Receptor
PDB id Resolution Class Description Source Keywords
4JAL 2 Å EC: 2.1.1.207 CRYSTAL STRUCTURE OF TRNA (UM34/CM34) METHYLTRANSFERASE TRML ESCHERICHIA COLI WITH SAH ESCHERICHIA COLI SPOUT METHYLTRANSFERASE TRNA MODIFICATION TRML DEEP TREFSAM BINDING METHYLATION TRANSFERASE
Ref.: THE TRNA RECOGNITION MECHANISM OF THE MINIMALIST SP METHYLTRANSFERASE, TRML NUCLEIC ACIDS RES. V. 41 7828 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SAH B:203;
A:201;
Valid;
Valid;
none;
none;
submit data
384.411 C14 H20 N6 O5 S c1nc(...
EDO B:202;
B:201;
Invalid;
Invalid;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
EPE A:202;
Invalid;
none;
submit data
238.305 C8 H18 N2 O4 S C1CN(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4JAL 2 Å EC: 2.1.1.207 CRYSTAL STRUCTURE OF TRNA (UM34/CM34) METHYLTRANSFERASE TRML ESCHERICHIA COLI WITH SAH ESCHERICHIA COLI SPOUT METHYLTRANSFERASE TRNA MODIFICATION TRML DEEP TREFSAM BINDING METHYLATION TRANSFERASE
Ref.: THE TRNA RECOGNITION MECHANISM OF THE MINIMALIST SP METHYLTRANSFERASE, TRML NUCLEIC ACIDS RES. V. 41 7828 2013
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4JAL - 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 1MXI - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 4JAL - 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 1MXI - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 4JAL - 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 : 4JAL; Ligand: SAH; Similar sites found: 75
This union binding pocket(no: 1) in the query (biounit: 4jal.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5AHW CMP 0.0001254 0.48028 None
2 2BOS GLA GAL GLC 0.01138 0.41923 None
3 2BOS GLA GAL GLC NBU 0.01353 0.41595 None
4 1MJH ATP 0.002218 0.40953 None
5 3KO0 TFP 0.02414 0.40908 None
6 2FKA BEF 0.0219 0.40796 None
7 5A7Y SAH 0.000001503 0.60529 1.79641
8 5A07 GDP 0.005946 0.42279 1.79641
9 5TWJ SAM 0.000000002512 0.63037 1.85185
10 5TVA AMP 0.004062 0.42622 2.39521
11 5TV6 PML 0.01775 0.40816 2.39521
12 1YRO UDP 0.02391 0.40776 2.99401
13 3BBD SAH 0.000006304 0.53723 3.59281
14 5UDS ATP 0.0001584 0.4987 3.59281
15 4JWJ SAH 0.000006721 0.49335 3.59281
16 1S4P GDP 0.004747 0.42303 3.59281
17 4KCT FDP 0.01289 0.40256 3.59281
18 3G6K FAD 0.0003491 0.4004 3.59281
19 5CGE 51F 0.01855 0.40719 3.97112
20 4JWH SAH 0.000001839 0.5031 4.19162
21 2C5S AMP 0.0002544 0.49515 4.19162
22 2D3Y DU 0.007509 0.44855 4.19162
23 4MCC 21X 0.0001683 0.42846 4.19162
24 2YBQ SAH 0.00185 0.41854 4.19162
25 3HGM ATP 0.0005489 0.43378 4.7619
26 3AIA SAM 0.0000001264 0.62004 4.79042
27 2YY8 MTA 0.000005318 0.56177 4.79042
28 2YY8 SAM 0.000001436 0.54674 4.79042
29 2WSI FAD 0.0004559 0.43671 4.79042
30 4LOC OXM 0.01162 0.42032 4.79042
31 1CBF SAH 0.004032 0.418 4.79042
32 3GUZ PAF 0.01715 0.40378 4.79042
33 3DCM SAM 0.0000003057 0.57547 5.38922
34 5H5F SAM 0.0000003337 0.54997 5.38922
35 2XG5 EC2 0.006677 0.43753 5.38922
36 2XG5 EC5 0.006677 0.43753 5.38922
37 5AOG IAC 0.005397 0.45776 5.98802
38 5FPE 3TR 0.0141 0.41506 5.98802
39 2F6U CIT 0.01361 0.41406 5.98802
40 1RYD GLC 0.01458 0.41055 5.98802
41 1P9P SAH 0.00006981 0.46194 6.13027
42 1YQC GLV 0.02679 0.41524 6.58683
43 3BBH SFG 0.000001114 0.57025 6.82927
44 5LFV SIA GAL NAG 0.00546 0.43322 7.18563
45 4WA2 SIA GAL NAG 0.02118 0.40576 7.18563
46 2PHR MAN MAN BMA MAN 0.02021 0.40102 7.18563
47 2PHX MAN MAN MAN MAN 0.02478 0.40073 7.18563
48 2PHF MAN MAN BMA MAN 0.02068 0.40052 7.18563
49 1O94 AMP 0.001173 0.43349 7.78443
50 2Z48 NGA 0.02553 0.40419 7.78443
51 2JAP J01 0.01989 0.40137 7.78443
52 1JBU BEN 0.02213 0.42443 7.93651
53 1CT9 AMP 0.0008758 0.4686 8.38323
54 5TCI MLI 0.03312 0.40309 8.38323
55 2AE2 NAP 0.01779 0.40792 8.98204
56 4PEG 5GP 0.02375 0.40334 8.98204
57 1GPM AMP 0.00198 0.46396 9.58084
58 3OII SAH 0.00000366 0.53124 9.88142
59 1H5R THM 0.014 0.40478 10.1796
60 4JWF SAH 0.000002071 0.51123 10.5991
61 5APG EEM 0.000004309 0.51626 10.7784
62 3HQP FDP 0.007665 0.41746 10.7784
63 3O7B SAH 0.000008756 0.52479 11.976
64 3RK1 ATP 0.001242 0.44556 11.976
65 2OQ2 A3P 0.0004829 0.43643 12.5749
66 3BP1 GUN 0.02162 0.40072 13.1737
67 5MGJ 7MX 0.02315 0.40493 13.3333
68 4CNE SAH 0.00000000001738 0.7695 14.9701
69 5F7J ADE 0.02145 0.40594 15.5689
70 1VBO MAN MAN MAN 0.01908 0.40729 16.1074
71 1VBO MAN 0.02594 0.40602 16.1074
72 1V2X SAM 0.0000000002651 0.70081 37.1257
73 4CNG SAH 0.0000000001526 0.61984 37.7246
74 3NK7 SAM 0.00000000008324 0.7218 38.3234
75 3GYQ SAM 0.00000002892 0.63126 41.3174
Pocket No.: 2; Query (leader) PDB : 4JAL; Ligand: SAH; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4jal.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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