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Receptor
PDB id Resolution Class Description Source Keywords
3RFA 2.05 Å EC: 2.1.1.192 X-RAY STRUCTURE OF RLMN FROM ESCHERICHIA COLI IN COMPLEX WIT ADENOSYLMETHIONINE ESCHERICHIA COLI RADICAL SAM S-ADENOSYLMETHIONINE IRON SULFUR CLUSTER METHYLTRANSFERASE OXIDOREDUCTASE
Ref.: STRUCTURAL BASIS FOR METHYL TRANSFER BY A RADICAL S ENZYME. SCIENCE V. 332 1089 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SAM A:406;
B:406;
Valid;
Valid;
none;
none;
submit data
398.437 C15 H22 N6 O5 S C[S@@...
SF4 A:405;
B:405;
Part of Protein;
Part of Protein;
none;
none;
submit data
351.64 Fe4 S4 [S]12...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3RFA 2.05 Å EC: 2.1.1.192 X-RAY STRUCTURE OF RLMN FROM ESCHERICHIA COLI IN COMPLEX WIT ADENOSYLMETHIONINE ESCHERICHIA COLI RADICAL SAM S-ADENOSYLMETHIONINE IRON SULFUR CLUSTER METHYLTRANSFERASE OXIDOREDUCTASE
Ref.: STRUCTURAL BASIS FOR METHYL TRANSFER BY A RADICAL S ENZYME. SCIENCE V. 332 1089 2011
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3RFA - SAM C15 H22 N6 O5 S C[S@@+](CC....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3RFA - SAM C15 H22 N6 O5 S C[S@@+](CC....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3RFA - 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 : 3RFA; Ligand: SAM; Similar sites found with APoc: 127
This union binding pocket(no: 1) in the query (biounit: 3rfa.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 2BS5 BGC GAL FUC None
2 3ZW2 NAG GAL FUC None
3 3AKK ADP 1.53846
4 2Y88 2ER 1.63934
5 4XZ3 ACP 1.73913
6 1Y7P RIP 1.79372
7 1JA9 NDP 1.82482
8 4FHD EEM 1.90217
9 4FHD 0TT 1.90217
10 5UR1 YY9 1.92926
11 1NJJ GET 1.9802
12 1IGW PYR 1.9802
13 2Q7D ANP 2.02312
14 3V4S ATP 2.06718
15 4WEI GLC GAL 2.16606
16 5VSM MET 2.20126
17 5VSM 5AD 2.20126
18 4UZI IMD 2.22772
19 4EN4 ATP 2.24359
20 4EN4 GT1 2.24359
21 4EN4 GT0 2.24359
22 2QK4 ATP 2.43363
23 1M0W ANP 2.47525
24 5IM3 DTP 2.47525
25 6E1Q CFA 2.47525
26 5EXK 5AD 2.71903
27 1Q6O LG6 2.77778
28 4GK9 MAN BMA MAN MAN MAN 2.86738
29 4S00 AKR 2.90828
30 5OES ADP 2.9703
31 1PK8 ATP 2.9703
32 3ZXE PGZ 3.00752
33 3QH2 3NM 3.16742
34 1JPA ANP 3.20513
35 5DEY 59T 3.367
36 1O9U ADZ 3.42857
37 5DZT AMP 3.46535
38 5BU2 ADP 3.46535
39 3VPC ADP 3.5461
40 3BNK FMN 3.57143
41 2ZX2 RAM 3.58974
42 3DNT ATP 3.71287
43 4K38 SAM 3.78378
44 4K37 SAM 3.78378
45 4K39 SAM 3.78378
46 3BRN SRO 3.82166
47 5F90 LMR 3.84615
48 5F90 GLA GAL BGC 5VQ 3.84615
49 5F90 GLA GAL 3.84615
50 1AUX AGS 3.85852
