Receptor
PDB id Resolution Class Description Source Keywords
2YY8 2.48 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF ARCHAEAL TRNA-METHYLASE FOR POSITION 56 (ATRM56) FROM PYROCOCCUS HORIKOSHII, COMPLEXED WITH S- A DENOSYL-L-METHIONINE PYROCOCCUS HORIKOSHII DEEP TREFOIL KNOT STRUCTURAL GENOMICS NPPSFA NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE RSGI TRANSFERASE
Ref.: CRYSTAL STRUCTURE AND MUTATIONAL STUDY OF A UNIQUE SPOU FAMILY ARCHAEAL METHYLASE THAT FORMS 2'-O-METHYLCYTIDINE AT POSITION 56 OF TRNA J.MOL.BIOL. V. 375 1064 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MTA A:400;
Valid;
none;
submit data
297.334 C11 H15 N5 O3 S CSC[C...
SAM B:500;
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
2YY8 2.48 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF ARCHAEAL TRNA-METHYLASE FOR POSITION 56 (ATRM56) FROM PYROCOCCUS HORIKOSHII, COMPLEXED WITH S- A DENOSYL-L-METHIONINE PYROCOCCUS HORIKOSHII DEEP TREFOIL KNOT STRUCTURAL GENOMICS NPPSFA NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE RSGI TRANSFERASE
Ref.: CRYSTAL STRUCTURE AND MUTATIONAL STUDY OF A UNIQUE SPOU FAMILY ARCHAEAL METHYLASE THAT FORMS 2'-O-METHYLCYTIDINE AT POSITION 56 OF TRNA J.MOL.BIOL. V. 375 1064 2008
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1579 families.
1 2YY8 - 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 1312 families.
1 2YY8 - 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 1130 families.
1 2YY8 - SAM C15 H22 N6 O5 S C[S@@+](CC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MTA; Similar ligands found: 290
No: Ligand ECFP6 Tc MDL keys Tc
1 MTA 1 1
2 DTA 0.786885 0.867647
3 3DH 0.777778 0.938462
4 ADN 0.758621 0.878788
5 XYA 0.758621 0.878788
6 RAB 0.758621 0.878788
7 DSH 0.705882 0.84507
8 5N5 0.704918 0.878788
9 5CD 0.693548 0.892308
10 A4D 0.693548 0.907692
11 EP4 0.6875 0.939394
12 M2T 0.676923 0.940298
13 A7D 0.657534 0.882353
14 5X8 0.64 0.895522
15 5AD 0.639344 0.857143
16 ZAS 0.628571 0.816901
17 LMS 0.628571 0.719512
18 AMP 0.628571 0.794521
19 A 0.628571 0.794521
20 A5D 0.623377 0.867647
21 SAH 0.615385 0.869565
22 J7C 0.60274 0.794521
23 ABM 0.60274 0.821918
24 45A 0.60274 0.821918
25 AAT 0.6 0.797297
26 6RE 0.597222 0.783784
27 SRA 0.597222 0.776316
28 S4M 0.594595 0.84
29 AOC 0.589041 0.880597
30 MAO 0.586667 0.805195
31 S8M 0.583333 0.833333
32 A2D 0.581081 0.773333
33 A3N 0.581081 0.867647
34 5AS 0.578947 0.697674
35 GJV 0.573333 0.773333
36 A12 0.565789 0.74359
37 AP2 0.565789 0.74359
38 BA3 0.565789 0.773333
39 M33 0.564103 0.810811
40 ADX 0.564103 0.719512
41 AU1 0.564103 0.753247
42 MHZ 0.564103 0.805195
43 AP5 0.558442 0.773333
44 ADP 0.558442 0.773333
45 B4P 0.558442 0.773333
46 7D7 0.553846 0.794118
47 Y3J 0.552239 0.80303
48 ADP MG 0.551282 0.794521
49 AT4 0.551282 0.766234
50 AN2 0.551282 0.763158
51 SON 0.551282 0.74359
52 SXZ 0.550562 0.849315
53 PRX 0.55 0.8
54 A6D 0.545455 0.766234
55 CA0 0.544304 0.753247
56 SA8 0.54321 0.873239
57 AD9 0.54321 0.753247
58 EEM 0.542169 0.849315
59 HEJ 0.5375 0.773333
60 SFG 0.5375 0.826087
61 ACP 0.5375 0.753247
62 KG4 0.5375 0.753247
63 50T 0.5375 0.763158
64 H1Q 0.5375 0.783784
65 ATP 0.5375 0.773333
66 AQP 0.530864 0.773333
67 APR 0.530864 0.773333
68 APC 0.530864 0.74359
69 AR6 0.530864 0.773333
70 5FA 0.530864 0.773333
71 SAM 0.53012 0.875
72 ANP 0.53012 0.753247
73 SMM 0.529412 0.84
74 3AM 0.527027 0.756757
75 NEC 0.526316 0.823529
76 ADV 0.52439 0.74359
77 SAP 0.52439 0.75641
78 AGS 0.52439 0.75641
79 APC MG 0.52439 0.773333
80 ATP MG 0.52439 0.794521
81 ADP PO3 0.52439 0.794521
82 RBY 0.52439 0.74359
83 8LE 0.52381 0.75641
84 5AL 0.52381 0.786667
85 54H 0.523256 0.705882
86 VMS 0.523256 0.705882
87 3AD 0.521739 0.863636
88 MTH 0.520548 0.984127
89 SAI 0.518072 0.830986
90 G5A 0.518072 0.678161
91 A5A 0.517647 0.722892
92 ME8 0.516484 0.797468
93 GAP 0.511905 0.753247
94 T99 0.511905 0.766234
95 TAT 0.511905 0.766234
96 ACQ 0.511905 0.753247
97 8LH 0.511628 0.789474
98 S7M 0.511628 0.824324
99 9ZA 0.511364 0.769231
100 9ZD 0.511364 0.769231
101 8QN 0.511364 0.786667
102 CC5 0.507463 0.876923
103 A3G 0.506494 0.828571
104 A3P 0.506329 0.77027
105 HQG 0.505747 0.763158
106 52H 0.505747 0.697674
107 NVA LMS 0.5 0.693182
108 8LQ 0.5 0.789474
109 MAP 0.5 0.734177
110 TSB 0.5 0.714286
111 53H 0.5 0.697674
112 ALF ADP 0.5 0.734177
113 DAL AMP 0.5 0.786667
114 8X1 0.5 0.655556
115 7D5 0.5 0.714286
116 ADP ALF 0.5 0.734177
117 ATF 0.5 0.74359
118 MTP 0.5 0.828571
119 25A 0.494382 0.773333
120 5SV 0.494382 0.759494
121 SRP 0.494253 0.74359
122 SSA 0.494253 0.678161
123 6YZ 0.494253 0.753247
124 VO4 ADP 0.494253 0.763158
125 ADP VO4 0.494253 0.763158
126 2AM 0.493333 0.746667
127 26A 0.492958 0.867647
128 0UM 0.488889 0.810811
129 ADQ 0.488889 0.753247
130 DSZ 0.488889 0.678161
131 A3R 0.488889 0.725
132 PAJ 0.488889 0.75
133 A1R 0.488889 0.725
134 LSS 0.488889 0.701149
135 N5O 0.487179 0.788732
136 3OD 0.483871 0.776316
137 62X 0.483516 0.815789
138 AHX 0.483516 0.716049
139 5CA 0.483146 0.678161
140 A22 0.483146 0.763158
141 2VA 0.481928 0.855072
142 A3T 0.481928 0.880597
143 SP1 0.480519 0.75
144 RP1 0.480519 0.75
145 3L1 0.478873 0.8
146 3D1 0.478873 0.8
147 OAD 0.478261 0.776316
148 9X8 0.478261 0.779221
149 K15 0.478261 0.813333
150 LEU LMS 0.478261 0.693182
151 GEK 0.477778 0.833333
152 OZV 0.477778 0.773333
153 OOB 0.477778 0.763158
154 A3S 0.47561 0.84058
155 N5A 0.475 0.785714
156 OVE 0.474359 0.74026
157 P5A 0.473118 0.648352
158 PR8 0.473118 0.698795
159 AMO 0.472527 0.74359
160 4AD 0.472527 0.734177
161 NSS 0.472527 0.678161
162 2FA 0.472222 0.816901
163 6MD 0.472222 0.893939
164 NOC 0.471429 0.791045
165 NVA 2AD 0.470588 0.833333
166 2BA 0.469136 0.767123
167 A2P 0.469136 0.756757
168 CMP 0.469136 0.777778
169 1ZZ 0.468085 0.731707
170 PTJ 0.468085 0.759494
171 TXA 0.468085 0.766234
172 9K8 0.468085 0.674157
173 QQX 0.467532 0.714286
174 00A 0.467391 0.725
175 DLL 0.467391 0.763158
176 5F1 0.465753 0.782609
177 MYR AMP 0.463158 0.731707
178 ADP BMA 0.462366 0.753247
179 3UK 0.462366 0.753247
180 ACK 0.461538 0.739726
181 QQY 0.461538 0.723684
182 A A 0.457447 0.773333
183 WAQ 0.457447 0.725
184 LAD 0.457447 0.707317
185 KAA 0.457447 0.655556
186 GSU 0.457447 0.678161
187 B5V 0.457447 0.74359
188 PPS 0.454545 0.698795
189 B5M 0.453608 0.75641
190 B5Y 0.453608 0.75641
191 PAP 0.453488 0.76
192 JB6 0.452632 0.746835
193 BIS 0.452632 0.725
194 FYA 0.452632 0.763158
195 NB8 0.452632 0.716049
196 1DA 0.452055 0.878788
197 XAH 0.44898 0.690476
198 VRT 0.448276 0.84507
199 SO8 0.448276 0.869565
200 25L 0.447917 0.763158
201 KB1 0.447917 0.786667
202 4UV 0.444444 0.734177
203 9SN 0.443299 0.716049
204 V3L 0.443182 0.773333
205 LAQ 0.441176 0.710843
206 7D3 0.439024 0.696203
207 ATP A A A 0.438776 0.783784
208 FA5 0.438776 0.74359
209 8PZ 0.438776 0.678161
210 ATP A 0.438776 0.783784
211 YAP 0.438776 0.734177
212 J1A 0.4375 0.740741
213 LPA AMP 0.436893 0.710843
214 J1C 0.435897 0.67033
215 GA7 0.435644 0.789474
216 4UU 0.435644 0.734177
217 AFH 0.435644 0.707317
218 7MD 0.435644 0.690476
219 J1B 0.434783 0.67033
220 B1U 0.434343 0.641304
221 YSA 0.434343 0.678161
222 TXD 0.432692 0.746835
223 4UW 0.432692 0.75
224 ARJ 0.432432 0.776119
225 MCF 0.432099 0.842857
226 GTA 0.431373 0.731707
227 4YB 0.431373 0.662921
228 TAD 0.431373 0.728395
229 KH3 0.431373 0.802632
230 AMP DBH 0.43 0.753247
231 TYR AMP 0.43 0.734177
232 IVH 0.428571 0.813333
233 AHZ 0.427184 0.731707
234 HZ2 0.427184 0.776316
235 3NZ 0.427083 0.833333
236 G3A 0.425743 0.716049
237 7C5 0.425743 0.773333
238 2A5 0.425287 0.708861
239 ERJ 0.425 0.835821
240 AP0 0.424528 0.7375
241 7MC 0.424528 0.694118
242 TT8 0.423913 0.898551
243 YLP 0.423077 0.694118
244 KOY 0.423077 0.805556
245 48N 0.423077 0.7375
246 CNA 0.422018 0.74359
247 G5P 0.421569 0.716049
248 ARG AMP 0.421569 0.682353
249 AR6 AR6 0.421569 0.773333
250 ATR 0.420455 0.746667
251 101 0.419753 0.714286
252 D3Y 0.419355 0.816901
253 NXX 0.419048 0.74359
254 NAX 0.419048 0.698795
255 NAI 0.419048 0.725
256 6V0 0.419048 0.716049
257 HY8 0.419048 0.776316
258 DND 0.419048 0.74359
259 7D4 0.418605 0.696203
260 DQV 0.417476 0.763158
261 A A A 0.416667 0.763158
262 TXE 0.415094 0.725
263 649 0.415094 0.648352
264 OMR 0.415094 0.722892
265 DA 0.414634 0.714286
266 D5M 0.414634 0.714286
267 T5A 0.412844 0.694118
268 139 0.412844 0.698795
269 ADJ 0.412844 0.702381
270 J4G 0.412371 0.734177
271 F0P 0.411215 0.797297
272 YLC 0.411215 0.710843
273 8Q2 0.411215 0.655556
274 YLB 0.411215 0.714286
275 J1D 0.410714 0.628866
276 OZP 0.409524 0.797297
277 AYB 0.409091 0.705882
278 A2R 0.408602 0.763158
279 A4P 0.407407 0.659091
280 UP5 0.40566 0.734177
281 F2R 0.405405 0.674419
282 6MZ 0.404762 0.808219
283 IOT 0.40367 0.666667
284 6CR 0.402597 0.805556
285 TYM 0.401869 0.74359
286 WSA 0.401869 0.686047
287 N37 0.401869 0.780822
288 AF3 ADP 3PG 0.401869 0.707317
289 4TA 0.401786 0.702381
290 YLA 0.4 0.674419
Ligand no: 2; Ligand: SAM; Similar ligands found: 221
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 XYA 0.565789 0.773333
9 RAB 0.565789 0.773333
10 ADN 0.565789 0.773333
11 5CD 0.564103 0.783784
12 EP4 0.5625 0.826667
13 SA8 0.56044 0.945205
14 5X8 0.555556 0.888889
15 SFG 0.555556 0.875
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 VMS 0.510204 0.673913
26 54H 0.510204 0.673913
27 0UM 0.51 0.857143
28 A 0.505747 0.707317
29 AMP 0.505747 0.707317
30 LMS 0.505747 0.666667
31 ABM 0.505618 0.753086
32 45A 0.505618 0.753086
33 A5A 0.505155 0.688889
34 SRP 0.5 0.746988
35 K15 0.5 0.883117
36 SON 0.5 0.746988
37 6RE 0.5 0.78481
38 SSA 0.5 0.684783
39 5AD 0.5 0.75
40 LSS 0.49505 0.706522
41 CA0 0.494624 0.714286
42 A12 0.494505 0.705882
43 AP2 0.494505 0.705882
44 ME8 0.490385 0.841463
45 53H 0.49 0.666667
46 5CA 0.49 0.684783
47 DAL AMP 0.49 0.765432
48 TSB 0.49 0.681319
49 ACP 0.489362 0.694118
50 KG4 0.489362 0.714286
51 5AS 0.48913 0.648936
52 ADP 0.48913 0.690476
53 J7C 0.488889 0.772152
54 A2D 0.488889 0.690476
55 ZAS 0.488636 0.769231
56 9ZA 0.485149 0.729412
57 9ZD 0.485149 0.729412
58 8QN 0.485149 0.743902
59 8LH 0.484848 0.746988
60 GAP 0.484536 0.73494
61 AN2 0.483871 0.682353
62 ADP MG 0.483871 0.728395
63 A7D 0.483871 0.851351
64 A3S 0.483871 0.813333
65 GJV 0.483516 0.775
66 SRA 0.483146 0.694118
67 KAA 0.480769 0.698925
68 LAD 0.480769 0.752941
69 GSU 0.480769 0.722222
70 DSZ 0.480392 0.703297
71 AMO 0.480392 0.746988
72 52H 0.48 0.666667
73 8LE 0.479592 0.717647
74 APC MG 0.479167 0.731707
75 M33 0.478723 0.722892
76 MAO 0.478261 0.82716
77 BA3 0.478261 0.690476
78 AOC 0.477778 0.776316
79 NEC 0.477778 0.75
80 DSH 0.477778 0.842105
81 SXZ 0.47619 0.894737
82 AHX 0.475728 0.701149
83 NVA LMS 0.475728 0.736264
84 Y3J 0.47561 0.706667
85 8LQ 0.475248 0.768293
86 G5A 0.474227 0.684783
87 A3T 0.473684 0.8
88 AP5 0.473118 0.690476
89 B4P 0.473118 0.690476
90 A3N 0.472527 0.766234
91 KB1 0.471698 0.833333
92 APC 0.46875 0.705882
93 PRX 0.46875 0.73494
94 AT4 0.468085 0.686047
95 PAJ 0.466019 0.712644
96 4AD 0.466019 0.759036
97 ADP PO3 0.463918 0.728395
98 RBY 0.463918 0.72619
99 ADV 0.463918 0.72619
100 ATP MG 0.463918 0.728395
101 MHZ 0.463158 0.82716
102 ADX 0.463158 0.666667
103 AU1 0.463158 0.674419
104 YAP 0.462963 0.738095
105 TXA 0.462264 0.72619
106 NB8 0.462264 0.72093
107 A3G 0.461538 0.802632
108 VRT 0.459184 0.842105
109 YSA 0.458716 0.684783
110 XAH 0.458716 0.715909
111 H1Q 0.458333 0.719512
112 50T 0.458333 0.682353
113 HEJ 0.458333 0.690476
114 ATP 0.458333 0.690476
115 LEU LMS 0.457143 0.717391
116 7D7 0.45679 0.723684
117 KH3 0.455357 0.871795
118 ACQ 0.454545 0.694118
119 AQP 0.453608 0.690476
120 AR6 0.453608 0.710843
121 5FA 0.453608 0.690476
