-->
Receptor
PDB id Resolution Class Description Source Keywords
3M6W 1.3 Å EC: 2.1.1.- MULTI-SITE-SPECIFIC 16S RRNA METHYLTRANSFERASE RSMF FROM THE THERMOPHILUS IN SPACE GROUP P21212 IN COMPLEX WITH S-ADENOSM ETHIONINE THERMUS THERMOPHILUS RRNA METHYLTRANSFERASE 5-METHYLCYTIDINE RSMF ADOMET MULTSPECIFIC METHYLTRANSFERASE TRANSFERASE
Ref.: MULTI-SITE-SPECIFIC 16S RRNA METHYLTRANSFERASE RSMF THERMUS THERMOPHILUS. RNA V. 16 1584 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL A:466;
Invalid;
none;
submit data
35.453 Cl [Cl-]
SAM A:465;
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
3M6W 1.3 Å EC: 2.1.1.- MULTI-SITE-SPECIFIC 16S RRNA METHYLTRANSFERASE RSMF FROM THE THERMOPHILUS IN SPACE GROUP P21212 IN COMPLEX WITH S-ADENOSM ETHIONINE THERMUS THERMOPHILUS RRNA METHYLTRANSFERASE 5-METHYLCYTIDINE RSMF ADOMET MULTSPECIFIC METHYLTRANSFERASE TRANSFERASE
Ref.: MULTI-SITE-SPECIFIC 16S RRNA METHYLTRANSFERASE RSMF THERMUS THERMOPHILUS. RNA V. 16 1584 2010
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 60 families.
1 3M6V - SAM C15 H22 N6 O5 S C[S@@+](CC....
2 3M6W - 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 54 families.
1 3M6V - SAM C15 H22 N6 O5 S C[S@@+](CC....
2 3M6W - 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 47 families.
1 3M6V - SAM C15 H22 N6 O5 S C[S@@+](CC....
2 3M6W - 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 : 3M6W; Ligand: SAM; Similar sites found with APoc: 321
This union binding pocket(no: 1) in the query (biounit: 3m6w.bio2) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 5C9P FUC 0.787402
2 3S1S SAH 1.07759
3 3C6K SPD 1.50862
4 3C6K MTA 1.50862
5 2EJU SAH 1.5873
6 1YQZ FAD 1.59817
7 1MUU NAD 1.6055
8 4LWP SAH 1.63043
9 6BQ6 TER 1.72414
10 1X87 NAD 1.72414
11 3AKI AH8 1.72414
12 4KRG SAH 1.72414
13 4IV9 TSR 1.72414
14 1SC6 NAD 1.73267
15 4DCM SAM 1.86667
16 1F8F NAD 1.88679
17 4UCI SAM 1.92771
18 2JHF NAD 1.93966
19 2GKS ADP 1.93966
20 1O5Q PYR 1.96721
21 1U2Z SAH 2.07852
22 1E3I CXF 2.12766
23 2G5C NAD 2.13523
24 3HB5 NAP 2.14067
25 2FZW NAD 2.14477
26 1UWK NAD 2.15517
27 1UWK URO 2.15517
28 3LAD FAD 2.15517
29 5M67 NAD 2.15517
30 4MRP GSH 2.15517
31 5M67 ADE 2.15517
32 5M67 3D1 2.15517
33 4PIO AVI 2.16718
34 4PIO SAH 2.16718
35 1NW5 SAM 2.19436
36 2IXB A2G 2.25225
37 2IXB NAD 2.25225
38 1R27 MGD 2.37069
39 3S5W FAD 2.37581
40 1U3U NAD 2.40642
41 1U3U BNF 2.40642
42 1D1T NAD 2.41287
43 2OBF SAH 2.42215
44 2OBF F83 2.42215
45 1T57 FMN 2.42718
46 5OCQ CIT 2.45614
47 2DPM SAM 2.46479
48 5E1M SAH 2.48963
49 5E1M PRO PRO LYS ARG ILE ALA 2.48963
50 1SAY PYR 2.49307
51 1LDN NAD 2.53165
52 6IS0 SAH 2.58621
53 4GKV NAD 2.67857
54 6CI9 NAP 2.7027
55 9LDB NAD 2.71084
56 5YF1 8V0 2.76243
57 5YF1 SFG 2.76243
58 3JWH SAH 2.76498
59 5JJR SAH 2.80172
60 4EDF UPG 2.80172
61 3QOX SAH 2.8169
62 6ECW SAH 2.85714
63 5U19 SAH 2.93255
64 5U19 827 2.93255
65 1CDO NAD 2.94118
