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Receptor
PDB id Resolution Class Description Source Keywords
3GYQ 2.45 Å EC: 2.1.1.66 STRUCTURE OF THE THIOSTREPTON-RESISTANCE METHYLTRANSFERASE S-ADENOSYL-L-METHIONINE COMPLEX STREPTOMYCES CYANEUS RRNA METHYLTRANSFERASE SPOUT MTASES SAM TREFOIL KNOT ANTIBIOTIC RESISTANCE METHYLTRANSFERASE S-ADENOSYL-L- METHIONINE TRANSFERASE
Ref.: STRUCTURE OF THE THIOSTREPTON-RESISTANCE METHYLTRANSFERASE-S-ADENOSYL-L-METHIONINE COMPLEX AND ITS INTERACTION WITH RIBOSOMAL RNA J.BIOL.CHEM. V. 284 17013 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SAM A:270;
B:270;
Valid;
Valid;
none;
none;
submit data
398.437 C15 H22 N6 O5 S C[S@@...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3GYQ 2.45 Å EC: 2.1.1.66 STRUCTURE OF THE THIOSTREPTON-RESISTANCE METHYLTRANSFERASE S-ADENOSYL-L-METHIONINE COMPLEX STREPTOMYCES CYANEUS RRNA METHYLTRANSFERASE SPOUT MTASES SAM TREFOIL KNOT ANTIBIOTIC RESISTANCE METHYLTRANSFERASE S-ADENOSYL-L- METHIONINE TRANSFERASE
Ref.: STRUCTURE OF THE THIOSTREPTON-RESISTANCE METHYLTRANSFERASE-S-ADENOSYL-L-METHIONINE COMPLEX AND ITS INTERACTION WITH RIBOSOMAL RNA J.BIOL.CHEM. V. 284 17013 2009
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3GYQ - SAM C15 H22 N6 O5 S C[S@@+](CC....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3GYQ - SAM C15 H22 N6 O5 S C[S@@+](CC....
2 3NK7 - SAM C15 H22 N6 O5 S C[S@@+](CC....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3GYQ - SAM C15 H22 N6 O5 S C[S@@+](CC....
2 3NK7 - 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 : 3GYQ; Ligand: SAM; Similar sites found with APoc: 109
This union binding pocket(no: 1) in the query (biounit: 3gyq.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 3BBD SAH None
2 2BOS GLA GAL GLC None
3 2BOS GLA GAL GLC NBU None
4 6GNO XDI None
5 5FII PHE None
6 4DS0 A2G GAL NAG FUC None
7 4CQK PIO None
8 3KIF GDL None
9 5APG EEM 1.62162
10 4JWH SAH 1.83824
11 4UCI ADN 1.83824
12 1QXA GLY GLY GLY 2.12766
13 4JWF SAH 2.30415
14 1RZ1 NAD 2.48447
15 4AP9 1PS 2.48756
16 5H5F SAM 2.5641
17 3BP1 GUN 2.57353
18 2C5S AMP 2.57353
19 1JGT APC 2.57353
20 1JGT CMA 2.57353
21 1D4D FAD 2.57353
22 5FPE 3TR 2.57353
23 5A04 BGC 2.57353
24 3O7B SAH 2.86885
25 6EMU SAM 3.04569
26 5NGZ 2BG 3.04569
27 1P9P SAH 3.06513
28 5TWJ SAM 3.08642
29 1GPM AMP 3.30882
30 1KOR ARG 3.30882
31 1KOR SIN 3.30882
32 1KOR ANP 3.30882
33 5WS9 AMP 3.30882
34 2YBQ UP2 3.30882
35 1ZDQ MSM 3.30882
