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Receptor
PDB id Resolution Class Description Source Keywords
2V3K 2 Å NON-ENZYME: OTHER THE YEAST RIBOSOME SYNTHESIS FACTOR EMG1 ALPHA BETA KNOT FOLD METHYLTRANSFERASE SACCHAROMYCES CEREVISIAE RIBOSOMAL PROTEIN EMG1 RRNA PROCESSING NUCLEAR PROTEIN RIBONUCLEOPROTEIN RIBOSOME BIOGENESIS ALPHA/BETA KNOT FOLD METHYLTRANSFERASE
Ref.: THE YEAST RIBOSOME SYNTHESIS FACTOR EMG1 IS A NOVEL MEMBER OF THE SUPERFAMILY OF ALPHA/BETA KNOT FOLD METHYLTRANSFERASES. NUCLEIC ACIDS RES. V. 36 629 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SAM A:1254;
Valid;
none;
submit data
398.437 C15 H22 N6 O5 S C[S@@...
SO4 A:1252;
A:1253;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3OII 1.85 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE NEP1/EMG1 BOUN ADENOSYLHOMOCYSTEINE SACCHAROMYCES CEREVISIAE EMG1 SCNEP1 SPOUT RIBOSOME BIOGENESIS METHYLTRANSFERASEPROCESSING RIBOSOMAL PROTEIN
Ref.: STRUCTURAL INSIGHT INTO THE FUNCTIONAL MECHANISM OF NEP1/EMG1 N1-SPECIFIC PSEUDOURIDINE METHYLTRANSFERA RIBOSOME BIOGENESIS. NUCLEIC ACIDS RES. V. 39 2445 2011
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 2V3K - SAM C15 H22 N6 O5 S C[S@@+](CC....
2 3OII - SAH C14 H20 N6 O5 S c1nc(c2c(n....
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 2V3K - SAM C15 H22 N6 O5 S C[S@@+](CC....
2 3OII - SAH C14 H20 N6 O5 S c1nc(c2c(n....
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 2V3K - SAM C15 H22 N6 O5 S C[S@@+](CC....
2 3OII - SAH C14 H20 N6 O5 S c1nc(c2c(n....
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 : 3OII; Ligand: SAH; Similar sites found with APoc: 76
This union binding pocket(no: 1) in the query (biounit: 3oii.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 4JWJ SAH None
2 2BOS GLA GAL GLC None
3 2BOS GLA GAL GLC NBU None
4 4P5E N6P None
5 1MFI FHC None
6 3NK7 SAM 1.18577
7 1SQL GUN 1.36986
8 5H5F SAM 1.7094
9 1GPM AMP 1.97628
10 1SZ2 BGC 1.97628
11 2YBQ UP2 1.97628
12 4NTD FAD 1.97628
13 4MCC 21X 2.03252
14 4JWH SAH 2.37154
15 5A7Y SAH 2.37154
16 1EB1 ZAL PRO MMO 2.37154
17 6GZD LCI 2.37154
18 1F6D UDP 2.7668
19 4CNE SAH 3.16206
20 3K6V CIT 3.16206
21 3COW 52H 3.16206
22 3UDG TMP 3.16206
23 2X1L MET 3.16206
24 3FJG 3PG 3.18725
25 3LKF PC 3.55731
26 5TTJ FAD 3.55731
27 2V7B BEZ 3.95257
28 4KCT FDP 3.95257
29 3G6K FAD 3.95257
30 3G6K POP 3.95257
31 3CV3 UDP 3.95257
32 5O96 SAM 4.08163
33 1P9P SAH 4.74308
34 3HQP FDP 4.74308
35 3BP1 GUN 4.74308
36 6FP4 E1T 4.74308
37 3GDN MXN 4.74308
38 4JWF SAH 5.06912
39 6EMU SAM 5.07614
40 3VSV XYS 5.13834
41 3RK1 ATP 5.48523
42 1T36 ORN 5.5336
43 4PTN GXV 5.92885
44 6HKE LMR 5.92885
45 4NBI D3Y 6.09756
46 4MIG G3F 6.32411
47 3A06 NDP 7.11462
48 2GEK GDP 7.11462
49 1CT9 AMP 7.11462
50 1RTF BEN 7.14286
51 1C4Q GLA GAL BGC 7.24638
52 1FQK ALF 8.16327
53 1FQJ ALF 8.16327
54 4CNG SAH 8.3004
55 2Z48 A2G 8.3004
56 1O5E 132 8.77193
57 5WS9 AMP 9.09091
58 1MXI SAH 9.375
59 3GYQ SAM 9.48617
60 3PTG 932 9.48617
61 4JAL SAH 9.88142
62 3M2W L8I 10.6719
63 6H45 QEI 10.6719
64 2W5P CL8 10.7383
65 5TWJ SAM 11.1111
66 4D04 FAD 12.253
67 4D04 NAP 12.253
68 1V2X SAM 12.3711
69 4RRG A3T 14.8936
70 1MID LAP 15.3846
71 2NU8 COA 16.2055
72 5TS5 FAD 16.996
73 4RLQ 3SK 17.3913
74 3O7B SAH 31.1475
75 3BBD SAH 40
76 3BBH SFG 40.9756
Pocket No.: 2; Query (leader) PDB : 3OII; Ligand: SAH; Similar sites found with APoc: 31
This union binding pocket(no: 2) in the query (biounit: 3oii.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 5MT9 SRO None
2 2FWP ICR 1.63934
3 4AG5 ADP 1.97628
4 1YXM ADE 1.97628
5 4M3P HCS 2.37154
6 4ZCC FAD 2.37154
7 3MMH SME 2.39521
8 4JLS 3ZE 2.63158
9 1KGZ PRP 3.16206
10 4M1U A2G MBG 3.16206
11 1Q8A HCS 3.95257
12 4UP4 GAL NAG 3.95257
13 2GU8 796 3.95257
14 1WHT BZS 4.57516
15 3EF0 ALF 4.74308
16 1RJW ETF 4.74308
17 1USR SIA WIA 4.74308
18 2I3G NAP 4.74308
19 5TKL G3H 4.74308
20 2WQ4 SFU 5.12821
21 3BOF HCS 5.13834
22 5G3U ITW 5.5336
23 1RSG FAD 5.92885
24 1PDZ PGA 6.71937
25 3AB4 LYS 6.74157
26 1YY5 FAD 7.50988
27 1S9D GDP 7.92683
28 5XHA FRU 8.3004
29 2Z49 AMG 8.3004
30 3BY9 SIN 12.253
31 1JBU BEN 19.0476
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