Receptor
PDB id Resolution Class Description Source Keywords
5A7Y 2.5 Å EC: 2.1.1.218 CRYSTAL STRUCTURE OF SULFOLOBUS ACIDOCALDARIUS TRM10 IN COMPLEX WITH S-ADENOSYLHOMOCYSTEINE SULFOLOBUS ACIDOCALDARIUS TRANSFERASE SPOUT TRNA METHYLTRANSFERASE TRM10
Ref.: STRUCTURAL AND FUNCTIONAL INSIGHTS INTO TRNA BINDIN ADENOSINE N1-METHYLATION BY AN ARCHAEAL TRM10 HOMOL NUCLEIC ACIDS RES. V. 44 940 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACT B:1294;
B:1293;
Invalid;
Invalid;
none;
none;
submit data
59.044 C2 H3 O2 CC(=O...
PEG A:1292;
B:1292;
Invalid;
Invalid;
none;
none;
submit data
106.12 C4 H10 O3 C(COC...
SAH B:1291;
A:1291;
Valid;
Valid;
none;
none;
submit data
384.411 C14 H20 N6 O5 S c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5A7Y 2.5 Å EC: 2.1.1.218 CRYSTAL STRUCTURE OF SULFOLOBUS ACIDOCALDARIUS TRM10 IN COMPLEX WITH S-ADENOSYLHOMOCYSTEINE SULFOLOBUS ACIDOCALDARIUS TRANSFERASE SPOUT TRNA METHYLTRANSFERASE TRM10
Ref.: STRUCTURAL AND FUNCTIONAL INSIGHTS INTO TRNA BINDIN ADENOSINE N1-METHYLATION BY AN ARCHAEAL TRM10 HOMOL NUCLEIC ACIDS RES. V. 44 940 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5A7Y - 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 1 families.
1 5A7Y - 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 1 families.
1 5A7Y - 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 : 5A7Y; Ligand: SAH; Similar sites found: 82
This union binding pocket(no: 1) in the query (biounit: 5a7y.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1BWO LPC 0.01132 0.41356 None
2 5DX0 SFG 0.02051 0.4101 1.60256
3 5DWQ SFG 0.02582 0.40062 1.60256
4 4JAL SAH 0.000001503 0.60529 1.79641
5 1Q19 APC 0.00565 0.43223 1.92308
6 1SBR VIB 0.01435 0.4 2
7 2F1K NAP 0.02615 0.40601 2.15054
8 1X7D ORN 0.02839 0.41533 2.24359
9 4WAS NAP 0.0291 0.41378 2.24359
10 4WAS COO 0.0301 0.41299 2.24359
11 2YQS UD1 0.02289 0.40899 2.24359
12 3OII SAH 0.0002556 0.49729 2.37154
13 5UDS ATP 0.001303 0.43495 2.44755
14 1LLU NAD 0.02488 0.41536 2.5641
15 2DFV NAD 0.03476 0.40086 2.59366
16 1CT9 AMP 0.003994 0.42203 2.88462
17 3EGI ADP 0.01158 0.40458 2.91262
18 4L2I NAD 0.004948 0.46261 3.20513
19 4L2I FAD 0.004312 0.45662 3.20513
20 5L4S NAP 0.048 0.40304 3.52564
21 5L4S 6KX 0.048 0.40304 3.52564
22 4RRG A3T 0.001081 0.40496 3.5461
23 3NK7 SAM 0.00001403 0.55994 3.61011
24 3GYQ SAM 0.00004549 0.45602 3.67647
25 1N07 FMN 0.02605 0.41214 3.68098
26 1N07 ADP 0.0127 0.41107 3.68098
27 2NYA MGD 0.04975 0.404 3.84615
28 3HGM ATP 0.002566 0.44939 4.08163
29 3G89 SAM 0.01469 0.40203 4.41767
30 4Y2H SAH 0.03615 0.41153 4.48718
31 4CNE SAH 0.00001221 0.56032 4.49438
32 5BW4 SAM 0.02286 0.40331 4.49438
33 3AIA SAM 0.00003071 0.53515 4.73934
34 5U8U FAD 0.04468 0.42263 4.80769
35 4JWJ SAH 0.00000985 0.44608 4.9505
36 1Z0N BCD 0.004402 0.43165 5.20833
37 1U7Z PMT 0.04228 0.40207 5.30973
38 5APG EEM 0.000008025 0.45795 5.40541
