 0.517647 0.849315
24 5AL 0.510417 0.743902
25 54H 0.510204 0.673913
26 VMS 0.510204 0.673913
27 0UM 0.51 0.857143
28 AMP 0.505747 0.707317
29 LMS 0.505747 0.666667
30 A 0.505747 0.707317
31 ABM 0.505618 0.753086
32 A5A 0.505155 0.688889
33 SON 0.5 0.746988
34 SSA 0.5 0.684783
35 6RE 0.5 0.78481
36 K15 0.5 0.883117
37 5AD 0.5 0.75
38 SRP 0.5 0.746988
39 LSS 0.49505 0.706522
40 CA0 0.494624 0.714286
41 A12 0.494505 0.705882
42 AP2 0.494505 0.705882
43 ME8 0.490385 0.841463
44 TSB 0.49 0.681319
45 53H 0.49 0.666667
46 DAL AMP 0.49 0.765432
47 5CA 0.49 0.684783
48 ACP 0.489362 0.694118
49 ADP 0.48913 0.690476
50 5AS 0.48913 0.648936
51 J7C 0.488889 0.772152
52 A2D 0.488889 0.690476
53 ZAS 0.488636 0.769231
54 9ZD 0.485149 0.729412
55 9ZA 0.485149 0.729412
56 8QN 0.485149 0.743902
57 GAP 0.484536 0.73494
58 AN2 0.483871 0.682353
59 A3S 0.483871 0.813333
60 A7D 0.483871 0.851351
61 GJV 0.483516 0.775
62 SRA 0.483146 0.694118
63 LAD 0.480769 0.752941
64 KAA 0.480769 0.698925
65 GSU 0.480769 0.722222
66 AMO 0.480392 0.746988
67 DSZ 0.480392 0.703297
68 52H 0.48 0.666667
69 M33 0.478723 0.722892
70 BA3 0.478261 0.690476
71 MAO 0.478261 0.82716
72 NEC 0.477778 0.75
73 AOC 0.477778 0.776316
74 DSH 0.477778 0.842105
75 SXZ 0.47619 0.894737
76 AHX 0.475728 0.701149
77 NVA LMS 0.475728 0.736264
78 Y3J 0.47561 0.706667
79 G5A 0.474227 0.684783
80 A3T 0.473684 0.8
81 B4P 0.473118 0.690476
82 AP5 0.473118 0.690476
83 A3N 0.472527 0.766234
84 KB1 0.471698 0.833333
85 PRX 0.46875 0.73494
86 APC 0.46875 0.705882
87 AT4 0.468085 0.686047
88 PAJ 0.466019 0.712644
89 4AD 0.466019 0.759036
90 RBY 0.463918 0.72619
91 ADP PO3 0.463918 0.728395
92 ADV 0.463918 0.72619
93 ADX 0.463158 0.666667
94 MHZ 0.463158 0.82716
95 AU1 0.463158 0.674419
96 YAP 0.462963 0.738095
97 TXA 0.462264 0.72619
98 NB8 0.462264 0.72093
99 A3G 0.461538 0.802632
100 VRT 0.459184 0.842105
101 XAH 0.458716 0.715909
102 YSA 0.458716 0.684783
103 HEJ 0.458333 0.690476
104 50T 0.458333 0.682353
105 ATP 0.458333 0.690476
106 LEU LMS 0.457143 0.717391
107 7D7 0.45679 0.723684
108 KH3 0.455357 0.871795
109 ACQ 0.454545 0.694118
110 AR6 0.453608 0.710843
111 APR 0.453608 0.710843
112 AQP 0.453608 0.690476
113 5FA 0.453608 0.690476
114 NSS 0.451923 0.703297
115 FA5 0.449541 0.746988
116 A5D 0.44898 0.789474
117 AD9 0.44898 0.674419
118 AGS 0.44898 0.678161
119 SAP 0.44898 0.678161
120 PTJ 0.448598 0.72093
121 YLB 0.448276 0.758621
