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Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:254;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
SAH A:253;
B:253;
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
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: 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 : 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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