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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 54 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 47 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: 211
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 DSH 0.692308 0.914286
6 SXZ 0.692308 0.916667
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 ADN 0.573333 0.84058
19 RAB 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 SMM 0.536842 0.88
28 SSA 0.536842 0.712644
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 A 0.529412 0.763158
36 LMS 0.529412 0.694118
37 AMP 0.529412 0.763158
38 5CA 0.525773 0.712644
39 ME8 0.524752 0.8125
40 M2T 0.52439 0.821918
41 6RE 0.523256 0.824324
42 GJV 0.522727 0.813333
43 AAT 0.515789 0.863014
44 LSS 0.515152 0.696629
45 KAA 0.514852 0.727273
46 J7C 0.511364 0.835616
47 A5A 0.510417 0.697674
48 SON 0.505495 0.805195
49 SRP 0.505155 0.805195
50 F0P 0.504505 0.915493
51 54H 0.5 0.681818
52 VMS 0.5 0.681818
53 ADX 0.5 0.694118
54 CA0 0.5 0.769231
55 AMO 0.5 0.805195
56 5AL 0.5 0.779221
57 KH3 0.5 0.866667
58 NVA LMS 0.49505 0.707865
59 AHX 0.49505 0.753086
60 TSB 0.494949 0.689655
61 53H 0.494949 0.674157
62 G5A 0.494737 0.712644
63 ABM 0.494382 0.74359
64 A2D 0.494382 0.74359
65 ZAS 0.494253 0.808219
66 A6D 0.490196 0.759494
67 8QN 0.49 0.779221
68 GEK 0.49 0.956522
69 GAP 0.489583 0.769231
70 AN2 0.48913 0.734177
71 A3S 0.48913 0.884058
72 S4M 0.488889 0.831169
73 SRA 0.488636 0.746835
74 LAD 0.485437 0.810127
75 52H 0.484848 0.674157
76 A12 0.483516 0.759494
77 BA3 0.483516 0.74359
78 AP2 0.483516 0.759494
79 NEC 0.483146 0.788732
80 AOC 0.483146 0.842857
81 Y3J 0.481481 0.768116
82 VRT 0.479167 0.861111
83 50T 0.478723 0.734177
84 B4P 0.478261 0.74359
85 ADP 0.478261 0.74359
86 5AS 0.478261 0.655556
87 AP5 0.478261 0.74359
88 A3N 0.477778 0.830986
89 YSA 0.476636 0.712644
90 XAH 0.476636 0.768293
91 0XU 0.473684 0.897059
92 AT4 0.473118 0.7375
93 WAQ 0.471154 0.807692
94 NSS 0.470588 0.712644
95 5AD 0.468354 0.791045
96 AU1 0.468085 0.725
97 M33 0.468085 0.734177
98 MAO 0.467391 0.797468
99 TXA 0.466667 0.759494
100 NB8 0.466667 0.775
101 A3G 0.466667 0.871429
102 3AM 0.465909 0.727273
103 DAL AMP 0.465347 0.779221
104 8X1 0.465347 0.707865
105 A3T 0.463158 0.842857
106 ATP 0.463158 0.74359
107 HEJ 0.463158 0.74359
108 ACP 0.463158 0.746835
109 7D7 0.4625 0.785714
110 LEU LMS 0.461538 0.688889
111 9ZA 0.460784 0.740741
112 9ZD 0.460784 0.740741
113 5FA 0.458333 0.74359
114 AQP 0.458333 0.74359
115 AR6 0.458333 0.766234
