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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: 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 : 5A7Y; Ligand: SAH; Similar sites found with APoc: 194
This union binding pocket(no: 1) in the query (biounit: 5a7y.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 1BWO LPC None
2 5GM1 SAH 0.673401
3 6ARJ BW4 1.60256
4 6ARJ SAH 1.60256
5 3LN0 52B 1.60256
6 5DX8 SFG 1.60256
7 5DX1 SFG 1.60256
8 5DXA SFG 1.60256
9 5DX0 SFG 1.60256
10 5DWQ SFG 1.60256
11 3G6K FAD 1.62338
12 3G6K POP 1.62338
13 1G63 FMN 1.65746
14 4JAL SAH 1.79641
15 1MXI SAH 1.875
16 1Q19 APC 1.92308
17 4A0M NAD 1.92308
18 2O4C NAD 1.92308
19 2C5S AMP 1.93705
20 1SBR VIB 2
21 2F1K NAP 2.15054
22 1X7D ORN 2.24359
23 4WAS NAP 2.24359
24 4WAS COO 2.24359
25 2YQS UD1 2.24359
26 3GAY P6T 2.24359
27 1X7D NAD 2.24359
28 1DJN FMN 2.24359
29 3H5N ATP 2.26629
30 5F2T PLM 2.27273
31 2WSI FAD 2.28758
32 3OII SAH 2.37154
33 2YBQ UP2 2.39726
34 2YBQ SAH 2.39726
35 6B2M COA 2.44755
36 1K97 CIR 2.5641
37 1K97 ASP 2.5641
38 1LLU NAD 2.5641
39 2DFV NAD 2.59366
40 3OJF NDP 2.72374
41 1K4M NAD 2.8169
42 1CT9 AMP 2.88462
43 3EGI ADP 2.91262
44 2ZAT NAP 3.07692
45 4L2I NAD 3.20513
46 4L2I FAD 3.20513
47 5HTX ADP 3.20513
48 5ETJ IM5 3.20513
49 1YZN GNP 3.24324
50 1KQF MGD 3.40136
51 1FUR MLT 3.52564
52 2Q7V FAD 3.52564
53 5L4S 6KX 3.52564
54 5L4S NAP 3.52564
55 4RRG A3T 3.5461
56 3NK7 SAM 3.61011
57 3GYQ SAM 3.67647
58 1N07 FMN 3.68098
59 1N07 ADP 3.68098
60 2RAB FAD 3.84615
61 1Q1R FAD 3.84615
62 4M0R 644 3.84615
63 2IV2 MGD 3.84615
64 2NYA MGD 3.84615
65 4OM8 NAD 3.8835
66 3HGM ATP 4.08163
67 4EA7 JB2 4.09091
68 4EA7 COA 4.09091
69 1JGT APC 4.16667
70 1JGT CMA 4.16667
71 5FUB SAH 4.16667
72 2NVK FAD 4.16667
73 5NII FAD 4.20712
74 4RR7 A3S 4.41176
75 3G89 SAM 4.41767
76 1WDK NAD 4.48718
77 5WS9 AMP 4.48718
78 4Y30 49L 4.48718
79 5A07 GDP 4.48718
80 1VKO NAD 4.48718
81 4TVD BGC 4.48718
82 4CNE SAH 4.49438
83 5BW4 SAM 4.49438
84 3AIA SAM 4.73934
85 3O7B SAH 4.80769
86 5N0O SAM 4.80769
87 3DJL FAD 4.80769
88 5U8U FAD 4.80769
89 5Y6Q MCN 4.93827
90 4JWJ SAH 4.9505
91 4GKV NAD 5.12821
92 1Z0N BCD 5.20833
93 5ZZ6 NAD 5.28846
94 1U7Z PMT 5.30973
95 6D5E GNP 5.38922
96 5APG EEM 5.40541
97 3RNM FAD 5.44872
98 4YEF 4CQ 5.61798
99 4MCC 21X 5.69106
100 1VM6 NAD 5.70175
101 1GPM AMP 5.76923
102 2F5Z FAD 5.76923
103 2G37 FAD 5.76923
104 3BBH SFG 5.85366
105 3BBD SAH 5.85366
106 5UFN SAH 5.88235
107 2J9C ATP 5.88235
108 2J9D AMP 5.88235
109 1N5D NDP 5.90278
110 3RK1 ATP 5.90717
111 1UAD GNP 6.06061
112 1R27 MGD 6.08974
113 1PJS SAH 6.08974
114 3CY2 MB9 6.08974
115 2OQ2 A3P 6.13027
116 3SBZ MLI 6.41026
117 2IVD FAD 6.41026
118 4HVA 4HV 6.41509
119 4W6Z 8ID 6.73077
120 1MJH ATP 6.79012
121 6GEW SFG 7.05128
122 6GEW SAH 7.05128
123 1D1G NDP 7.14286
124 4XT8 TMQ 7.36434
125 1KEV NDP 7.37179
126 2YY8 SAM 7.46269
127 2YY8 MTA 7.46269
128 3WXB NDP 7.52688
129 5TSH ADP 7.69231
130 5F7J ADE 7.8125
131 4XZ3 COA 7.82609
132 5SZH GNP 7.84314
133 1VCE SAH 7.92453
134 1O94 AMP 8.01282
135 1V59 FAD 8.01282
136 1O97 AMP 8.01282
137 1O97 FAD 8.01282
138 1WNG SAH 8.30189