122 YLP 0.447368 0.738636
123 8X1 0.446602 0.680851
124 D3Y 0.446602 0.792208
125 ADP ALF 0.445545 0.678161
126 ALF ADP 0.445545 0.678161
127 3AM 0.444444 0.674699
128 MYR AMP 0.444444 0.776471
129 OAD 0.443396 0.73494
130 2VA 0.443299 0.779221
131 S8M 0.442308 0.831169
132 OOB 0.442308 0.722892
133 TYR AMP 0.441441 0.759036
134 6YZ 0.441176 0.694118
135 ADP VO4 0.441176 0.702381
136 VO4 ADP 0.441176 0.702381
137 T99 0.44 0.686047
138 TAT 0.44 0.686047
139 ANP 0.44 0.674419
140 WAQ 0.439252 0.75
141 B5Y 0.436364 0.717647
142 8PZ 0.436364 0.684783
143 F0P 0.435897 0.844156
144 YLC 0.435897 0.755814
145 AAT 0.435644 0.797468
146 1ZZ 0.435185 0.755814
147 9K8 0.435185 0.663158
148 3OD 0.435185 0.73494
149 NVA 2AD 0.434343 0.855263
150 00A 0.433962 0.689655
151 DLL 0.433962 0.722892
152 ARG AMP 0.433628 0.727273
153 7MD 0.433628 0.715909
154 ATF 0.431373 0.666667
155 SO8 0.43 0.792208
156 3UK 0.429907 0.714286
157 A6D 0.429907 0.72619
158 9X8 0.429907 0.717647
159 F2R 0.429752 0.7
160 5SV 0.428571 0.741176
161 AMP DBH 0.428571 0.714286
162 TYM 0.42735 0.746988
163 WSA 0.42735 0.692308
164 9SN 0.427273 0.681818
165 AHZ 0.426087 0.755814
166 P5A 0.425926 0.691489
167 B5V 0.425926 0.705882
168 PR8 0.425926 0.744186
169 A A 0.425926 0.710843
170 3NZ 0.425926 0.807692
171 A1R 0.424528 0.709302
172 2A5 0.424242 0.674419
173 7MC 0.423729 0.719101
174 B5M 0.423423 0.717647
175 7D5 0.422222 0.658824
176 JB6 0.422018 0.709302
177 FYA 0.422018 0.722892
178 AYB 0.421488 0.75
179 A22 0.419048 0.682353
180 MAP 0.419048 0.659091
181 2AM 0.417582 0.666667
182 TAD 0.417391 0.712644
183 A3P 0.416667 0.686747
184 ADP BMA 0.416667 0.714286
185 25A 0.415094 0.690476
186 YLA 0.413223 0.719101
187 8Q2 0.411765 0.663158
188 A3R 0.411215 0.709302
189 ADQ 0.411215 0.694118
190 48N 0.410256 0.72093
191 0XU 0.41 0.824324
192 GA7 0.408696 0.72619
193 7D3 0.40625 0.643678
194 PAP 0.405941 0.678571
195 DQV 0.405172 0.702381
196 OVE 0.404255 0.662791
197 4UV 0.403509 0.697674
198 AF3 ADP 3PG 0.403361 0.712644
199 3AD 0.402299 0.783784
200 CMP 0.402062 0.691358
201 2BA 0.402062 0.682927
202 7C5 0.4 0.731707
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3DCM; Ligand: SAM; Similar sites found with APoc: 121
This union binding pocket(no: 1) in the query (biounit: 3dcm.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 1P9P SAH None
2 4MCC 21X None
3 5MT9 ARG None
4 5MT9 SRO None
5 1LNX URI None
6 2QZ4 ADP 1.04167
7 1A0J BEN 1.5625