36 2YBQ SAH 3.30882
37 1YQC GLV 3.52941
38 1EFV AMP 3.52941
39 1EFV FAD 3.52941
40 4MCC 21X 3.65854
41 5A7Y SAH 3.67647
42 1ZX5 LFR 3.67647
43 3BBH SFG 3.90244
44 1RYD GLC 4.04412
45 4G5H UD7 4.04412
46 3RK1 ATP 4.21941
47 3GDN MXN 4.41176
48 2OQ2 A3P 4.5977
49 3DCM SAM 4.6875
50 2WSI FAD 4.77941
51 1T57 FMN 4.85437
52 1ELI PYC 5.14706
53 1CT9 AMP 5.14706
54 5JBE MAL 5.14706
55 5CGE 51F 5.14706
56 4L2I NAD 5.32319
57 4L2I FAD 5.32319
58 6F97 FAD 5.51471
59 5O96 SAM 5.71429
60 6B2M COA 5.88235
61 4K49 HFQ 5.88235
62 2RKV ZBA 5.88235
63 2CBO TH2 6.08696
64 2Z49 AMG 6.25
65 2Z48 NGA 6.25
66 6H3O FAD 6.61765
67 2W5P CL8 6.71141
68 1M26 GAL A2G 6.76692
69 1TL2 NDG 6.77966
70 2RCU BUJ 7.35294
71 6MJF SAH 7.35294
72 3K1X DBX 7.69231
73 3G6K FAD 7.72059
74 3G6K POP 7.72059
75 1O97 FAD 7.72059
76 1O97 AMP 7.72059
77 5X2N ALA 8.08823
78 4JWJ SAH 8.41584
79 1Q19 APC 8.45588
80 1JG3 ADN 8.51064
81 3AIA SAM 8.53081
82 1KGZ PRP 8.82353
83 6GR0 F8W 9.1954
84 3OII SAH 9.48617
85 1S4P GDP 9.55882
86 4CNG SAH 9.80392
87 1MJH ATP 9.87654
88 1RJW ETF 10.2941
89 2XG5 EC2 10.4046
90 2XG5 EC5 10.4046
91 5C2N NAG 10.4167
92 5AHW CMP 10.8844
93 1F6D UDP 11.3971
94 1T0S BML 11.6279
95 1O94 AMP 11.7647
96 1YFS ALA 13.9706
97 2YY8 SAM 14.9254
98 2YY8 MTA 14.9254
99 5O2Z FLC 15.126
100 2ART LPA AMP 15.2672
101 3HGM ATP 15.6463
102 1SQL GUN 16.4384
103 5YRV 5AD 18.2482
104 5TVF PUT 18.8235
105 4R2M ANP 23.4177
106 4CNE SAH 24.3446
107 1V2X SAM 36.0825
108 4JAL SAH 41.3174
109 1MXI SAH 42.5
Pocket No.: 2; Query (leader) PDB : 3GYQ; Ligand: SAM; Similar sites found with APoc: 36
This union binding pocket(no: 2) in the query (biounit: 3gyq.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 2IHK CSF 2.20588
2 5WXU FLC 2.57353
3 2PW0 TRC 2.57353
4 1XF1 CIT 2.57353
5 1FL2 FAD 2.57353
6 1RTF BEN 2.77778
7 2BWN SIN 2.94118
8 3G2Y GF4 3.04183
9 2J0W ASP 3.30882
10 1Q9I FAD 3.30882
11 1Q9I TEO 3.30882
12 5HSA FAS 3.67647
13 5A07 GDP 3.67647
14 5G3U ITW 4.04412
15 2WTX UDP 4.04412
16 2WTX VDO 4.04412
17 3GDN FAD 4.41176
18 3GDN HBX 4.41176
19 3Q9T FAY 5.14706
20 3HP8 SUC 5.45455
21 5AOG IAC 5.88235
22 4LZB URA 6.30252
23 3VSV XYS 6.61765
24 4HA6 FAD 6.98529
25 4YUW 4JU 7.35294
26 4YUW S4M 7.35294
27 2HYQ MAN MAN 7.37705
28 2OFW ADX 7.69231
29 5T85 44G 9.20245
30 3B6C SDN 9.82906
31 5E5U MLI 11.5578
32 5YB7 ORN 11.7647
33 1NU4 MLA 13.4021
34 2CHT TSA 14.9606
35 2GEK GDP 15.0735
36 2NU8 COA 18.3824
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