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Receptor
PDB id Resolution Class Description Source Keywords
4JWF 2.4 Å EC: 2.1.1.221 CRYSTAL STRUCTURE OF SPTRM10(74)-SAH COMPLEX SCHIZOSACCHAROMYCES POMBE TRNA MTASE DOMAIN TRANSFERASE
Ref.: CRYSTAL STRUCTURE OF TRNA M1G9 METHYLTRANSFERASE TR INSIGHT INTO THE CATALYTIC MECHANISM AND RECOGNITIO SUBSTRATE. NUCLEIC ACIDS RES. V. 42 509 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SAH B:301;
A:301;
Valid;
Valid;
none;
none;
submit data
384.411 C14 H20 N6 O5 S c1nc(...
ACY B:302;
A:302;
A:303;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
60.052 C2 H4 O2 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4JWF 2.4 Å EC: 2.1.1.221 CRYSTAL STRUCTURE OF SPTRM10(74)-SAH COMPLEX SCHIZOSACCHAROMYCES POMBE TRNA MTASE DOMAIN TRANSFERASE
Ref.: CRYSTAL STRUCTURE OF TRNA M1G9 METHYLTRANSFERASE TR INSIGHT INTO THE CATALYTIC MECHANISM AND RECOGNITIO SUBSTRATE. NUCLEIC ACIDS RES. V. 42 509 2014
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4JWF - 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 3 families.
1 4JWF - 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 3 families.
1 4JWF - 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 : 4JWF; Ligand: SAH; Similar sites found with APoc: 155
This union binding pocket(no: 1) in the query (biounit: 4jwf.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 5TWJ SAM None
2 3AIA SAM None
3 2FKA BEF None
4 3FGZ BEF None
5 1ZEI CRS None
6 5OFI 9TQ None
7 5MT9 SRO None
8 4PPF FLC 0.921659
9 3BPX SAL 1.35135
10 6DIO CIT 1.38249
11 4MUS 2D8 1.4218
12 4MUS LY0 1.4218
13 2JBM SRT 1.84332
14 2F5X ASP 1.84332
15 2DC1 CIT 1.84332
16 4IP7 FBP 1.84332
17 5K8P 6R8 1.84332
18 5AHW CMP 2.04082
19 3GYQ SAM 2.30415
20 2C5S AMP 2.30415
21 3HQP FDP 2.30415
22 2CBZ ATP 2.30415
23 3A16 PXO 2.30415
24 3IB1 IMN 2.30415
25 4KFU ACP 2.35849
26 5F6U 5VK 2.54777
27 5OCG 9R5 2.6455
28 1P9P SAH 2.76498
29 1TE2 PGA 2.76498
30 5EXK 5AD 2.76498
31 1OSS BEN 2.76498
32 1AUA BOG 2.76498
33 6FA4 D1W 2.89017
34 1XPJ TLA 3.1746
35 4CNE SAH 3.22581
36 5TCI MLI 3.22581
37 3SRV S19 3.22581
38 3ALN ANP 3.22581
39 2J5V RGP 3.22581
40 6AC9 ANP 3.22581
41 4B2D FBP 3.22581
42 3A4M ADP 3.22581
43 5WXU FLC 3.22581
44 5APG EEM 3.24324
45 2HYR BGC GLC 3.27869
46 3F81 STT 3.27869
47 2NUO BGC 3.27869
48 2GUC MAN 3.27869
49 2GUD MAN 3.27869
50 2GUD BMA 3.27869
51 2NU5 NAG 3.27869
52 1MID LAP 3.2967
53 4PTN GXV 3.49854
54 1BO4 COA 3.57143
55 2QQC AG2 3.57143
56 4CNG SAH 3.68664
57 1K0E TRP 3.68664
58 1G51 AMP 3.68664
59 2AWN ADP 3.68664
60 5LFV SIA GAL NAG 3.68664
61 5ZXD ATP 3.68664
62 1MXI SAH 3.75
63 5X80 SAL 3.75
64 4URX HXY 3.78378
65 1NXJ TLA 3.82514
66 4IF4 BEF 3.84615
67 5F90 LMR 3.84615
68 5YW5 ADE 3.91061
69 2YY8 SAM 3.9801
70 2YY8 MTA 3.9801
71 5XG5 A2G 4.13793
72 1VQ2 DDN 4.14508
73 6EKZ SNP 4.14747
74 5LXT GTP 4.14747
75 1Z4O GL1 4.14747
76 2V7B BEZ 4.14747
77 1UTJ ABN 4.14747
78 4KCT FDP 4.14747
79 4I7E PEP 4.14747
80 1B74 DGN 4.60829
81 6CGN DA 4.60829
82 1H5R THM 4.60829
83 5W6Y TRP 4.60829
84 1F0X FAD 4.60829
85 1H5T TYD 4.60829
86 5ZI9 FLC 4.60829
87 6I6X H6B 4.60829
88 3FXU TSU 4.60829
89 1H5S TMP 4.60829
90 1OXV ANP 4.60829
91 4RL4 PPV 4.71698
92 2CHT TSA 4.72441
93 6DF7 G9V 4.79042
94 4RRG A3T 4.96454
95 3OII SAH 5.06912
96 3O7B SAH 5.06912
97 1GPM AMP 5.06912
98 1C3X 8IG 5.06912
99 4NAE 1GP 5.06912
100 4FXQ G9L 5.06912
101 6C0B MLI 5.12821
102 4RR7 A3S 5.14706
103 3EGI ADP 5.33981
104 3NK7 SAM 5.52995
105 5TVA AMP 5.52995
106 3RK1 ATP 5.52995
107 1R27 MGD 5.52995
108 2OQ2 A3P 5.52995
109 3N8K D1X 5.81395
110 4RDN 6MD 5.98802
111 4WEI GLC GAL 5.99078
112 2V7O DRN 5.99078
113 1KQR MNA 6.14525
114 2ZX2 RAM 6.15385
115 1L7N ALF 6.63507
116 3GUZ PAF 6.81818
117 2FR6 CTN 6.84932
118 5Z20 OXM 6.91244
119 2BGM MAX 6.91244
120 2BD0 BIO 6.91244
121 6F5W KG1 7.37327
122 4F9C 0SX 7.37327
123 3G6K POP 7.37327
124 3G6K FAD 7.37327
125 1IWE IMP 7.37327
126 5LWY OLB 7.56302
127 1L5Y BEF 7.74194
128 1QH9 LAC 7.8341
129 4MCC 21X 8.13008
130 1V2X SAM 8.24742
131 2NU8 COA 8.29493
132 2HVW DDN 8.69565
133 2FDW D3G 8.75576
134 1QO0 BMD 8.75576
135 2BOI MFU 8.84956
136 3DCM SAM 10.4167
137 4JAL SAH 10.5991
138 2W5P CL8 10.7383
139 5H4S RAM 11.5207
140 1MQ0 BRD 12.8571
141 5O96 SAM 13.3641
142 2IVF MGD 13.8249
143 5CIC 51R 13.8249
144 1XVB BHL BHL 14.7059
145 5H5F SAM 15.2074
146 3B6C SDN 16.129
147 1RDL MMA 19.469
148 1PVC ILE SER GLU VAL 20.5882
149 3BBD SAH 23.0415
150 3BBH SFG 23.4146
151 4NST ADP 23.5023
152 2BOS GLA GAL GLC 26.4706
153 2BOS GLA GAL GLC NBU 26.4706
154 5A7Y SAH 33.6406
155 6EMU SAM 40.6091
Pocket No.: 2; Query (leader) PDB : 4JWF; Ligand: SAH; Similar sites found with APoc: 25
This union binding pocket(no: 2) in the query (biounit: 4jwf.bio2) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 5A7C 5D4 None
2 4NTC FAD 2.30415
3 1SZO CAX 2.76498
4 3G3N TC8 2.76498
5 6BMN PAP 3.22581
6 5M8T 0TR 3.22581
7 2HYQ MAN MAN 3.27869
8 2YN4 39J 3.81356
9 1NXJ GLV 3.82514
10 5A9A UTP 4.14747
11 3HQ9 OXL 4.14747
12 2UYQ SAM 4.60829
13 3QH2 3NM 4.60829
14 5C9P FUC 5.06912
15 1NSA BEN 5.06912
16 6BND OPE 5.06912
17 3OF1 CMP 5.52995
18 1D1Q 4NP 6.21118
19 3FIU POP 6.45161
20 5FQK 6NT 6.91244
21 1YQC GLV 7.05882
22 1OBD AMP 8.29493
23 3QDY CBS 11.1888
24 2TOH HBI 13.3641
25 1SQL GUN 13.6986
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