139 2E0N SAH 8.49421
140 6AA8 NAD 8.60927
141 5TVA AMP 8.65385
142 5FM0 WAQ 8.65385
143 1T36 U 8.65385
144 3EEL 53T 8.81057
145 3PD2 A3S 8.84354
146 3BGD PM6 8.84615
147 3BGD SAH 8.84615
148 6MJF SAH 8.97436
149 4CNG SAH 9.01961
150 1T57 FMN 9.2233
151 1KOR ANP 9.29487
152 1KOR ARG 9.29487
153 1KOR SIN 9.29487
154 1YQD NAP 9.29487
155 5H5F SAM 9.40171
156 1EFV AMP 9.41177
157 1EFV FAD 9.41177
158 5YW5 ADE 9.49721
159 1S4P GDP 9.61539
160 1S4P MMA 9.61539
161 5O96 SAM 9.79592
162 4R2M ANP 10.1266
163 1VG8 GNP 10.1449
164 5AHW CMP 10.2041
165 5L2Z 70C 10.2362
166 2Q46 NAP 10.2767
167 2QTR NXX 10.582
168 1D9I 00P 10.7639
169 4NBI D3Y 10.9756
170 1P9P SAH 11.1111
171 4KM2 TOP 11.7318
172 5Z2M GTP 11.9318
173 2FZH DH1 12.1359
174 1LNX URI 12.3457
175 1ZC3 GNP 12.3894
176 5O4J SAH 12.4088
177 5O4J PJL 12.4088
178 5O4J 9KH 12.4088
179 2A9K GDP 12.5561
180 1V2X SAM 12.8866
181 5TWJ SAM 12.963
182 1LFD GNP 13.7931
183 2BL9 NDP 14.2857
184 5LLT DND 14.554
185 2BZG SAH 15.5172
186 3IA4 NDP 17.9012
187 4PXL NAD 18.9103
188 3L9R L9R 27.551
189 4JWH SAH 28.8462
190 1J3I NDP 31.7857
191 1J3I WRA 31.7857
192 4JWF SAH 33.6406
193 4AX9 N5N 42.8571
194 6EMU SAM 44.1624
Pocket No.: 2; Query (leader) PDB : 5A7Y; Ligand: SAH; Similar sites found with APoc: 85
This union binding pocket(no: 2) in the query (biounit: 5a7y.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 5HSA FAS 1.92308
2 4K38 SAM 1.92308
3 1ZK7 FAD 1.92308
4 1OAA OAA 1.9305
5 3BP1 GUN 2.06897
6 3NUG NAD 2.42915
7 1GEE NAD 2.68199
8 4A91 GLU 2.68456
9 3OJF IMJ 2.72374
10 4J7U YTZ 2.77778
11 4J7U NAP 2.77778
12 2Z48 A2G 2.88462
13 2Z48 NGA 2.88462
14 2VN9 GVD 2.99003
15 2PV7 NAD 3.02013
16 1UA4 AMP 3.20513
17 3ICC NAP 3.52941
18 5EJ2 NAD 3.57143
19 5OFW 9TW 3.58744
20 1W8D NAP 3.64238
21 1W6U NAP 3.64238
22 6GNO XDI 3.7037
23 3AY6 BGC 3.71747
24 3AY6 NAI 3.71747
25 2RAB NAD 3.84615
26 5YSS NAD 3.90625
27 4FC7 NAP 3.97112
28 4FC7 COA 3.97112
29 4ONA UW1 4.16667
30 1X87 NAD 4.16667
31 3EKK GS2 4.23453
32 3OVR 5SP 4.38596
33 4ITH RCM 4.42177
34 1LVL FAD 4.48718
35 4PTN GXV 4.48718
36 1YY5 FAD 4.48718
37 4XYM COA 4.78261
38 3ZV6 NAD 4.80769
39 4UP3 FAD 4.80769
40 2CVZ NDP 4.84429
41 1BDB NAD 5.12821
42 1EZ0 NAP 5.12821
43 1WP4 NDP 5.19031
44 1E5Q NDP 5.44872
45 5ZYN FAD 5.76923
46 3VSV XYS 5.76923
47 4I6H 1C8 5.84416
48 2Q2V NAD 5.88235
49 5N2D 8J8 6.25
50 1GZ6 NAI 6.41026
51 1ZBQ NAD 6.42202
52 4C3Y ANB 6.73077
53 4C3Y FAD 6.73077
54 4JBI NDP 6.73077
55 5WQP NCA 6.83761
56 5WQP NAP 6.83761
57 5MW4 5JU 7.05128
58 2DXU BT5 7.23404
59 3DCM SAM 7.29167
60 2RCU BUJ 7.37179
61 6H3O FAD 7.37179
62 1FL2 FAD 7.41935
63 2B4Q NAP 7.6087
64 4CQM NAP 7.66284
65 1BZL FAD 8.33333
66 1WMA AB3 8.33333
67 1WMA NDP 8.33333
68 4YVZ 3AT 8.65385
69 2ZJ1 ARJ 8.65385
70 2ZJ1 NAD 8.65385
71 4CNK FAD 8.65385
72 3ORF NAD 8.76494
73 1NB9 RBF 8.84354
74 1NB9 ADP 8.84354
75 1LSH PLD 8.97436
76 2GKS ADP 8.97436
77 3K56 IS3 9.02256
78 5DI3 GNP 9.5057
79 4Z87 GDP 9.61539
80 3LF0 ATP 9.64912
81 4KM2 ATR 11.7318
82 2RIF AMP 12.0567
83 3B1F NAD 13.1034
84 2BOS GLA GAL GLC 13.2353
85 1B74 DGN 17.3228
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