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Receptor
PDB id Resolution Class Description Source Keywords
1V2X 1.5 Å EC: 2.1.1.34 TRMH THERMUS THERMOPHILUS DEEP TREFOIL KNOT RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITRSGI STRUCTURAL GENOMICS TRANSFERASE
Ref.: DEEP KNOT STRUCTURE FOR CONSTRUCTION OF ACTIVE SITE COFACTOR BINDING SITE OF TRNA MODIFICATION ENZYME STRUCTURE V. 12 593 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PO4 A:201;
A:202;
Invalid;
Invalid;
none;
none;
submit data
94.971 O4 P [O-]P...
SAM A:400;
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
1V2X 1.5 Å EC: 2.1.1.34 TRMH THERMUS THERMOPHILUS DEEP TREFOIL KNOT RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITRSGI STRUCTURAL GENOMICS TRANSFERASE
Ref.: DEEP KNOT STRUCTURE FOR CONSTRUCTION OF ACTIVE SITE COFACTOR BINDING SITE OF TRNA MODIFICATION ENZYME STRUCTURE V. 12 593 2004
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1V2X - SAM C15 H22 N6 O5 S C[S@@+](CC....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1V2X - SAM C15 H22 N6 O5 S C[S@@+](CC....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1V2X - 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 : 1V2X; Ligand: SAM; Similar sites found with APoc: 111
This union binding pocket(no: 1) in the query (biounit: 1v2x.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 5TWJ SAM None
2 5AHW CMP None
3 2BOS GLA GAL GLC None
4 2BOS GLA GAL GLC NBU None
5 1SQL GUN None
6 4GAH 0ET 1.03093
7 2PHX MAN MAN MAN MAN 1.03093
8 1Q8V MAN MAN MAN 1.03093
9 2PHR MAN MAN BMA MAN 1.03093
10 2PHF MAN MAN BMA MAN 1.03093
11 2PHT MAN MAN MAN BMA MAN 1.03093
12 2GND MAN 1.03093
13 2PHW MAN MAN MAN BMA MAN MAN MAN 1.03093
14 2PHU MAN MAN MAN BMA MAN 1.03093
15 1USR SIA WIA 1.54639
16 1GZF NIR 1.54639
17 5APG EEM 2.06186
18 1CT9 AMP 2.06186
19 1Y7P RIP 2.06186
20 1VJE MSE 2.40964
21 1XXR MAN 2.48447
22 6EMU SAM 2.57732
23 3BOS CDP 2.57732
24 5NM7 GLY 3.09278
25 3HQP FDP 3.09278
26 1GPM AMP 3.09278
27 5TQZ GLC 3.33333
28 1VBO MAN MAN MAN 3.3557
29 1VBO MAN 3.3557
30 3GUZ PAF 3.40909
31 3BBH SFG 3.60825
32 3BBD SAH 3.60825
33 5H5F SAM 3.60825
34 3O7B SAH 3.60825
35 3FSY SCA 3.60825
36 2XHK AKG 3.60825
37 4PZ2 NAD 3.60825
38 2NGR AF3 3.60825
39 1CBK ROI 3.75
40 4FK7 P34 4.12371
41 4FXQ G9L 4.12371
42 2FJK 13P 4.12371
43 2OWZ CIT 4.12371
44 1U6R IOM 4.12371
45 1P6O HPY 4.34783
46 2V7B BEZ 4.63918
47 2IZ1 ATR 4.63918
48 5TVA AMP 4.63918
49 4JWH SAH 5.11182
50 2WSI FAD 5.15464
51 2C5S AMP 5.15464
52 5XHA FRU 5.15464
53 1KGZ PRP 5.15464
54 2CUN 3PG 5.15464
55 2JK0 ASP 5.15464
56 5CGE 51F 5.15464
57 4UZI IMD 5.6701
58 5WXU FLC 5.6701
59 2CJU PHX 5.78512
60 4X1Z FUC GAL NDG 6.0241
61 1EFV AMP 6.18557
62 1EFV FAD 6.18557
63 1QMG DMV 6.18557
64 3HP8 SUC 6.36364
65 1Z08 GNP 6.47059
66 3G6K POP 6.70103
67 3G6K FAD 6.70103
68 1K3A ACP 6.70103
69 1JGT APC 6.70103
70 4PTN GXV 6.70103
71 1JGT CMA 6.70103
72 5A07 GDP 6.70103
73 1SZ2 BGC 7.2165
74 3QH2 3NM 7.73196
75 4JWF SAH 8.24742
76 1RJW ETF 8.24742
77 5WS9 AMP 8.24742
78 4GNC ASO 8.24742
79 4W6Z ETF 8.76289
80 1P9P SAH 8.81226
81 5CIC 51R 9.25926
82 5O96 SAM 9.27835
83 3AIA SAM 9.27835
84 2OQ2 A3P 9.27835
85 5FPE 3TR 9.79381
86 5CEO 50D 9.79381
87 4W9F 3JU 10.5769
88 6MJF SAH 10.8247
89 3HGM ATP 11.5646
90 3OII SAH 12.3711
91 4JWJ SAH 12.8713
92 5A7Y SAH 12.8866
93 4CNE SAH 13.4021
94 2YY8 SAM 13.9175
95 2YY8 MTA 13.9175
96 3RK1 ATP 13.9241
97 4MCC 21X 14.9485
98 1O94 AMP 15.9794
99 4NBI D3Y 16.4634
100 1T0S BML 18.0412
101 2CHT TSA 19.0722
102 3ZZH NLG 23.7113
103 3M2W L8I 24.2268
104 2IDO TMP 24.7312
105 4C2W ANP 25
106 3DCM SAM 27.0833
107 3NK7 SAM 30.9278
108 4CNG SAH 31.9588
109 3GYQ SAM 36.0825
110 4JAL SAH 37.1257
111 1MXI SAH 41.875
Pocket No.: 2; Query (leader) PDB : 1V2X; 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: 1v2x.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
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