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Receptor
PDB id Resolution Class Description Source Keywords
4CNE 1.9 Å EC: 2.1.1.200 CRYSTAL STRUCTURE OF E.COLI TRMJ IN COMPLEX WITH S-ADENOSYL- HOMOCYSTEINE ESCHERICHIA COLI TRANSFERASE SPOUT
Ref.: CHARACTERIZATION OF TWO HOMOLOGOUS 2'-O-METHYLTRANS SHOWING DIFFERENT SPECIFICITIES FOR THEIR TRNA SUBS RNA V. 20 1257 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SAH B:400;
A:400;
Valid;
Valid;
none;
none;
submit data
384.411 C14 H20 N6 O5 S c1nc(...
PEG B:1200;
Invalid;
none;
submit data
106.12 C4 H10 O3 C(COC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4CNE 1.9 Å EC: 2.1.1.200 CRYSTAL STRUCTURE OF E.COLI TRMJ IN COMPLEX WITH S-ADENOSYL- HOMOCYSTEINE ESCHERICHIA COLI TRANSFERASE SPOUT
Ref.: CHARACTERIZATION OF TWO HOMOLOGOUS 2'-O-METHYLTRANS SHOWING DIFFERENT SPECIFICITIES FOR THEIR TRNA SUBS RNA V. 20 1257 2014
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4CNE - SAH C14 H20 N6 O5 S c1nc(c2c(n....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4CNE - SAH C14 H20 N6 O5 S c1nc(c2c(n....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4CNE - 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 : 4CNE; Ligand: SAH; Similar sites found with APoc: 104
This union binding pocket(no: 1) in the query (biounit: 4cne.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 2CHT TSA None
2 4CQK PIO None
3 2VN9 GVD 1.1236
4 1XXR MAN 1.24224
5 2F6U CIT 1.28205
6 3LTW HLZ 1.49813
7 4JWH SAH 1.87266
8 1F5N GNP 1.87266
9 3KL3 GCU 1.87266
10 6GNO XDI 2.22222
11 1G51 AMP 2.24719
12 5EJ2 NAD 2.24719
13 1MRH FMC 2.28137
14 4OKD GLC GLC GLC 2.62172
15 1LTZ HBI 2.62172
16 4GAH 0ET 2.87081
17 5TVA AMP 2.91667
18 1KGZ PRP 2.99625
19 5N0O SAM 2.99625
20 2YBQ UP2 2.99625
21 3OII SAH 3.16206
22 3LL5 IP8 3.21285
23 4JWF SAH 3.22581
24 3AIA SAM 3.31754
25 4Y4V DAL 3.37079
26 1JGT CMA 3.37079
27 4G9N NGA 3.4965
28 6EMU SAM 3.5533
29 4NBI D3Y 3.65854
30 3O7B SAH 3.68852
31 1RJW ETF 3.74532
32 3HQP FDP 3.74532
33 6B2M COA 4.11985
34 1K7T NAG GAL 4.30108
35 1EFV FAD 4.31373
36 1EFV AMP 4.31373
37 5F6U 5VK 4.4586
38 5A7Y SAH 4.49438
39 1USR SIA WIA 4.49438
40 1K0E TRP 4.49438
41 5OVK NDP 4.6875
42 5H5F SAM 4.70085
43 5FPE 3TR 4.86891
44 6MJF SAH 4.86891
45 1KOR ARG 4.86891
46 1KOR SIN 4.86891
47 1KOR ANP 4.86891
48 3G6K POP 4.87013
49 3G6K FAD 4.87013
50 1MJH ATP 4.93827
51 2CFI ZZZ 5.24345
52 2OQ2 A3P 5.36398
53 1U70 MTX 5.37634
54 1U70 NDP 5.37634
55 5AHW CMP 5.44218
56 2YY8 MTA 5.47264
57 2YY8 SAM 5.47264
58 2C5S AMP 5.56901
59 2B6N ALA PRO THR 5.61798
60 4CQM NAP 5.74713
61 1Q19 APC 5.99251
62 3HRD NIO 5.99251
63 4MCC 21X 6.09756
64 2PZE ATP 6.11354
65 5CGE 51F 6.13718
66 5YW5 ADE 6.14525
67 5TWJ SAM 6.17284
68 3AJ4 SEP 6.25
69 1GPM AMP 6.36704
70 2FJK 13P 6.36704