116 APC 0.458333 0.759494
117 APR 0.458333 0.766234
118 PRX 0.458333 0.746835
119 F2R 0.457627 0.75
120 IOT 0.456897 0.761905
121 4AD 0.456311 0.794872
122 PAJ 0.456311 0.722892
123 WSA 0.45614 0.72093
124 YAP 0.453704 0.794872
125 8PZ 0.453704 0.712644
126 FA5 0.453704 0.805195
127 ADP PO3 0.453608 0.763158
128 ADV 0.453608 0.782051
129 NVA 2AD 0.453608 0.849315
130 SAP 0.453608 0.728395
131 AGS 0.453608 0.728395
132 RBY 0.453608 0.782051
133 AD9 0.453608 0.725
134 PTJ 0.45283 0.731707
135 MHZ 0.452632 0.797468
136 00A 0.451923 0.740741
137 A3P 0.451613 0.74026
138 YLP 0.451327 0.771084
139 7MD 0.45045 0.768293
140 ALF ADP 0.45 0.707317
141 ADP ALF 0.45 0.707317
142 2VA 0.447917 0.819444
143 OOB 0.446602 0.779221
144 ANP 0.444444 0.725
145 T99 0.444444 0.7375
146 ACQ 0.444444 0.746835
147 TAT 0.444444 0.7375
148 P5A 0.443396 0.719101
149 7D5 0.443182 0.708861
150 A1R 0.442308 0.7625
151 YLC 0.439655 0.790123
152 2AM 0.438202 0.717949
153 DLL 0.438095 0.779221
154 ARG AMP 0.4375 0.759036
155 A22 0.436893 0.734177
156 D3Y 0.436893 0.859155
157 ATF 0.435644 0.716049
158 MYR AMP 0.435185 0.746988
159 80F 0.434426 0.75
160 SO8 0.434343 0.808219
161 OAD 0.433962 0.769231
162 3UK 0.433962 0.769231
163 TAD 0.433628 0.765432
164 25A 0.432692 0.74359
165 6YZ 0.431373 0.746835
166 VO4 ADP 0.431373 0.734177
167 ADP VO4 0.431373 0.734177
168 9SN 0.431193 0.731707
169 TYM 0.431034 0.805195
170 B5V 0.429907 0.759494
171 PR8 0.429907 0.8
172 ADQ 0.428571 0.746835
173 YLB 0.42735 0.771084
174 9K8 0.425926 0.67033
175 1ZZ 0.425926 0.746988
176 FYA 0.425926 0.779221
177 3OD 0.425926 0.769231
178 PPS 0.425743 0.674419
179 MAP 0.423077 0.707317
180 A2P 0.421053 0.727273
181 4YB 0.421053 0.735632
182 9X8 0.420561 0.75
183 ADP BMA 0.420561 0.746835
184 TYR AMP 0.419643 0.794872
185 5SV 0.419048 0.731707
186 3NZ 0.416667 0.824324
187 YLA 0.416667 0.771084
188 8Q2 0.415254 0.688889
189 A3R 0.415094 0.7625
190 B5Y 0.414414 0.75
191 B5M 0.414414 0.75
192 48N 0.413793 0.753086
193 LPA AMP 0.413793 0.768293
194 AYB 0.413223 0.761905
195 ACK 0.413043 0.710526
196 QQY 0.413043 0.696203
197 BIS 0.412844 0.719512
198 JB6 0.412844 0.7625
199 PAP 0.41 0.730769
200 DQV 0.408696 0.75641
201 OVE 0.408602 0.7125
202 AMP DBH 0.40708 0.746835
203 4UV 0.40708 0.75
204 3AD 0.406977 0.852941
205 AF3 ADP 3PG 0.40678 0.743902
206 OMR 0.40678 0.738095
207 LAQ 0.405172 0.768293
208 A A 0.40367 0.74359
209 7C5 0.403509 0.789474
210 7MC 0.403361 0.75
211 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 with APoc: 145