51 3WG3 A2G GAL NAG FUC 3.93258
52 4NBU NAI 4
53 4QM9 CYS 4.04624
54 6D61 4AA 4.10256
55 3T7V SAM 4.28571
56 4JYD SAH 4.31034
57 4XYM A12 4.31034
58 5A5W GUO 4.34783
59 5HVJ ANP 4.44444
60 3DLS ADP 4.47761
61 5H4S RAM 4.57746
62 4H6B 10Y 4.61538
63 4H6B 10X 4.61538
64 4PIV NDP 4.70297
65 5XWV 8H6 4.83871
66 5XWV NDP 4.83871
67 5USZ SKE 4.84429
68 2XI7 XI7 4.8913
69 1ZBQ NAD 4.89297
70 3ZS7 ATP 5
71 3HAV ATP 5.01672
72 4M7T SAM 5.18518
73 5YSI NCA 5.26316
74 3X01 AMP 5.34351
75 3CF6 SP1 5.38922
76 4EUE NAI 5.44554
77 6HTO MET 5.5
78 6HTO 5AD 5.5
79 4BVA NDP 5.67164
80 4FK7 P34 5.67686
81 1E6W NAD 5.76923
82 4CS9 AMP 5.82011
83 3LQV ADE 6.08696
84 3VPD ANP 6.40569
85 3K5I ADP 6.45161
86 3K5I AIR 6.45161
87 2XVE FAD 6.46552
88 4UTW RFW 6.55022
89 1WUW TSU 6.66667
90 4X3R 686 6.68317
91 2QX0 PH2 6.91824
92 1RP0 AHZ 7.39437
93 4NFE BEN 7.59494
94 1OLT SAM 7.67327
95 4HXY NDP 7.92079
96 3QWI NAP 8.14815
97 3QWI CUE 8.14815
98 5KK4 44E 8.33333
99 4CQM NAP 8.42912
100 3KDM TES 8.44444
101 6CZI 38E 8.92857
102 2WG9 OCA 9.23077
103 1DQX BMP 9.3633
104 5K2M ADP 9.43396
105 1VKF CIT 9.57447
106 3H0L ADP 9.57447
107 5ZCT ANP 9.80392
108 4CJN QNZ 10.6436
109 5WGG SAM 11.8812
110 5TH5 MET 12.1673
111 5TH5 7C5 12.1673
112 3PPQ CHT 12.2186
113 5LXT ACP 13.2867
114 2FB3 GTP 13.5294
115 2FB3 5AD 13.5294
116 2FB3 MET 13.5294
117 4Y24 TD2 13.6364
118 1IOW PHY 14.3791
119 1IOW ADP 14.3791
120 3VPB ADP 16.0714
121 4BKS X6C 17.5258
122 1Z6Z NAP 18.0851
123 4NJH SAM 18.6957
124 4NJH 2K8 18.6957
125 4WCX SAM 23.2673
126 2HO2 PRO PRO PRO PRO PRO PRO PRO PRO PRO LEU 23.6842
127 1PVC ILE SER GLU VAL 30.8824
Pocket No.: 2; Query (leader) PDB : 3RFA; Ligand: SAM; Similar sites found with APoc: 31
This union binding pocket(no: 2) in the query (biounit: 3rfa.bio2) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 3V4S ADP 2.06718
2 3FPZ AHZ 2.14724
3 4Y7E BMA BMA BMA 2.31214
4 5NMX NAP 2.72277
5 4REP FAD 2.72277
6 4NZN 2OU 2.72727
7 4NZN ANP 2.72727
8 3GNE FLC 2.77778
9 4NBT NAD 2.91667
10 3FU7 KIA 3.21782
11 5MRH Q9Z 3.9604
12 3GQK ATP 4.29448
13 1QO0 BMD 4.59184
14 1K7T NAG GAL 4.83871
15 1UPR 4IP 4.87805
16 5OPJ AHR 4.9505
17 1E3W NAD 5.74713
18 5LY1 PPI 6.03675
19 6C1S EFV 6.43564
20 3A4V NAD 6.62461
21 4YEE 4CQ 6.66667
22 6C4A PYR 6.68317
23 3QJ4 FAD 6.72515
24 3UYW TAU 7.00935
25 5EJ2 NAD 8.76623
26 3BZ3 YAM 10.8696
27 4R78 AMP 14.8867
28 4J7U YTZ 17.7083
29 4J7U NAP 17.7083
30 3C8F MT2 22.449
31 4M1U A2G MBG 22.8571
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