Receptor
PDB id Resolution Class Description Source Keywords
3FRH 1.2 Å EC: 2.1.1.- STRUCTURE OF THE 16S RRNA METHYLASE RMTB, P21 ESCHERICHIA COLI METHYLTRANSFERASE DOMAIN HELICAL N-TERMINAL DOMAIN METHYLTRANSFERASE PLASMID TRANSFERASE
Ref.: STRUCTURAL BASES FOR 16 S RRNA METHYLATION CATALYZED BY ARMA AND RMTB METHYLTRANSFERASES J.MOL.BIOL. V. 388 570 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SAH A:260;
Valid;
none;
submit data
384.411 C14 H20 N6 O5 S c1nc(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3FRH 1.2 Å EC: 2.1.1.- STRUCTURE OF THE 16S RRNA METHYLASE RMTB, P21 ESCHERICHIA COLI METHYLTRANSFERASE DOMAIN HELICAL N-TERMINAL DOMAIN METHYLTRANSFERASE PLASMID TRANSFERASE
Ref.: STRUCTURAL BASES FOR 16 S RRNA METHYLATION CATALYZED BY ARMA AND RMTB METHYLTRANSFERASES J.MOL.BIOL. V. 388 570 2009
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 57 families.
1 3FRI - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 3FRH - SAH C14 H20 N6 O5 S c1nc(c2c(n....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 50 families.
1 3FRI - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 3FRH - SAH C14 H20 N6 O5 S c1nc(c2c(n....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 44 families.
1 3FRI - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 3FRH - SAH C14 H20 N6 O5 S c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SAH; Similar ligands found: 197
No: Ligand ECFP6 Tc MDL keys Tc
1 SAH 1 1
2 5X8 0.759494 0.969697
3 A7D 0.734177 0.926471
4 TT8 0.709302 0.970588
5 SXZ 0.692308 0.916667
6 DSH 0.692308 0.914286
7 DTA 0.666667 0.857143
8 3DH 0.662338 0.869565
9 S8M 0.655556 0.901408
10 SFG 0.635294 0.954545
11 SA8 0.62069 0.915493
12 EEM 0.617977 0.890411
13 MTA 0.615385 0.869565
14 SAI 0.613636 0.955882
15 S7M 0.586957 0.916667
16 36A 0.586538 0.90411
17 K15 0.583333 0.878378
18 RAB 0.573333 0.84058
19 ADN 0.573333 0.84058
20 XYA 0.573333 0.84058
21 62X 0.572917 0.855263
22 5CD 0.571429 0.852941
23 0UM 0.5625 0.876712
24 5N5 0.558442 0.84058
25 A4D 0.551282 0.867647
26 SAM 0.537634 0.916667
27 SSA 0.536842 0.712644
28 SMM 0.536842 0.88
29 KB1 0.534653 0.902778
30 A5D 0.532609 0.857143
31 SIB 0.53125 0.928571
32 EP4 0.530864 0.819444
33 DSZ 0.530612 0.732558
34 GSU 0.53 0.752941
35 AMP 0.529412 0.763158
36 A 0.529412 0.763158
37 5CA 0.525773 0.712644
38 ME8 0.524752 0.8125
39 M2T 0.52439 0.821918
40 6RE 0.523256 0.824324
41 GJV 0.522727 0.813333
42 AAT 0.515789 0.863014
43 LSS 0.515152 0.696629
44 KAA 0.514852 0.727273
45 J7C 0.511364 0.835616
46 A5A 0.510417 0.697674
47 SON 0.505495 0.805195
48 SRP 0.505155 0.805195
49 5AL 0.5 0.779221
50 VMS 0.5 0.681818
51 KH3 0.5 0.866667
52 ADX 0.5 0.694118
53 CA0 0.5 0.769231
54 AMP MG 0.5 0.74359
55 AMO 0.5 0.805195
56 54H 0.5 0.681818
57 AHX 0.49505 0.753086
58 TSB 0.494949 0.689655
59 53H 0.494949 0.674157
60 G5A 0.494737 0.712644
61 A2D 0.494382 0.74359
62 ABM 0.494382 0.74359
63 ZAS 0.494253 0.808219
64 A6D 0.490196 0.759494
65 8QN 0.49 0.779221
66 GEK 0.49 0.956522
67 GAP 0.489583 0.769231
68 A3S 0.48913 0.884058
69 AN2 0.48913 0.734177
70 S4M 0.488889 0.831169
71 SRA 0.488636 0.746835
72 LAD 0.485437 0.810127
73 52H 0.484848 0.674157
74 A12 0.483516 0.759494
75 BA3 0.483516 0.74359
76 AP2 0.483516 0.759494
77 AOC 0.483146 0.842857
78 NEC 0.483146 0.788732
79 Y3J 0.481481 0.768116
80 NVA LMS 0.480392 0.696629
81 VRT 0.479167 0.861111
82 50T 0.478723 0.734177
83 5AS 0.478261 0.655556
84 B4P 0.478261 0.74359
85 ADP 0.478261 0.74359
86 AP5 0.478261 0.74359
87 A3N 0.477778 0.830986
88 YSA 0.476636 0.712644
89 XAH 0.476636 0.768293
90 0XU 0.473684 0.897059
91 WAQ 0.471154 0.807692
92 NSS 0.470588 0.712644
93 5AD 0.468354 0.791045
94 ADP MG 0.468085 0.734177
95 AU1 0.468085 0.725
96 M33 0.468085 0.734177
97 MAO 0.467391 0.797468
98 TXA 0.466667 0.759494
99 A3G 0.466667 0.871429
100 NB8 0.466667 0.775
101 3AM 0.465909 0.727273
102 DAL AMP 0.465347 0.779221
103 ATP 0.463158 0.74359
104 ADP BEF 0.463158 0.716049
105 A3T 0.463158 0.842857
106 BEF ADP 0.463158 0.716049
107 ACP 0.463158 0.746835
108 7D7 0.4625 0.785714
109 LEU LMS 0.461538 0.677778
110 APC 0.458333 0.759494
111 AQP 0.458333 0.74359
112 APR 0.458333 0.766234
113 PRX 0.458333 0.746835
114 AR6 0.458333 0.766234
115 5FA 0.458333 0.74359
116 IOT 0.456897 0.761905
117 4AD 0.456311 0.794872
118 PAJ 0.456311 0.722892
119 WSA 0.45614 0.72093
120 FA5 0.453704 0.805195
121 YAP 0.453704 0.794872
122 RBY 0.453608 0.782051
123 ADV 0.453608 0.782051
124 ADP PO3 0.453608 0.763158
125 AD9 0.453608 0.725
126 SAP 0.453608 0.728395
127 AGS 0.453608 0.728395
128 PTJ 0.45283 0.731707
129 MHZ 0.452632 0.797468
130 00A 0.451923 0.740741
131 A3P 0.451613 0.74026
132 YLP 0.451327 0.771084
133 7MD 0.45045 0.768293
134 ALF ADP 0.45 0.707317
135 ADP ALF 0.45 0.707317
136 ATP MG 0.44898 0.734177
137 2VA 0.447917 0.819444
138 OOB 0.446602 0.779221
139 ANP 0.444444 0.725
140 ACQ 0.444444 0.746835
141 TAT 0.444444 0.7375
142 P5A 0.443396 0.719101
143 7D5 0.443182 0.708861
144 ARG AMP 0.442478 0.759036
145 A1R 0.442308 0.7625
146 YLC 0.439655 0.790123
147 2AM 0.438202 0.717949
148 DLL 0.438095 0.779221
149 A22 0.436893 0.734177
150 D3Y 0.436893 0.859155
151 TYR AMP 0.436364 0.782051
152 ATF 0.435644 0.716049
153 MYR AMP 0.435185 0.746988
154 SO8 0.434343 0.808219
155 3UK 0.433962 0.769231
156 OAD 0.433962 0.769231
157 TAD 0.433628 0.765432
158 25A 0.432692 0.74359
159 ANP MG 0.431373 0.707317
160 VO4 ADP 0.431373 0.734177
161 ADP VO4 0.431373 0.734177
162 9SN 0.431193 0.731707
163 TYM 0.431034 0.805195
164 PR8 0.429907 0.8
165 ADQ 0.428571 0.746835
166 YLB 0.42735 0.771084
167 3OD 0.425926 0.769231
168 FYA 0.425926 0.779221
169 1ZZ 0.425926 0.746988
170 PPS 0.425743 0.674419
171 NVA 2AD 0.424242 0.808219
172 MAP 0.423077 0.707317
173 A2P 0.421053 0.727273
174 4YB 0.421053 0.735632
175 ADP BMA 0.420561 0.746835
176 5SV 0.419048 0.731707
177 3NZ 0.416667 0.824324
178 YLA 0.416667 0.771084
179 48N 0.413793 0.753086
180 LPA AMP 0.413793 0.768293
181 AYB 0.413223 0.761905
182 QQY 0.413043 0.696203
183 ACK 0.413043 0.710526
184 JB6 0.412844 0.7625
185 BIS 0.412844 0.719512
186 PAP 0.41 0.730769
187 OVE 0.408602 0.7125
188 4UV 0.40708 0.75
189 AMP DBH 0.40708 0.746835
190 3AD 0.406977 0.852941
191 AF3 ADP 3PG 0.40678 0.743902
192 OMR 0.40678 0.738095
193 LAQ 0.405172 0.768293
194 A A 0.40367 0.74359
195 7C5 0.403509 0.789474
196 7MC 0.403361 0.75
197 4UU 0.4 0.75
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3FRH; Ligand: SAH; Similar sites found: 193
This union binding pocket(no: 1) in the query (biounit: 3frh.bio1) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1L0I PSR 0.003161 0.45103 None
2 1LSS NAD 0.00205 0.42325 None
3 2HMT NAI 0.002595 0.41556 None
4 3KIF GDL 0.01827 0.4141 None
5 4JGX PLM 0.01554 0.4017 None
6 1MAI I3P 0.03449 0.40069 None
7 1UCD U5P 0.01502 0.41987 1.05263
8 3C3Y SAH 0.006267 0.40593 1.26582
9 4PIO AVI 0.00008253 0.41966 1.58103
10 4PIO SAH 0.00007477 0.41682 1.58103
11 3LST SAH 0.000001292 0.59322 1.97628
12 2ZFU SAH 0.00003518 0.49769 2.32558
13 5E9W SAH 0.000006344 0.56821 2.37154
14 5FTW SAH 0.000001243 0.5589 2.37154
15 2AOT SAH 0.00001813 0.53289 2.37154
16 3TKY SAH 0.00000101 0.53141 2.37154
17 3T7S SAM 0.00001712 0.5219 2.37154
18 5THY SAH 0.00001414 0.51439 2.37154
19 5THZ SAH 0.000009297 0.51153 2.37154
20 1G60 SAM 0.00005378 0.49488 2.37154
21 4DCM SAM 0.0008269 0.45681 2.37154
22 1Q0S SAH 0.0001469 0.45644 2.37154
23 1I9G SAM 0.0009674 0.43701 2.37154
24 2PWY SAH 0.0009915 0.42929 2.37154
25 1JQD HSM 0.0006355 0.41989 2.37154
26 5IL1 SAM 0.003682 0.41943 2.37154
27 5K7U SAM 0.004272 0.41659 2.37154
28 3P9C SAH 0.0002041 0.41485 2.37154
29 1JQD SAH 0.0003512 0.41435 2.37154
30 4N49 SAM 0.003781 0.41202 2.37154
31 1V6A TRE 0.02467 0.40915 2.37154
32 2WTN FER 0.0154 0.41356 2.39044
33 3GWZ SAH 0.000001419 0.59131 2.7668
34 3GXO SAH 0.000001882 0.578 2.7668
35 5XVK SAH 0.0002332 0.45479 2.7668
36 3QOX SAH 0.0002913 0.45087 2.7668
37 5GWX SAR 0.000321 0.43335 2.7668
38 5GWX SAM 0.000321 0.43335 2.7668
39 4RDH AMP 0.002887 0.43189 2.7668
40 2BO4 FLC 0.01334 0.4236 2.7668
41 4RDI ATP 0.005799 0.41074 2.7668
42 3EYK EYK 0.009188 0.40558 2.7668
43 5BRP PNG 0.0396 0.40063 2.7668
44 1R18 SAH 0.0008907 0.43477 3.0837
45 2UYQ SAM 0.000000247 0.67516 3.16206
46 4KRG SAH 0.000006825 0.54574 3.16206
47 1KYZ SAH 0.00002154 0.51752 3.16206
48 5BW4 SAM 0.00003538 0.51367 3.16206
49 1NW5 SAM 0.000126 0.47898 3.16206
50 5E72 SAM 0.000282 0.45542 3.16206
51 2WA2 SAM 0.000844 0.45187 3.16206
52 2ZIF SAM 0.001456 0.43324 3.16206
53 1J78 OLA 0.003788 0.42883 3.16206
54 2EJU SAH 0.002499 0.42683 3.16206
55 2PX8 SAH 0.002554 0.42642 3.16206
56 1KYZ FER 0.0003405 0.42577 3.16206
57 4D79 ATP 0.003547 0.42014 3.16206
58 5F2K OCA 0.0002676 0.40906 3.16206
59 5F2K SAH 0.0002676 0.40906 3.16206
60 3V1S 0LH 0.02306 0.40498 3.16206
61 1UAY ADN 0.007228 0.41738 3.30579
62 5F8F SFG 0.000003388 0.56629 3.55731
63 1XDS SAM 0.000006165 0.56139 3.55731
64 1QZZ SAM 0.00001505 0.54321 3.55731
65 4PNE SAH 0.000002631 0.53375 3.55731
66 4E70 N7I 0.00004323 0.44692 3.55731
67 5DX8 SFG 0.0004791 0.4421 3.55731
68 5DWQ SFG 0.0004211 0.43898 3.55731
69 5DX1 SFG 0.0003929 0.43495 3.55731
70 5DX0 SFG 0.0004071 0.43462 3.55731
71 5DXA SFG 0.0007895 0.43331 3.55731
72 1TZD ADP 0.01313 0.43059 3.55731
73 4XDY HIO 0.02901 0.40882 3.55731
74 5KVA SAM 0.004426 0.40596 3.55731
75 3TKA SAM 0.006794 0.40126 3.55731
76 1O5I NAD 0.00138 0.43425 3.61446
77 1UZN NAP 0.003195 0.42987 3.64372
78 5E1M SAH 0.00004158 0.43039 3.73444
79 5E1M PRO PRO LYS ARG ILE ALA 0.00004158 0.43039 3.73444
80 1JJV ATP 0.006507 0.43975 3.8835
81 3VYW SAM 0.006342 0.40253 3.8961
82 5KOK SAH 0.0000001274 0.60782 3.95257
83 1YXM ADE 0.0001141 0.54805 3.95257
84 5MPT SAH 0.00001514 0.52425 3.95257
85 1L1E SAH 0.000009418 0.52182 3.95257
86 1TPY SAH 0.00002413 0.49956 3.95257
87 3MB5 SAM 0.00005089 0.48159 3.95257
88 5KOK R9T 0.000001397 0.47547 3.95257
89 5KOK S9T 0.000001483 0.46888 3.95257
90 1G55 SAH 0.0002439 0.46664 3.95257
91 3RKR NAP 0.001302 0.46233 3.95257
92 4BQS K2Q 0.02332 0.40438 3.97727
93 4POO SAM 0.001017 0.42308 4
94 2VDV SAM 0.000001802 0.58644 4.06504
95 1ZGA SAH 0.00004973 0.51887 4.34783
96 3GCZ SAM 0.0006431 0.45274 4.34783
97 2A14 SAH 0.0004332 0.44772 4.34783
98 1Y8Q ATP 0.0006586 0.43129 4.34783
99 1U2Z SAH 0.001789 0.41889 4.34783
100 5ULP KB1 0.001709 0.41468 4.34783
101 2PT9 S4M 0.00222 0.40667 4.34783
102 4JWK CTN 0.0287 0.40237 4.34783
103 1I1N SAH 0.0008883 0.41108 4.42478
104 3DXY SAM 0.00002922 0.53636 4.58716
105 3MQ2 SAH 0.00002386 0.52135 4.58716
106 3OU2 SAH 0.000004276 0.50822 4.58716
107 4A6D SAM 0.00000098 0.56971 4.74308
108 1XTP SAI 0.00004473 0.50358 4.74308
109 1KPG SAH 0.00002003 0.50291 4.74308
110 1KPH SAH 0.00002362 0.49995 4.74308
111 5JJR SAH 0.0009827 0.44465 4.74308
112 4R6W SAH 0.00007063 0.43092 4.74308
113 3VSE SAH 0.004663 0.43056 4.74308
114 5CUQ NSC 0.002519 0.4247 4.74308
115 3A27 SAM 0.005179 0.41291 4.74308
116 1QAN SAH 0.0007526 0.4378 4.91803
117 5L95 AMP 0.002113 0.42628 5.01792
118 2XVM SAH 0.0000008512 0.60172 5.02513
119 1SQF SAM 0.0003342 0.46522 5.13834
120 3EVG SAH 0.0007144 0.45073 5.13834
121 2P41 SAH 0.001516 0.43638 5.13834
122 4LIK CIT 0.01655 0.4261 5.13834
123 3W9F I3P 0.02768 0.40544 5.13834
124 3AKK ADP 0.01422 0.40003 5.13834
125 5LOG SAH 0.002083 0.42655 5.15021
126 2BZG SAH 0.00005022 0.50138 5.17241
127 2YX1 SFG 0.0007247 0.46429 5.5336
128 3H8V ATP 0.0007842 0.44895 5.5336
129 4DMG SAM 0.002026 0.44797 5.5336
130 2WPB ZZI 0.01777 0.41473 5.5336
131 4BWL MN9 0.02077 0.41328 5.5336
132 5FA8 SAM 0.0005379 0.44007 5.59006
133 4NEC SAH 0.000001754 0.57941 5.92885
134 5XVQ SAH 0.0003169 0.44939 5.92885
135 3P2E SAH 0.00005022 0.49118 6.22222
136 5X62 SAH 0.00002089 0.52394 6.32411
137 1BC5 SAH 0.000009284 0.51155 6.32411
138 4KIB SAH 0.000005211 0.48998 6.32411
139 3PT9 SAH 0.0005574 0.45547 6.32411
140 3S1S SAH 0.0003195 0.44924 6.32411
141 4UCI SAM 0.004269 0.41312 6.32411
142 1Z3C SA8 0.0004506 0.41142 6.32411
143 5JGL SAM 0.000005896 0.54859 6.71937
144 1F3L SAH 0.00009902 0.47421 6.71937
145 4V3I ASP LEU THR ARG PRO 0.01638 0.41359 6.71937
146 1SQL GUN 0.01679 0.41835 6.84932
147 2PXX SAH 0.000002893 0.54949 6.97674
148 3BXO SAM 0.00001576 0.54227 7.11297
149 5HJM MTA 0.0001574 0.47482 7.11462
150 3A25 SAM 0.003418 0.42085 7.11462
151 5MGZ SAH 0.00000809 0.53027 7.20339
152 4II2 ATP 0.00077 0.44119 7.22892
153 5KAX RHQ 0.02322 0.40865 7.22892
154 3JWH SAH 0.000003538 0.58038 7.37327
155 4YMH SAH 0.003582 0.41301 7.5
156 5DNK SAH 0.0003006 0.49366 7.50988
157 3BGD SAH 0.00007368 0.47508 7.50988
158 3BGD PM6 0.0001669 0.4375 7.50988
159 3BP1 GUN 0.02594 0.41083 7.50988
160 4N9Z V3L 0.02624 0.40246 7.90514
161 2DPM SAM 0.0005806 0.44246 8.3004
162 5DZT AMP 0.02442 0.40949 8.3004
163 2OUA AES 0.03007 0.40101 8.51064
164 3LKZ SFG 0.001861 0.42866 9.09091
165 4O08 PO6 0.03014 0.40309 9.09091
166 3H2B SAH 0.00002466 0.50945 9.35961
167 1L3I SAH 0.002745 0.40156 9.89583
168 2VDJ HSE 0.009934 0.42583 10.2767
169 4OBW SAM 0.000213 0.47382 10.6719
170 5KOD IAC 0.03014 0.41507 10.6719
171 1JG3 ADN 0.001566 0.43575 11.0638
172 4LWP SAH 0.0004252 0.46063 11.0672
173 3X01 AMP 0.0173 0.41836 11.0672
174 3G2O SAM 0.000008203 0.53594 11.8577
175 4AZW SAM 0.000007415 0.5319 11.8577
176 4AZT SAM 0.00001161 0.52931 11.8577
177 3WV8 ATP 0.005293 0.40909 11.8577
178 5XLX SAH 0.00001032 0.53155 12.6482
179 4KRI SAH 0.00002344 0.50513 13.0435
180 5GM1 SAH 0.00001156 0.50769 13.4387
181 2IX0 C5P 0.01073 0.41587 13.4387
182 3Q87 SAM 0.0001214 0.46629 14.2292
183 1FP1 SAH 0.000001701 0.58001 16.2055
184 1VE3 SAM 0.000009688 0.53277 16.2996
185 5JE0 AZ8 0.000009433 0.46512 17.004
186 5JE0 SAH 0.000009433 0.46512 17.004
187 5C9J DAO 0.02095 0.40279 17.1717
188 3PMA SCR 0.004651 0.44616 17.2414
189 2JHP SAH 0.004229 0.42043 17.7866
190 5E8J SAH 0.000006746 0.55956 20.4545
191 4GQB 0XU 0.0001942 0.4519 22.7273
192 5FA5 MTA 0.0003573 0.47353 25
193 3FZG SAM 0.000000007084 0.68917 45.5
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