66 5XNC MTA 2.96496
67 6FDF SAH 2.99401
68 5N6C NAD 3
69 4KRI SAH 3.00231
70 3G2O SAM 3.01003
71 1JQD SAH 3.08219
72 2AOT SAH 3.08219
73 5L53 NAP 3.08642
74 4TQG NDP 3.09598
75 5MPT SAH 3.1401
76 6DUB SAH 3.15315
77 5YJI SAH 3.16901
78 5YJI 8WO 3.16901
79 2DFV NAD 3.17003
80 5E9W SAH 3.20513
81 5THY SAH 3.20988
82 5THZ SAH 3.20988
83 3LZW FAD 3.23276
84 3LZW NAP 3.23276
85 1DLJ NAI 3.23383
86 1DLJ UGA 3.23383
87 5JE0 SAH 3.23887
88 5JE0 AZ8 3.23887
89 2WA2 SAM 3.26087
90 1P77 ATR 3.30882
91 6GAS FAD 3.32326
92 3ELW SAM 3.33333
93 3ELW GP3 3.33333
94 1SOW NAD 3.35366
95 3T7S SAM 3.35821
96 2ZIF SAM 3.367
97 3ENV ABF 3.40426
98 3LKZ SFG 3.42679
99 5TOW ADN 3.4398
100 5TOW NAI 3.4398
101 1V59 FAD 3.44828
102 4POO SAM 3.5
103 5FUB SAH 3.56083
104 3VYW SAM 3.57143
105 2P41 SAH 3.60656
106 5WP4 SAH 3.66379
107 2ZJ1 ARJ 3.66379
108 2ZJ1 NAD 3.66379
109 5O9F 9ON 3.66379
110 5O9F NAD 3.66379
111 3DXY SAM 3.66972
112 3FPF TNA 3.69128
113 3FPF MTA 3.69128
114 2VT3 ATP 3.72093
115 5E72 SAM 3.75723
116 1A5Z NAD 3.76176
117 2GN4 UD1 3.77907
118 5W7M SAH 3.84615
119 5W7K SAH 3.84615
120 1V6A TRE 3.91566
121 3EVF GTA 3.97112
122 3EVF SAH 3.97112
123 3EVG SAH 4
124 2A92 NAI 4.04984
125 5TWB FAD 4.06977
126 3HVJ 705 4.0724
127 2PX8 SAH 4.08922
128 4MIG G3F 4.09483
129 4XUC 43G 4.12844
130 4XUC SAM 4.12844
131 3NJ4 AFX 4.13793
132 3NJ4 NAD 4.13793
133 5JGL SAM 4.15225
134 4YMH SAH 4.16667
135 4NEC SAH 4.16667
136 2HIM ASP 4.18994
137 2HIM ASN 4.18994
138 3VPH NAD 4.19355
139 3VPH OXM 4.19355
140 1GV0 NAD 4.19355
141 4ZVV GN0 4.21687
142 4ZVV NAD 4.21687
143 1KOL NAD 4.27136
144 1LSS NAD 4.28571
145 2PT9 2MH 4.36137
146 2PT9 S4M 4.36137
147 1Z3C SA8 4.36242
148 4PI8 NAG AMU 4.38596
149 5O98 NAP 4.4164
150 1O5I NAD 4.41767
151 4ZGR NGA GAL 4.45344
152 3AJ4 SEP 4.46429
153 5ULP KB1 4.47761
154 5CUQ NSC 4.49438
155 1KPH SAH 4.52962
156 2ZL4 ALA ALA ALA ALA 4.59184
157 3L9W GSH 4.60048
158 3L9W AMP 4.60048
159 3BXO SAM 4.60251
160 1XCL SAH 4.68085
161 4C3Y FAD 4.74138
162 5MW4 5JU 4.79042
163 1NYT NAP 4.79705
164 3QWI NAP 4.81482
165 3QWI CUE 4.81482
166 1KPG SAH 4.87805
167 1Y8Q ATP 4.91329
168 2I7C AAT 4.947
169 1G0N NDP 4.947
170 1G0N PHH 4.947
171 3OND NAD 4.9569
172 3OND ADN 4.9569
173 4N49 SAM 5.14019
174 3PT9 SAH 5.17241
175 1YY5 FAD 5.17241
176 1MV8 NAD 5.27523
177 3VSE SAH 5.27638
178 5YJF SAH 5.28169
179 5YJF 8WO 5.28169
180 2VHW NAI 5.30504
181 3GCZ SAM 5.31915
182 1EDO NAP 5.32787
183 5L4S 6KX 5.34591
184 5L4S NAP 5.34591
185 5ERG SAM 5.38793
186 5GWX SAM 5.38793
187 5GWX SAR 5.38793
188 5GWT SIN 5.39568
189 5GWT NAD 5.39568
190 3GFB NAD 5.42857
191 1E6E FAD 5.46875
192 3A27 SAM 5.51471
193 6AR9 3L4 5.51471
194 1P1C SAH 5.52764
195 4YAG NAI 5.53633
196 1GTE FAD 5.60345
197 1V8B NAD 5.60345
198 4PNE SAH 5.62914
199 2YX1 SFG 5.65476
200 5N5D SAM 5.75221
201 4ITU 1HS 5.94796
202 4ITU NAI 5.94796
203 5BSZ SAH 6
204 3TKA SAM 6.05187
205 4YT4 FE9 6.13333
206 1QAN SAH 6.14754
207 5AHO TLA 6.25
208 5UFN SAH 6.30252
209 5YRL GLC GLC 6.33803
210 5YRM BGC GLC 6.33803
211 5YRJ BGC GLC 6.33803
212 5YRG BGC GLC 6.33803
213 5YRF GLC GLC 6.33803
214 4HXY NDP 6.39269
215 4HKP TKW 6.41026
216 1JQ3 AAT 6.41892
217 1I9G SAM 6.42857
218 4KIB SAH 6.44258
219 2A14 SAH 6.46388
220 1R18 SAH 6.60793
221 4PLT NAI 6.64653
222 4PLT OXM 6.64653
223 6F7X MFU 6.66667
224 1VL8 NAP 6.74157
225 6ECT SAM 6.85358
226 3GGO ENO 6.89655
227 3GGO NAI 6.89655
228 3Q87 SAM 7.05882
229 3ITJ CIT 7.10059
230 3RFV 15L 7.11611
231 5BW4 SAM 7.11611
232 3RFV NAI 7.11611
233 4OM8 NAD 7.11974
234 3ABI NAD 7.12329
235 1T26 GBD 7.14286
236 1T26 NAI 7.14286
237 6F3N NAD 7.20339
238 6F3N ADN 7.20339
239 2JK0 ASP 7.38462
240 3H2B SAH 7.38916
241 6F3M NAD 7.3913
242 5FWA J7C 7.3991
243 4YAC NAI 7.40741
244 3NUG NAD 7.69231
245 1Q0S SAH 7.72201
246 3AB1 FAD 7.75862
247 4Y9D NAI 7.86885
248 1DL5 SAH 7.88644
249 3MQ2 SAH 8.25688
250 3A25 SAM 8.30565
251 6B92 SAH 8.5034
252 1DQX BMP 8.61423
253 2HNK SAH 8.62069
254 2BZ1 TAU 8.67347
255 1G55 SAH 8.74636
256 2RGO FAD 8.83621
257 1LTH NAD 9.09091
258 3PFG TLO 9.12547
259 3PFG SAM 9.12547
260 5EIN NAP 9.25926
261 1JG3 ADN 9.3617
262 3MAG SAH 9.44625
263 6ARJ BW4 9.45559
264 6ARJ SAH 9.45559
265 5DX8 SFG 9.45559
266 5DWQ SFG 9.45559
267 5DXA SFG 9.45559
268 5DX0 SFG 9.45559
269 5DX1 SFG 9.45559
270 1PL6 572 9.48276
271 1PL6 NAD 9.48276
272 5ZZ6 ADP 9.61539
273 5HJM MTA 9.65909
274 2PWY SAH 9.68992
275 6GAR FAD 9.74212
276 1H2B NAJ 9.7493
277 3MCT SAH 9.76431
278 1N07 FMN 9.81595
279 1N07 ADP 9.81595
280 4YUW S4M 9.86842
281 4YUW 4JU 9.86842
282 5UAV NDP 9.93789
283 6GFK SAH 9.96016
284 4BLW SAH 10.0346
285 4BLW AMP 10.0346
286 2IZ1 ATR 10.1293
287 1KYZ SAH 10.137
288 1G60 SAM 10.3846
289 1L3I SAH 10.4167
290 2HMT NAI 10.4167
291 1IY8 NAD 10.4869
292 4JLS 3ZE 10.5263
293 2XVM SAH 10.5528
294 1F3L SAH 10.5919
295 4R6W PC 10.8527
296 4R6W SAH 10.8527
297 5E5U MLI 11.0553
298 1BDB NAD 11.5523
299 4URF NAD 11.6935
300 4FN4 NAD 11.811
301 3OU2 SAH 11.9266
302 3P2E SAH 12
303 3C3Y SAH 12.2363
304 1VE3 SAM 12.7753
305 2O07 SPD 12.8289
306 2O07 MTA 12.8289
307 5KVA SAM 13.3094
308 5FA8 SAM 13.6646
309 2HK9 ATR 14.1818
310 2VDV SAM 14.2276
311 4OBW SAM 15.9533
312 4DMG SAM 16.285
313 6F5Z SAH 16.3934
314 3DZ6 M8E 17.9104
315 5GM1 SAH 18.1818
316 5E8J SAH 18.1818
317 3MB5 SAM 19.2157
318 4GQB 0XU 22.7273
319 1I1N SAH 24.7788
320 5FA5 MTA 25
321 1SQF SAM 27.2727
Pocket No.: 2; Query (leader) PDB : 3M6W; 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: 3m6w.bio2) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3M6W; Ligand: SAM; Similar sites found with APoc: 1
This union binding pocket(no: 3) in the query (biounit: 3m6w.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 1ZGA SAH 2.80112
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