8 4YMJ 4EJ 1.5625
9 3WB0 FEG 1.80723
10 3O7B SAH 2.08333
11 3BP1 GUN 2.08333
12 1M26 GAL A2G 2.25564
13 1V59 FAD 2.60417
14 1O5O U5P 2.60417
15 2GJ5 VD3 3.08642
16 3NK7 SAM 3.125
17 2QB8 ATP 3.125
18 3THR C2F 3.125
19 3LAD FAD 3.125
20 2Z48 NGA 3.125
21 5U8U FAD 3.125
22 6FP4 FAD 3.125
23 6FP4 E1T 3.125
24 3AKI AH8 3.125
25 1SQL GUN 3.42466
26 5O96 SAM 3.64583
27 1F6D UDP 3.64583
28 2F5Z FAD 3.64583
29 5J5Z FAD 3.64583
30 2GEK GDP 3.64583
31 3CTY FAD 3.64583
32 4M52 M52 4.16667
33 2A8X FAD 4.16667
34 4M52 FAD 4.16667
35 5NA1 FAD 4.16667
36 3QFA FAD 4.16667
37 1I8T FAD 4.16667
38 4HZ0 1AV 4.16667
39 5TWJ SAM 4.32099
40 3I7V B4P 4.47761
41 3GYQ SAM 4.6875
42 3BBD SAH 4.6875
43 3BBH SFG 4.6875
44 4C2C ALA ALA ALA 4.6875
45 1KGZ PRP 4.6875
46 2WSI FAD 4.6875
47 4XDA RIB 4.6875
48 1O9U ADZ 4.6875
49 1T3D CYS 4.84429
50 3G2Y GF4 5.20833
51 1ZX5 LFR 5.20833
52 3G6K FAD 5.20833
53 3G6K POP 5.20833
54 6DWI HD4 5.20833
55 3KCC CMP 5.20833
56 2HXW FLC 5.20833
57 1FEC FAD 5.20833
58 1T36 ORN 5.20833
59 5TH5 MET 5.20833
60 4JAL SAH 5.38922
61 1ZK7 FAD 5.72917
62 4J56 FAD 5.72917
63 1LVL FAD 5.72917
64 5T85 44G 6.13497
65 1MJH ATP 6.17284
66 5H5F SAM 6.25
67 2ZZV LAC 6.25
68 4C2G ALA ALA ALA ALA 6.25
69 3RI1 3RH 6.25
70 1GPJ CIT 6.25
71 2FJK 13P 6.25
72 5X2N ALA 6.77083
73 2RAB NAD 6.77083
74 2RAB FAD 6.77083
75 5A7Y SAH 7.29167
76 5U97 PIT 7.29167
77 1H82 GZZ 7.29167
78 4RPL 3UC 7.29167
79 1P4V GLY 7.29167
80 1H82 FAD 7.29167
81 4RPL FAD 7.29167
82 4OVZ P85 7.8125
83 2P3V SRT 7.8125
84 4V1F BQ1 8.13953
85 2HQM FAD 8.33333
86 6BOX SAH 8.33333
87 6EMU SAM 8.33333
88 2CE7 ADP 8.85417
89 2W3L DRO 9.02778
90 2HHP FLC 9.375
91 5A04 BGC 9.375
92 5BUK FAD 9.375
93 1ZDQ MSM 9.375
94 2NVK FAD 9.375
95 1ZEI CRS 9.43396
96 5LY1 PPI 9.89583
97 1MXI SAH 10
98 4JWH SAH 10.4167
99 4JWF SAH 10.4167
100 2NU8 COA 10.4167
101 4UX9 ANP 10.4167
102 4JWJ SAH 10.9375
103 3I6B KDO 11.1111
104 1SBR VIB 11.4583
105 3GDN MXN 11.4583
106 3HQP FDP 11.4583
107 1T0S BML 11.9792
108 3RNM FAD 13.7931
109 1G4U AF3 14.0625
110 3ESS 18N 15.1042
111 1GET NAP 15.625
112 1GET FAD 15.625
113 1USR SIA 16.6667
114 4CNG SAH 18.75
115 1BZL GCG 18.75
116 1BZL FAD 18.75
117 1CT9 AMP 19.7917
118 2WPF FAD 21.875
119 2WPF WPF 21.875
120 4CNE SAH 25
121 1V2X SAM 27.0833
Pocket No.: 2; Query (leader) PDB : 3DCM; Ligand: SAM; 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: 3dcm.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback