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Receptor
PDB id Resolution Class Description Source Keywords
3AIA 1.4 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF DUF358 REVEALS A PUTATIVE SPOUT-CLASS METHLTRANSFERASE METHANOCALDOCOCCUS JANNASCHII DUF358 RRNA METHYLTRANSFERASE SPOUT-CLASS FOLD TRANSFERAS
Ref.: CRYSTAL STRUCTURE OF MJ1640/DUF358 PROTEIN REVEALS PUTATIVE SPOUT-CLASS RNA METHYLTRANSFERASE J MOL CELL BIOL V. 2 366 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PBL A:207;
B:207;
Invalid;
Invalid;
none;
none;
submit data
136.146 C5 H12 O4 CC(CC...
SAM A:206;
B:206;
Valid;
Valid;
none;
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
3AIA 1.4 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF DUF358 REVEALS A PUTATIVE SPOUT-CLASS METHLTRANSFERASE METHANOCALDOCOCCUS JANNASCHII DUF358 RRNA METHYLTRANSFERASE SPOUT-CLASS FOLD TRANSFERAS
Ref.: CRYSTAL STRUCTURE OF MJ1640/DUF358 PROTEIN REVEALS PUTATIVE SPOUT-CLASS RNA METHYLTRANSFERASE J MOL CELL BIOL V. 2 366 2010
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 3AI9 - SAM C15 H22 N6 O5 S C[S@@+](CC....
2 3AIA - SAM C15 H22 N6 O5 S C[S@@+](CC....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 3AI9 - SAM C15 H22 N6 O5 S C[S@@+](CC....
2 3AIA - SAM C15 H22 N6 O5 S C[S@@+](CC....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 3AI9 - SAM C15 H22 N6 O5 S C[S@@+](CC....
2 3AIA - 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 : 3AIA; Ligand: SAM; Similar sites found with APoc: 162
This union binding pocket(no: 1) in the query (biounit: 3aia.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 4JWF SAH None
2 1BW9 NAD None
3 1OSS BEN 1.4218
4 2QTR NXX 1.5873
5 6GAS FAD 1.89573
6 4NTD FAD 2.36967
7 3FIU AMP 2.36967
8 1Q19 APC 2.8436
9 2OQ2 A3P 2.8436
10 1J39 UPG 2.8436
11 1TL2 NDG 2.8436
12 2IID FAD 2.8436
13 5ZZ6 NAD 2.88462
14 1Z08 GNP 2.94118
15 3I7V B4P 2.98507
16 4CNG SAH 3.31754
17 4CNE SAH 3.31754
18 1USR SIA 3.31754
19 1USR SIA WIA 3.31754
20 1EB1 ZAL PRO MMO 3.31754
21 4AX9 N5N 3.31754
22 4KBA 1QM 3.31754
23 2XCU C5P 3.31754
24 2GEK GDP 3.31754
25 3AB4 THR 3.31754
26 3HQP FDP 3.31754
27 1A2C 34H LEU PRJ OAR 3.31754
28 3AB4 LYS 3.31754
29 2WSI FAD 3.79147
30 3BP1 GUN 3.79147
31 1K97 ASP 3.79147
32 1K97 CIR 3.79147
33 1MV8 NAD 3.79147
34 5UPK GNP 3.79147
35 2A8X FAD 3.79147
36 5BVE 4VG 3.79147
37 6F3M NAD 3.79147
38 4F8L AES 4.13793
39 5OCG GNP 4.2328
40 3RK1 ATP 4.2654
41 4NAE 1GP 4.2654
42 5ZBC FAD 4.2654
43 4JWJ SAH 4.45545
44 5A7Y SAH 4.73934
45 2NU8 COA 4.73934
46 5TS5 FAD 4.73934
47 3QVP FAD 4.73934
48 2WTX VDO 4.73934
49 2WTX UDP 4.73934
50 4JAL SAH 4.79042
51 6D5H GNP 4.79042
52 6D5M GNP 4.79042
53 6D5E GNP 4.79042
54 6D59 GNP 4.79042
55 6D55 GNP 4.79042
56 6BVJ GNP 4.79042
57 1MXI SAH 5
58 1MRH FMC 5.21327
59 1EFV FAD 5.21327
60 1EFV AMP 5.21327
61 1CT9 AMP 5.21327
62 1RTF BEN 5.21327
63 6EK3 OUL 5.21327
64 3OKP GDD 5.21327
65 2W5P CL8 5.36913
66 1P9P SAH 5.6872
67 1EU1 GLC 5.6872
68 5WS9 AMP 5.6872
69 5TWB FAD 5.6872
70 5ZYN FAD 5.6872
71 6F5W KG1 5.6872
72 1XUJ BOZ 5.6872
73 4J7U YTZ 5.6872
74 4J7U NAP 5.6872
75 4RR7 A3S 5.88235
76 5H5F SAM 5.98291
77 1NXJ GLV 6.01093
78 1GPE FAD 6.16114
79 5YB7 ORN 6.16114
80 5YB7 FAD 6.16114
81 1MJH ATP 6.17284
82 5J60 FAD 6.63507
83 4RFM 3P6 6.63507
84 2E5V FAD 6.63507
85 3IB1 IMN 6.63507
86 3QJ4 FAD 6.63507
87 4C2C ALA ALA ALA 7.109
88 1JPA ANP 7.109
89 3CV3 UDP 7.109
90 5O96 SAM 7.58294
91 4W6Z ETF 7.58294
92 6F97 FAD 7.58294
93 3HRD NIO 7.58294
94 1HFU NAG NDG 7.58294
95 4W6Z 8ID 7.58294
96 3O7B SAH 7.78689
97 3LAD FAD 8.05687
98 1T3Q MCN 8.05687
99 3BBD SAH 8.29268
100 4RRG A3T 8.51064
101 3GYQ SAM 8.53081
102 2XG5 EC5 8.53081
103 2XG5 EC2 8.53081
104 4U44 3D9 8.53081
105 1T36 ORN 8.53081
106 1RJW ETF 9.00474
107 1JGT CMA 9.00474
108 1JGT APC 9.00474
109 1O94 AMP 9.00474
110 1UTJ ABN 9.00474
111 4BCQ TJF 9.00474
112 5DIF GNP 9.00474
113 6CIT GNP 9.00474
114 1IBR GNP 9.00474
115 5UWP GNP 9.00474
116 5DHF GNP 9.00474
117 5DI9 GNP 9.00474
118 5UWW GNP 9.00474
119 5UWI GNP 9.00474
120 5UWT GNP 9.00474
121 5UWJ GNP 9.00474
122 5UWH GNP 9.00474
123 5UWU GNP 9.00474
124 4HAT GNP 9.00474
125 5UWO GNP 9.00474
126 5UWS GNP 9.00474
127 4CFU 2WC 9.00474
128 4BCN T9N 9.00474
129 6GUE FB8 9.00474
130 6EMU SAM 9.13706
131 1V2X SAM 9.27835
132 1YVZ JPC 9.47867
133 4NBI D3Y 9.7561
134 5TWJ SAM 9.87654
135 3G6K FAD 9.95261
136 3G6K POP 9.95261
137 3UDG TMP 9.95261
138 4JWH SAH 10.4265
139 3PTG 932 10.4265
140 2F5Z FAD 10.9375
141 3NK7 SAM 11.3744
142 4MCC 21X 11.3744
143 1GPM AMP 11.3744
144 2GJ8 ALF GDP 11.6279
145 4GUT FAD 11.8483
146 3SBD GNP 12.2995
147 1NU4 MLA 12.3711
148 1WA5 GTP 12.7962
149 1REO FAD 12.7962
150 1GPJ CIT 13.2701
151 2POC UD1 13.2701
152 1UNH IXM 14.218
153 1KOR ANP 15.6398
154 1KOR SIN 15.6398
155 1KOR ARG 15.6398
156 3AB1 FAD 16.5877
157 2RAB FAD 17.0616
158 3BBH SFG 17.0732
159 5UWR GNP 22.2222
160 3RNM FAD 22.4138
161 1GJC 130 26.087
162 5UWQ GNP 27.2727
Pocket No.: 2; Query (leader) PDB : 3AIA; Ligand: SAM; Similar sites found with APoc: 35
This union binding pocket(no: 2) in the query (biounit: 3aia.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 3SBZ MLI 0.947867
2 5G3U ITW 1.4218
3 6CB2 OLC 2.36967
4 2FV5 541 2.8436
5 1YZN GNP 3.24324
6 2D3N GLC GLC GLC 3.31754
7 1U6R IOM 3.31754
8 3ENV ABF 3.31754
9 1NAA 6FA 3.79147
10 1NAA ABL 3.79147
11 4UCF GLA 3.79147
12 1VRP IOM 3.79147
13 3RAB GNP 4.14201
14 4YZC STU 4.2654
15 6FA4 GNP 4.62428
16 1GAR U89 4.73934
17 1NVV GNP 4.81928
18 5L4S 6KX 5.21327
19 5L4S NAP 5.21327
20 5OCQ CIT 5.61404
21 3E3U NVC 6.09137
22 3BGD PM6 6.16114
23 3BGD SAH 6.16114
24 2GJP MAL 6.63507
25 1JBU BEN 6.63507
26 3B6R CRN 7.109
27 4ZOH MCN 9.52381
28 2QQC AG2 9.82143
29 2GJ5 VD3 9.87654
30 6AMI TRP 9.95261
31 5C9P FUC 10.9005
32 2Z48 A2G 12.3223
33 2Z49 AMG 12.3223
34 2Z48 NGA 12.3223
35 4YSX FAD 13.2701
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