71 6HKE LMR 6.36704
72 1P9P SAH 6.74157
73 3HGM ATP 6.80272
74 4JWJ SAH 6.93069
75 1O94 AMP 7.49064
76 3LAD FAD 7.49064
77 4UZI IMD 7.49064
78 4CNK FAD 7.86517
79 5O96 SAM 8.2397
80 1CT9 AMP 8.61423
81 1T57 FMN 9.2233
82 1ELI PYC 9.3633
83 3BBD SAH 9.7561
84 5TQZ GLC 10
85 3BBH SFG 10.2439
86 4R2M ANP 10.7595
87 2WSI FAD 11.1111
88 3KCC CMP 11.1538
89 5X2N ALA 11.6105
90 5CIC 51R 11.6105
91 2BOS GLA GAL GLC 11.7647
92 2BOS GLA GAL GLC NBU 11.7647
93 2UUU PL3 11.985
94 2NU8 COA 12.3596
95 1V2X SAM 13.4021
96 2CBZ ATP 13.9241
97 4JAL SAH 14.9701
98 5WXU FLC 15.3558
99 1MXI SAH 16.25
100 3RK1 ATP 16.8539
101 5APG EEM 18.9189
102 3GYQ SAM 24.3446
103 3NK7 SAM 24.7191
104 3DCM SAM 25
Pocket No.: 2; Query (leader) PDB : 4CNE; Ligand: SAH; Similar sites found with APoc: 90
This union binding pocket(no: 2) in the query (biounit: 4cne.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 4YAG NAI 1.87266
2 1SBR VIB 2
3 3PD2 A3S 2.04082
4 4RRG A3T 2.12766
5 4RR7 A3S 2.20588
6 2OG2 MLI 2.24719
7 4PTN GXV 2.24719
8 1Z08 GNP 2.35294
9 4O0L NDP 2.54545
10 1IWE IMP 2.62172
11 3O26 NDP 2.62172
12 4PLT NAI 2.62172
13 4PLT OXM 2.62172
14 3OID NDP 2.71318
15 1YQC GLV 2.94118
16 5W75 SUC 2.99625
17 5XWV 8H6 2.99625
18 5XWV NDP 2.99625
19 6GEW SAH 2.99625
20 6GEW SFG 2.99625
21 2X3F APC 2.99625
22 2RHO GSP 2.99625
23 4L2I FAD 3.04183
24 1N07 ADP 3.06748
25 3ZV6 NAD 3.37079
26 4FMS BDP 3.37079
27 4FK7 P34 3.49345
28 6MJ7 ARG 3.63636
29 1WMA AB3 3.74532
30 1WMA NDP 3.74532
31 3V1U NAD 3.74532
32 1UH4 GLC GLC GLC GLC GLC GLC 3.74532
33 5CX6 CDP 3.74532
34 1H5Q NAP 3.77358
35 1D8C SOR 4.11985
36 3BP1 GUN 4.11985
37 1ZX5 LFR 4.11985
38 5J6D 6H5 4.11985
39 1QF5 GDP 4.11985
40 1QF5 RPL 4.11985
41 4FXQ G9L 4.11985
42 4G31 0WH 4.11985
43 1QXA GLY GLY GLY 4.25532
44 5ZWP GSH 4.32692
45 5CEO 50D 4.33333
46 2Q37 3AL 4.49438
47 1PVS 7HP 4.49438
48 2Z48 NGA 4.49438
49 1GEG NAD 4.6875
50 1F6D UDP 4.86891
51 5YEC ATP 4.86891
52 5OJI NAP 5.38462
53 5OJI ISN 5.38462
54 6CI9 NAP 5.40541
55 3NB0 G6P 5.61798
56 1US5 GLU 5.61798
57 3PE2 E1B 5.61798
58 3GD8 GOL 5.8296
59 1NML CIT 5.99251
60 4K26 NDP 5.99251
61 3SBZ MLI 6.34921
62 3TN7 NJP 6.61479
63 6BYF CIT 7.05882
64 1XVB BHL 7.11611
65 1VL8 NAP 7.11611
66 1O97 AMP 7.19697
67 1O97 FAD 7.19697
68 5WQP NCA 7.26496
69 5WQP NAP 7.26496
70 1ZBQ NAD 7.86517
71 1QAW TRP 8.10811
72 2BGM NAJ 8.2397
73 1UAY ADN 8.26446
74 5XDT MB3 8.76623
75 5O98 NAP 8.98876
76 3ZZS TRP 9.23077
77 3WXB NDP 9.73783
78 3COW 52H 9.73783
79 3OKP GDD 10.1124
80 2TOH HBI 10.1124
81 1P9B HDA 10.4869
82 4R0M FA5 12.3596
83 3A28 NAD 12.4031
84 3KO0 TFP 12.8713
85 4FN4 NAD 13.8577
86 3OKA GDD 19.0476
87 1WAP TRP 20
88 5WS9 AMP 20.9738
89 1WDK N8E 22.4719
90 3ZZQ TRP 23.0769
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