39 4MCC 21X 0.0002537 0.50736 5.69106
40 1GPM AMP 0.005636 0.42609 5.76923
41 1ZMD FAD 0.02651 0.42231 5.76923
42 2F5Z FAD 0.03077 0.41879 5.76923
43 3BBD SAH 0.0001491 0.50418 5.85366
44 3BBH SFG 0.000009699 0.48245 5.85366
45 1N5D NDP 0.03657 0.40324 5.90278
46 3RK1 ATP 0.005143 0.42426 5.90717
47 1UAD GNP 0.007208 0.43184 6.06061
48 2OQ2 A3P 0.007393 0.42638 6.13027
49 1MJH ATP 0.01038 0.41899 6.79012
50 2PAV ATP 0.0232 0.41247 7.37179
51 1KEV NDP 0.04227 0.40311 7.37179
52 1NVM NAD 0.04153 0.40033 7.37179
53 2YY8 SAM 0.00001319 0.56127 7.46269
54 2YY8 MTA 0.00004808 0.5198 7.46269
55 5SZH GNP 0.02925 0.40216 7.84314
56 1O94 AMP 0.003133 0.44122 8.01282
57 2E0N SAH 0.01081 0.41266 8.49421
58 5TVA AMP 0.00512 0.40121 8.65385
59 1T36 U 0.02107 0.40012 8.65385
60 4CNG SAH 0.00009525 0.53086 9.01961
61 1KOR SIN 0.01366 0.46089 9.29487
62 1KOR ANP 0.01392 0.46089 9.29487
63 1KOR ARG 0.01366 0.46089 9.29487
64 1YQD NAP 0.04314 0.4016 9.29487
65 5H5F SAM 0.00001141 0.44645 9.40171
66 1EFV AMP 0.01101 0.45238 9.41177
67 1EFV FAD 0.01393 0.44672 9.41177
68 1VG8 GNP 0.03105 0.40082 10.1449
69 5AHW CMP 0.002269 0.44606 10.2041
70 5L2Z 70C 0.04806 0.40012 10.2362
71 4NBI D3Y 0.0005353 0.48539 10.9756
72 1P9P SAH 0.0001064 0.51621 11.1111
73 4KM2 TOP 0.04211 0.40704 11.7318
74 1ZC3 GNP 0.01807 0.41293 12.3894
75 5O4J PJL 0.03251 0.40814 12.4088
76 5O4J SAH 0.03425 0.40798 12.4088
77 5O4J 9KH 0.03425 0.40798 12.4088
78 5TWJ SAM 0.000003404 0.59564 12.963
79 2BZG SAH 0.01942 0.40188 15.5172
80 3L9R L9R 0.0493 0.40148 27.551
81 4JWH SAH 0.0000007618 0.63331 28.8462
82 4JWF SAH 0.0000004127 0.47952 33.6406
Pocket No.: 2; Query (leader) PDB : 5A7Y; Ligand: SAH; Similar sites found: 28
This union binding pocket(no: 2) in the query (biounit: 5a7y.bio2) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5DX1 SFG 0.01547 0.41225 1.60256
2 4J7U YTZ 0.04655 0.40461 2.77778
3 4J7U NAP 0.04655 0.40461 2.77778
4 5HTX ADP 0.004492 0.41746 3.20513
5 1UA4 AMP 0.01023 0.40536 3.20513
6 5OFW 9TW 0.0173 0.40114 3.58744
7 4FC7 COA 0.04895 0.40344 3.97112
8 4FC7 NAP 0.04895 0.40344 3.97112
9 5A07 GDP 0.009904 0.40141 4.48718
10 4UP3 FAD 0.04129 0.4057 4.80769
11 1WP4 NDP 0.02828 0.40173 5.19031
12 3VSV XYS 0.01812 0.40132 5.76923
13 4I6H 1C8 0.004413 0.42703 5.84416
14 4C3Y FAD 0.03504 0.41034 6.73077
15 4C3Y ANB 0.04167 0.41034 6.73077
16 5MW4 5JU 0.03381 0.4103 7.05128
17 5J8O 6GZ 0.01247 0.40336 7.25806
18 2B4Q NAP 0.03132 0.4019 7.6087
19 4CNK FAD 0.04545 0.40171 8.65385
20 1NB9 ADP 0.03525 0.4066 8.84354
21 1NB9 RBF 0.03525 0.4066 8.84354
22 1LSH PLD 0.02135 0.40918 8.97436
23 2GKS ADP 0.01838 0.40247 8.97436
24 3K56 IS3 0.01072 0.40439 9.02256
25 4KM2 ATR 0.04552 0.40076 11.7318
26 2RIF AMP 0.009314 0.40729 12.0567
27 1V2X SAM 0.01251 0.43574 12.8866
28 2BOS GLA GAL GLC 0.01568 0.40127 13.2353
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