122 APR 0.453608 0.710843
123 NSS 0.451923 0.703297
124 FA5 0.449541 0.746988
125 A5D 0.44898 0.789474
126 AGS 0.44898 0.678161
127 SAP 0.44898 0.678161
128 AD9 0.44898 0.674419
129 PTJ 0.448598 0.72093
130 YLB 0.448276 0.758621
131 YLP 0.447368 0.738636
132 OZP 0.447368 0.844156
133 8X1 0.446602 0.680851
134 D3Y 0.446602 0.792208
135 N5O 0.445652 0.789474
136 ADP ALF 0.445545 0.678161
137 ALF ADP 0.445545 0.678161
138 MYR AMP 0.444444 0.776471
139 3AM 0.444444 0.674699
140 HY8 0.443478 0.822785
141 OAD 0.443396 0.73494
142 2VA 0.443299 0.779221
143 OOB 0.442308 0.722892
144 S8M 0.442308 0.831169
145 TYR AMP 0.441441 0.759036
146 6YZ 0.441176 0.694118
147 VO4 ADP 0.441176 0.702381
148 ADP VO4 0.441176 0.702381
149 ANP 0.44 0.674419
150 T99 0.44 0.686047
151 TAT 0.44 0.686047
152 N37 0.439655 0.828947
153 WAQ 0.439252 0.75
154 HZ2 0.438596 0.822785
155 8PZ 0.436364 0.684783
156 B5Y 0.436364 0.717647
157 N5A 0.43617 0.786667
158 F0P 0.435897 0.844156
159 YLC 0.435897 0.755814
160 AAT 0.435644 0.797468
161 1ZZ 0.435185 0.755814
162 9K8 0.435185 0.663158
163 3OD 0.435185 0.73494
164 NVA 2AD 0.434343 0.855263
165 00A 0.433962 0.689655
166 DLL 0.433962 0.722892
167 ARG AMP 0.433628 0.727273
168 7MD 0.433628 0.715909
169 ATF 0.431373 0.666667
170 SO8 0.43 0.792208
171 3UK 0.429907 0.714286
172 A6D 0.429907 0.72619
173 9X8 0.429907 0.717647
174 F2R 0.429752 0.7
175 AMP DBH 0.428571 0.714286
176 5SV 0.428571 0.741176
177 OZV 0.428571 0.690476
178 TYM 0.42735 0.746988
179 WSA 0.42735 0.692308
180 9SN 0.427273 0.681818
181 AHZ 0.426087 0.755814
182 P5A 0.425926 0.691489
183 J4G 0.425926 0.759036
184 PR8 0.425926 0.744186
185 A A 0.425926 0.710843
186 3NZ 0.425926 0.807692
187 B5V 0.425926 0.705882
188 A1R 0.424528 0.709302
189 2A5 0.424242 0.674419
190 7MC 0.423729 0.719101
191 B5M 0.423423 0.717647
192 HQG 0.423077 0.702381
193 7D5 0.422222 0.658824
194 JB6 0.422018 0.709302
195 FYA 0.422018 0.722892
196 AYB 0.421488 0.75
197 B1U 0.419643 0.632653
198 A22 0.419048 0.682353
199 MAP 0.419048 0.659091
200 2AM 0.417582 0.666667
201 TAD 0.417391 0.712644
202 ADP BMA 0.416667 0.714286
203 A3P 0.416667 0.686747
204 25A 0.415094 0.690476
205 YLA 0.413223 0.719101
206 8Q2 0.411765 0.663158
207 ADQ 0.411215 0.694118
208 A3R 0.411215 0.709302
209 48N 0.410256 0.72093
210 0XU 0.41 0.824324
211 GA7 0.408696 0.72619
212 7D3 0.40625 0.643678
213 PAP 0.405941 0.678571
214 DQV 0.405172 0.702381
215 OVE 0.404255 0.662791
216 4UV 0.403509 0.697674
217 AF3 ADP 3PG 0.403361 0.712644
218 3AD 0.402299 0.783784
219 CMP 0.402062 0.691358
220 2BA 0.402062 0.682927
221 7C5 0.4 0.731707
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2YY8; Ligand: MTA; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 2yy8.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2YY8; 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: 2yy8.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback