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Receptor
PDB id Resolution Class Description Source Keywords
4JWH 2.04 Å EC: 2.1.1.221 CRYSTAL STRUCTURE OF SPTRM10(FULL LENGTH)-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 A:401;
B:401;
Valid;
Valid;
none;
none;
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384.411 C14 H20 N6 O5 S c1nc(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4JWH 2.04 Å EC: 2.1.1.221 CRYSTAL STRUCTURE OF SPTRM10(FULL LENGTH)-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 4JWH - 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 4JWH - 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 4JWH - 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 : 4JWH; Ligand: SAH; Similar sites found with APoc: 176
This union binding pocket(no: 1) in the query (biounit: 4jwh.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 1ZEI CRS None
2 5WHT SIA None
3 5OFI 9TQ None
4 2JBM SRT 1.33779
5 1H5R THM 1.36519
6 1H5T TYD 1.36519
7 1H5S TMP 1.36519
8 1IIM TTP 1.36986
9 5EY0 ILE 1.45985
10 4IP7 FBP 1.59744
11 1G51 AMP 1.59744
12 1EWK GLU 1.59744
13 5UI2 SUC 1.59744
14 2F5X ASP 1.60256
15 1UTJ ABN 1.65289
16 3QH2 3NM 1.80995
17 3GYQ SAM 1.83824
18 5TWJ SAM 1.85185
19 4CNE SAH 1.87266
20 5EXK 5AD 1.91693
21 6FDF SAH 1.91693
22 3WRB GDE 1.91693
23 4ITH RCM 2.04082
24 2CBZ ATP 2.1097
25 5TCI MLI 2.23642
26 3KRQ 3TR 2.23642
27 1F6D UDP 2.23642
28 3ALN ANP 2.23642
29 5IHE D5M 2.23642
30 5XXH E0D 2.25564
31 1P9P SAH 2.29885
32 4KFU ACP 2.35849
33 3OII SAH 2.37154
34 5D63 FUC GLA GLA 2.38908
35 3SRV S19 2.52708
36 4B2D FBP 2.55591
37 4PPF FLC 2.55591
38 1K0E TRP 2.55591
39 5LFV SIA GAL NAG 2.55591
40 1C1X HFA 2.55591
41 1BW9 PPY 2.55591
42 2GEK GDP 2.55591
43 2X1L MET 2.55591
44 1TE2 PGA 2.65487
45 2BD0 BIO 2.86885
46 6EKZ SNP 2.8754
47 5HVJ ANP 2.8754
48 3HQP FDP 2.8754
49 4YMU ARG 2.8754
50 4KCT FDP 2.8754
51 3HQ9 OXL 2.8754
52 6I6X H6B 2.8754
53 2V7B BEZ 2.8754
54 6FA4 D1W 2.89017
55 5XK9 GST 3.01724
56 4NAE 1GP 3.11111
57 4CNG SAH 3.13725
58 1XPJ TLA 3.1746
59 1F0X FAD 3.19489
60 2UYQ SAM 3.22581
61 5APG EEM 3.24324
62 3BZ3 YAM 3.26087
63 2GUC MAN 3.27869
64 2GUD BMA 3.27869
65 2GUD MAN 3.27869
66 2HYQ MAN MAN 3.27869
67 4ZNL BEF ADP 3.28467
68 1EXF GLY 3.30579
69 5H5F SAM 3.4188
70 2TPI ILE VAL 3.49345
71 6CGN DA 3.51438
72 3GDN MXN 3.51438
73 5WP5 SAH 3.51438
74 1N13 AG2 3.53982
75 1BO4 COA 3.57143
76 2QQC AG2 3.57143
77 1MXI SAH 3.75
78 1NXJ TLA 3.82514
79 3OKP GDD 3.83387
80 3ITA AIC 3.83387
81 3Q3H UDP 3.83387
82 6DIO CIT 3.83387
83 4IF4 BEF 3.84615
84 5ZI9 FLC 3.84615
85 3BBH SFG 3.90244
86 3BBD SAH 3.90244
87 5AHW CMP 4.08163
88 1VQ2 DDN 4.14508
89 5Z20 OXM 4.15335
90 2PZI AXX 4.15335
91 4JAL SAH 4.19162
92 1B74 DGN 4.33071
93 3NK7 SAM 4.33213
94 1GPM AMP 4.47284
95 5Z5I XYP 4.47284
96 3CV3 UDP 4.47284
97 2YY8 SAM 4.47761
98 2YY8 MTA 4.47761
99 1OSS BEN 4.4843
100 4F06 PHB 4.58221
101 2FKA BEF 4.65116
102 2YN4 39J 4.66102
103 2CHT TSA 4.72441
104 5C9P FUC 4.72441
105 3B6R CRN 4.79233
106 4FK7 P34 4.80349
107 3OF1 CMP 4.87805
108 2EW5 Y12 4.97238
109 1V2X SAM 5.11182
110 2NU8 COA 5.11182
111 4Y2B EPK 5.11182
112 4F9C 0SX 5.11182
113 5XLS URA 5.11182
114 4CFT H4B 5.11182
115 3DCJ THH 5.11628
116 3O7B SAH 5.32787
117 3EGI ADP 5.33981
118 3FGZ BEF 5.46875
119 5L3S G 5.7047
120 4WEI GLC GAL 5.7508
121 3N8K D1X 5.81395
122 5TVA AMP 5.83333
123 1OBD AMP 5.88235
124 2X2T GAL NGA 5.88235
125 4RR7 A3S 5.88235
126 1QH9 LAC 6.03448
127 2C5S AMP 6.07029
128 3VSV XYS 6.07029
129 2OQ2 A3P 6.13027
130 3NW7 LGV 6.18893
131 1RDL MMA 6.19469
132 4RRG A3T 6.38298
133 2BGM MAX 6.47482
134 5CIC 51R 6.48148
135 2FR6 CTN 6.84932
136 2FR6 URI 6.84932
137 1CT9 AMP 7.02875
138 4RDN 6MD 7.18563
139 6C0B MLI 7.34824
140 1P6O HPY 7.45342
141 4O48 ASP 7.66773
142 1L5Y BEF 7.74194
143 4MCC 21X 8.13008
144 1GG6 APL 8.24742
145 5TQZ GLC 8.66667
146 2HVW DDN 8.69565
147 2ZX2 RAM 8.71795
148 1T57 FMN 8.73786
149 5H4S RAM 8.80282
150 2Z49 AMG 8.94569
151 5LXT GTP 9.09091
152 6GR0 F8W 9.1954
153 6F5W KG1 9.26518
154 2IVF MGD 9.58466
155 2BOI MFU 9.73451
156 1MID LAP 9.89011
157 3DCM SAM 10.4167
158 3AIA SAM 10.4265
159 2W5P CL8 10.7383
160 6MJ7 ARG 10.9091
161 3QPB URA 11.5016
162 5O96 SAM 11.8367
163 1MQ0 BRD 12.8571
164 2PIE GLU LEU LYS TPO GLU ARG TYR 13.0435
165 1SQL GUN 13.6986
166 3R4S SIA 13.738
167 1L7N ALF 13.7441
168 2ZZV LAC 14.0575
169 1XVB BHL BHL 14.1176
170 1T36 ORN 14.377
171 3B6C SDN 14.9573
172 3OKA GDD 23.8095
173 2BOS GLA GAL GLC 26.4706
174 2BOS GLA GAL GLC NBU 26.4706
175 5A7Y SAH 28.8462
176 6EMU SAM 34.0102
Pocket No.: 2; Query (leader) PDB : 4JWH; Ligand: SAH; Similar sites found with APoc: 42
This union binding pocket(no: 2) in the query (biounit: 4jwh.bio2) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 1A5V Y3 1.89873
2 6F97 FAD 1.91693
3 4IA6 EIC 2.23642
4 2RCU BUJ 2.23642
5 3L8H FX1 2.7933
6 1M5B BN1 3.04183
7 2HYR BGC GLC 3.27869
8 2NUO BGC 3.27869
9 2NU5 NAG 3.27869
10 5OF1 SAL 3.33333
11 4FXQ G9L 3.51438
12 1NXJ GLV 3.82514
13 2AJ4 GLA 3.83387
14 1Z4O GL1 4.0724
15 6HKE LMR 4.15335
16 5M8T 0TR 4.15335
17 1MFI FHC 4.38596
18 3AB4 THR 4.49438
19 1W6F ISZ 5.03597
20 5A89 FMN 5.12821
21 5A89 ADP 5.12821
22 3G6K FAD 5.19481
23 3G6K POP 5.19481
24 4UXM BE7 5.30303
25 5FQK 6NT 5.57621
26 1D1Q 4NP 6.21118
27 2Y7P SAL 6.42202
28 3G89 SAM 7.22892
29 2XG5 EC2 7.51445
30 2XG5 EC5 7.51445
31 3RK1 ATP 7.59494
32 2C2A ADP 7.75194
33 4L77 CNL 8.30671
34 3WLV AZA 8.97436
35 5OCG 9R5 9.52381
36 5A7C 5D4 9.73451
37 3QDV NDG 11.1888
38 3QDX CBS 11.1888
39 3QPB R1P 11.5016
40 4YAG NAI 11.7647
41 1VAY AZA 13.2404
42 1PVC ILE SER GLU VAL 20.5882
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