This union binding pocket(no: 1) in the query (biounit: 4jal.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 5AHW CMP None
2 2BOS GLA GAL GLC None
3 2BOS GLA GAL GLC NBU None
4 1MJH ATP None
5 3KO0 TFP None
6 2FKA BEF None
7 6BKK 308 None
8 5A7Y SAH 1.79641
9 5A07 GDP 1.79641
10 5XC5 GTP 1.79641
11 5TWJ SAM 1.85185
12 5TVA AMP 2.39521
13 5TV6 PML 2.39521
14 2XTZ GSP 2.39521
15 6EMU SAM 2.99401
16 4M3P HCS 2.99401
17 1YRO UDP 2.99401
18 5O96 SAM 3.59281
19 3BBD SAH 3.59281
20 4JWJ SAH 3.59281
21 3G6K FAD 3.59281
22 3G6K POP 3.59281
23 1S4P GDP 3.59281
24 6B2M COA 3.59281
25 2PV7 NAD 3.59281
26 4KCT FDP 3.59281
27 5NM7 GLY 3.59281
28 5CGE 51F 3.97112
29 4JWH SAH 4.19162
30 2C5S AMP 4.19162
31 4MCC 21X 4.19162
32 2D3Y DU 4.19162
33 2YBQ UP2 4.19162
34 3A06 NDP 4.19162
35 2YBQ SAH 4.19162
36 2FR1 NDP 4.19162
37 5DNK SAH 4.19162
38 6GNO XDI 4.44444
39 3HGM ATP 4.7619
40 3AIA SAM 4.79042
41 2YY8 MTA 4.79042
42 2YY8 SAM 4.79042
43 2WSI FAD 4.79042
44 4LOC OXM 4.79042
45 1AE1 NAP 4.79042
46 3GUZ PAF 4.79042
47 2FJK 13P 4.79042
48 3G5N PB2 4.79042
49 3DCM SAM 5.38922
50 5H5F SAM 5.38922
51 2XG5 EC5 5.38922
52 2XG5 EC2 5.38922
53 4HA6 FAD 5.38922
54 1T57 FMN 5.38922
55 1K97 CIR 5.38922
56 1K97 ASP 5.38922
57 4AP3 FAD 5.38922
58 4AP3 NAP 5.38922
59 3WB0 FEG 5.42169
60 5AOG IAC 5.98802
61 5FPE 3TR 5.98802
62 2F6U CIT 5.98802
63 1RYD GLC 5.98802
64 1Q19 APC 5.98802
65 4HXY NDP 5.98802
66 5CIC 51R 5.98802
67 5J60 FAD 5.98802
68 4YNU FAD 5.98802
69 1JNR FAD 6
70 1P9P SAH 6.13027
71 1EFV AMP 6.58683
72 1EFV FAD 6.58683
73 1KOR ANP 6.58683
74 1KOR ARG 6.58683
75 1YQC GLV 6.58683
76 1KOR SIN 6.58683
77 5FM0 WAQ 6.58683
78 4M52 M52 6.58683
79 3BBH SFG 6.82927
80 5LFV SIA GAL NAG 7.18563
81 6E0D XXX 7.18563
82 5YW5 ADE 7.18563
83 1MJT ITU 7.18563
84 4PTN GXV 7.18563
85 1Q8V MAN MAN MAN 7.18563
86 4WA2 SIA GAL NAG 7.18563
87 4HDO GNP 7.18563
88 1BH2 GSP 7.18563
89 2PHR MAN MAN BMA MAN 7.18563
90 2PHX MAN MAN MAN MAN 7.18563
91 2PHF MAN MAN BMA MAN 7.18563
92 1O97 AMP 7.78443
93 1O97 FAD 7.78443
94 1O94 AMP 7.78443
95 2Z49 AMG 7.78443
96 3LZW FAD 7.78443
97 3LZW NAP 7.78443
98 2Z48 NGA 7.78443
99 2JAP J01 7.78443
100 1JBU BEN 7.93651
101 1CT9 AMP 8.38323
102 6H3O FAD 8.38323
103 5TCI MLI 8.38323
104 3I3X U22 8.38323
105 4L2I FAD 8.98204
106 2AE2 NAP 8.98204
107 2AE2 PTO 8.98204
108 5U97 PIT 8.98204
109 4PEG 5GP 8.98204
110 4R2M ANP 9.49367
111 1GPM AMP 9.58084
112 5HSA FAS 9.58084
113 3OII SAH 9.88142
114 1JGT APC 10.1796
115 1JGT CMA 10.1796
116 1H5R THM 10.1796
117 4JWF SAH 10.5991
118 5APG EEM 10.7784
119 3HQP FDP 10.7784
120 4RR7 A3S 11.7647
121 3O7B SAH 11.976
122 3RK1 ATP 11.976
123 6APL C5P 11.976
124 2OQ2 A3P 12.5749
125 6GAS FAD 12.5749
126 5N0O SAM 12.5749
127 6MJF SAH 13.1737
128 6GEW SFG 13.1737
129 6GEW SAH 13.1737
130 3BP1 GUN 13.1737
131 4CNE SAH 14.9701
132 5F7J ADE 15.5689
133 1VBO MAN MAN MAN 16.1074
134 1VBO MAN 16.1074
135 1TAD GDP 16.7665
136 1TAD ALF 16.7665
137 2NU8 COA 17.3653
138 5UWS GNP 17.9641
139 4NBI D3Y 18.2927
140 3WYG GTP 19.1617
141 3QH2 3NM 32.9341
142 1V2X SAM 37.1257
143 4CNG SAH 37.7246
144 3NK7 SAM 38.3234
145 3GYQ SAM 41.3174
Pocket No.: 2; Query (leader) PDB : 4JAL; Ligand: SAH; Similar sites found with APoc: 87
This union binding pocket(no: 2) in the query (biounit: 4jal.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 2CHT TSA None
2 2WZV FMN None
3 1D1G NDP None
4 5ZZ6 NAD None
5 1U70 NDP 1.79641
6 1U70 MTX 1.79641
7 4RRG A3T 2.12766
8 4M7V RAR 2.39521
9 4M7V NAP 2.39521
10 3PD2 A3S 2.72109
11 3W6X HZP 2.99401
12 2X3F APC 2.99401
13 4USR FAD 2.99401
14 4IP7 FBP 2.99401
15 5WS9 AMP 2.99401
16 2VVL FAD 2.99401
17 2BL9 NDP 2.99401
18 5O2Z FLC 3.36134
19 5ZYN FAD 3.59281
20 2Q7V FAD 3.59281
21 1P4V GLY 3.59281
22 3ITJ FAD 3.59281
23 1S4P MMA 3.59281
24 5FEU NAP 3.59281
25 1QO8 FAD 4.19162
26 2RKV ZBA 4.19162
27 1TDF FAD 4.19162
28 2CFI ZZZ 4.19162
29 3COW 52H 4.19162
30 1XG5 NAP 4.19162
31 1VPM COA 4.19162
32 5FJN FAD 4.60526
33 5FJN BE2 4.60526
34 2B6N ALA PRO THR 4.79042
35 6IS0 SAH 4.79042
36 3MJH GTP 4.79042
37 5YEC ATP 5.04202
38 1EK6 UPG 5.38922
39 1EK6 NAI 5.38922
40 4YKG FAD 5.38922
41 4POO SAM 5.5
42 3Q9T FAY 5.98802
43 1F5N GNP 5.98802
44 5T9F TYR 5.98802
45 1C3Q TZE 5.98802
46 3APT FAD 5.98802
47 1OAA OAA 5.98802
48 5NII FAD 6.58683
49 1Z45 NAD 6.58683
50 2IVD FAD 6.58683
51 1XVB BHL 6.58683
52 6CI9 NAP 6.58683
53 1GZ6 NAI 6.58683
54 4QED NAP 6.58683
55 4M52 FAD 6.58683
56 1V59 FAD 7.18563
57 5DOZ NDP 7.18563
58 2Q1S NAI 7.78443
59 6F97 FAD 7.78443
60 5ECP ATP 7.78443
61 5ECP JAA 7.78443
62 5ECP MET 7.78443
63 1BXK NAD 7.78443
64 4L2I NAD 8.98204
65 4CNK FAD 8.98204
66 1PJS SAH 8.98204
67 2RCU BUJ 8.98204
68 5ZBC FAD 8.98204
69 5G3U ITW 8.98204
70 5THQ NDP 8.98204
71 1ZEM NAD 8.98204
72 1Z0J GTP 9.58084
73 3E5P PPI 10.1796
74 3IT6 ORN 10.1796
75 2RGO FAD 11.3772
76 5TS5 FAD 11.3772
77 2JB2 PHE 11.976
78 2JB2 FAD 11.976
79 4CQM NAP 11.976
80 1GPE FAD 11.976
81 5A89 FMN 12.8205
82 2F5Z FAD 13.1737
83 3AXB FAD 14.3713
84 5OC1 FAD 14.9701
85 2GAG FOA 18.5714
86 1NAA 6FA 20.3593
87 3RNM FAD 25.8621
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