Receptor
PDB id Resolution Class Description Source Keywords
5K7U 1.7 Å EC: 2.1.1.62 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAINS OF METTL3/METTL14 WITH SAM HOMO SAPIENS METHYLTRANSFERASE METHYLADENOSINE M6A TRANSFERASE
Ref.: STRUCTURAL BASIS FOR COOPERATIVE FUNCTION OF METTL3 METTL14 METHYLTRANSFERASES. MOL.CELL V. 63 306 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SAM A:601;
 Valid;
 none;
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398.437 C15 H22 N6 O5 S C[S@@...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5K7U 1.7 Å EC: 2.1.1.62 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAINS OF METTL3/METTL14 WITH SAM HOMO SAPIENS METHYLTRANSFERASE METHYLADENOSINE M6A TRANSFERASE
Ref.: STRUCTURAL BASIS FOR COOPERATIVE FUNCTION OF METTL3 METTL14 METHYLTRANSFERASES. MOL.CELL V. 63 306 2016
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5K7U - SAM C15 H22 N6 O5 S C[S@@+](CC....
2 5K7W - SAH C14 H20 N6 O5 S c1nc(c2c(n....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5IL2 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 5IL1 Kd = 1.5 uM SAM C15 H22 N6 O5 S C[S@@+](CC....
3 5L6D - SAH C14 H20 N6 O5 S c1nc(c2c(n....
4 5L6E - SAM C15 H22 N6 O5 S C[S@@+](CC....
5 5K7U - SAM C15 H22 N6 O5 S C[S@@+](CC....
6 5K7W - SAH C14 H20 N6 O5 S c1nc(c2c(n....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5IL2 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 5IL1 Kd = 1.5 uM SAM C15 H22 N6 O5 S C[S@@+](CC....
3 5L6D - SAH C14 H20 N6 O5 S c1nc(c2c(n....
4 5L6E - SAM C15 H22 N6 O5 S C[S@@+](CC....
5 5K7U - SAM C15 H22 N6 O5 S C[S@@+](CC....
6 5K7W - SAH C14 H20 N6 O5 S c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SAM; Similar ligands found: 192
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 XYA 0.565789 0.773333
9 ADN 0.565789 0.773333
10 RAB 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 AMP MG 0.511364 0.710843
25 5AL 0.510417 0.743902
26 VMS 0.510204 0.673913
27 54H 0.510204 0.673913
28 0UM 0.51 0.857143
29 A 0.505747 0.707317
30 AMP 0.505747 0.707317
31 ABM 0.505618 0.753086
32 A5A 0.505155 0.688889
33 DAL AMP 0.50505 0.765432
34 NVA LMS 0.504951 0.725275
35 K15 0.5 0.883117
36 6RE 0.5 0.78481
37 5AD 0.5 0.75
38 SSA 0.5 0.684783
39 SON 0.5 0.746988
40 SRP 0.5 0.746988
41 LSS 0.49505 0.706522
42 CA0 0.494624 0.714286
43 A12 0.494505 0.705882
44 AP2 0.494505 0.705882
45 ME8 0.490385 0.841463
46 5CA 0.49 0.684783
47 TSB 0.49 0.681319
48 53H 0.49 0.666667
49 ACP 0.489362 0.694118
50 5AS 0.48913 0.648936
51 ADP 0.48913 0.690476
52 A2D 0.488889 0.690476
53 J7C 0.488889 0.772152
54 ZAS 0.488636 0.769231
55 8QN 0.485149 0.743902
56 GAP 0.484536 0.73494
57 AN2 0.483871 0.682353
58 A3S 0.483871 0.813333
59 A7D 0.483871 0.851351
60 GJV 0.483516 0.775
61 SRA 0.483146 0.694118
62 LAD 0.480769 0.752941
63 KAA 0.480769 0.698925
64 GSU 0.480769 0.722222
65 AMO 0.480392 0.746988
66 DSZ 0.480392 0.703297
67 52H 0.48 0.666667
68 ADP MG 0.478723 0.702381
69 M33 0.478723 0.722892
70 MAO 0.478261 0.82716
71 BA3 0.478261 0.690476
72 AOC 0.477778 0.776316
73 DSH 0.477778 0.842105
74 NEC 0.477778 0.75
75 SXZ 0.47619 0.894737
76 AHX 0.475728 0.701149
77 Y3J 0.47561 0.706667
78 G5A 0.474227 0.684783
79 A3T 0.473684 0.8
80 ADP BEF 0.473684 0.686047
81 BEF ADP 0.473684 0.686047
82 B4P 0.473118 0.690476
83 AP5 0.473118 0.690476
84 A3N 0.472527 0.766234
85 KB1 0.471698 0.833333
86 LEU LMS 0.471154 0.706522
87 APC 0.46875 0.705882
88 PRX 0.46875 0.73494
89 PAJ 0.466019 0.712644
90 4AD 0.466019 0.759036
91 RBY 0.463918 0.72619
92 ADP PO3 0.463918 0.728395
93 ADV 0.463918 0.72619
94 ADX 0.463158 0.666667
95 MHZ 0.463158 0.82716
96 AU1 0.463158 0.674419
97 YAP 0.462963 0.738095
98 TXA 0.462264 0.72619
99 NB8 0.462264 0.72093
100 A3G 0.461538 0.802632
101 VRT 0.459184 0.842105
102 ATP MG 0.459184 0.702381
103 YSA 0.458716 0.684783
104 XAH 0.458716 0.715909
105 50T 0.458333 0.682353
106 ATP 0.458333 0.690476
107 7D7 0.45679 0.723684
108 ANP MG 0.455446 0.678161
109 KH3 0.455357 0.871795
110 ACQ 0.454545 0.694118
111 AQP 0.453608 0.690476
112 5FA 0.453608 0.690476
113 AR6 0.453608 0.710843
114 APR 0.453608 0.710843
115 NSS 0.451923 0.703297
116 FA5 0.449541 0.746988
117 AGS 0.44898 0.678161
118 SAP 0.44898 0.678161
119 A5D 0.44898 0.789474
120 AD9 0.44898 0.674419
121 PTJ 0.448598 0.72093
122 YLB 0.448276 0.758621
123 YLP 0.447368 0.738636
124 D3Y 0.446602 0.792208
125 ADP ALF 0.445545 0.678161
126 ALF ADP 0.445545 0.678161
127 TYR AMP 0.445455 0.746988
128 MYR AMP 0.444444 0.776471
129 3AM 0.444444 0.674699
130 OAD 0.443396 0.73494
131 2VA 0.443299 0.779221
132 OOB 0.442308 0.722892
133 S8M 0.442308 0.831169
134 ADP VO4 0.441176 0.702381
135 VO4 ADP 0.441176 0.702381
136 ANP 0.44 0.674419
137 TAT 0.44 0.686047
138 WAQ 0.439252 0.75
139 ARG AMP 0.438596 0.727273
140 YLC 0.435897 0.755814
141 AAT 0.435644 0.797468
142 3OD 0.435185 0.73494
143 1ZZ 0.435185 0.755814
144 NVA 2AD 0.434343 0.815789
145 DLL 0.433962 0.722892
146 00A 0.433962 0.689655
147 7MD 0.433628 0.715909
148 ATF 0.431373 0.666667
149 SO8 0.43 0.792208
150 3UK 0.429907 0.714286
151 A6D 0.429907 0.72619
152 5SV 0.428571 0.741176
153 AMP DBH 0.428571 0.714286
154 WSA 0.42735 0.692308
155 TYM 0.42735 0.746988
156 9SN 0.427273 0.681818
157 AHZ 0.426087 0.755814
158 A A 0.425926 0.710843
159 3NZ 0.425926 0.807692
160 P5A 0.425926 0.691489
161 PR8 0.425926 0.744186
162 A1R 0.424528 0.709302
163 2A5 0.424242 0.674419
164 7MC 0.423729 0.719101
165 7D5 0.422222 0.658824
166 FYA 0.422018 0.722892
167 JB6 0.422018 0.709302
168 AYB 0.421488 0.75
169 PLP AAD 0.419355 0.764045
170 A22 0.419048 0.682353
171 MAP 0.419048 0.659091
172 2AM 0.417582 0.666667
173 TAD 0.417391 0.712644
174 A3P 0.416667 0.686747
175 ADP BMA 0.416667 0.714286
176 25A 0.415094 0.690476
177 YLA 0.413223 0.719101
178 ADQ 0.411215 0.694118
179 48N 0.410256 0.72093
180 0XU 0.41 0.824324
181 NAD IBO 0.406504 0.717647
182 7D3 0.40625 0.643678
183 PAP 0.405941 0.678571
184 OVE 0.404255 0.662791
185 4UV 0.403509 0.697674
186 ALF ADP 3PG 0.403361 0.712644
187 AF3 ADP 3PG 0.403361 0.712644
188 LA8 ALF 3PG 0.403361 0.712644
189 3AD 0.402299 0.783784
190 CMP 0.402062 0.691358
191 2BA 0.402062 0.682927
192 7C5 0.4 0.731707
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5K7U; Ligand: SAM; Similar sites found: 199
This union binding pocket(no: 1) in the query (biounit: 5k7u.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3C3Y SAH 0.00005616 0.49258 1.68776
2 4E70 N7I 0.00333 0.43037 2.22222
3 1NFQ NAI 0.01049 0.41024 2.22222
4 3FRH SAH 0.004272 0.41659 2.37154
5 4KIB SAH 0.002632 0.41447 2.52101
6 1U2Z SAH 0.001029 0.44376 2.5788
7 3O7W SAM 0.0002703 0.44307 2.66667
8 4KRG SAH 0.001383 0.42595 2.66667
9 2EJU SAH 0.002809 0.41721 2.66667
10 4NEC SAH 0.002165 0.41235 2.66667
11 5E9W SAH 0.003267 0.40078 2.66667
12 5JE0 AZ8 0.001878 0.443 2.83401
13 5JE0 SAH 0.001878 0.443 2.83401
14 3LCV SAM 0.002139 0.42981 2.84698
15 3GU3 SAH 0.0004684 0.47601 2.86533
16 5JJR SAH 0.0007571 0.44166 2.86533
17 5DM1 5D7 0.002293 0.44863 2.99625
18 5DM1 SAH 0.00292 0.44266 2.99625
19 5HJM MTA 0.0005268 0.44143 3.11111
20 3LCC SAH 0.0005967 0.44116 3.11111
21 4ONQ SFG 0.001516 0.42872 3.11111
22 4Y2H SAH 0.01109 0.41664 3.11111
23 4Y2H 49K 0.0111 0.4166 3.11111
24 3TKY SAH 0.000274 0.46286 3.15186
25 5CUQ NSC 0.0004054 0.47465 3.37079
26 3EGI ADP 0.0005497 0.48495 3.39806
27 4IWN GEK 0.0003398 0.46491 3.49345
28 4NBW NAD 0.00478 0.42053 3.50195
29 3TLJ SAH 0.0003321 0.43328 3.55556
30 3VC1 GST 0.01227 0.41553 3.55556
31 3VC1 SAH 0.01227 0.41553 3.55556
32 4PNE SAH 0.002122 0.42996 3.97351
33 3A25 SAM 0.001074 0.43514 3.98671
34 3A27 SAM 0.001479 0.42918 4
35 4QED NAP 0.009097 0.41061 4
36 1R18 SAH 0.006052 0.40828 4
37 4PIO SAH 0.008742 0.41265 4.02477
38 4PIO AVI 0.009281 0.41021 4.02477
39 5DNK SAH 0.0009703 0.4152 4.29799
40 4X7Y SAH 0.019 0.40748 4.37956
41 1KYQ NAD 0.007828 0.40146 4.37956
42 4N49 SAM 0.0001994 0.4509 4.44444
43 3C6K SPD 0.003313 0.4379 4.44444
44 3C6K MTA 0.003313 0.4379 4.44444
45 4BLW AMP 0.00801 0.41794 4.44444
46 4BLW SAH 0.006212 0.41401 4.44444
47 3MJE NDP 0.01366 0.40259 4.44444
48 5E8J SAH 0.004065 0.4219 4.54545
49 3GXO SAH 0.001747 0.41175 4.60705
50 3GWZ SAH 0.002142 0.40752 4.60705
51 4FN4 NAD 0.005155 0.42179 4.72441
52 3VYW SAM 0.002686 0.4068 4.87013
53 5ULP KB1 0.00001858 0.46841 4.88889
54 5KVA SAM 0.00031 0.4647 4.88889
55 4FZV SAM 0.0003049 0.46298 4.88889
56 3DMH GMP 0.002137 0.43621 4.88889
57 3DMH SAM 0.001346 0.43496 4.88889
58 1DL5 SAH 0.004036 0.42237 4.88889
59 2ZIF SAM 0.001719 0.42089 4.88889
60 2EG5 SAH 0.005774 0.41489 4.88889
61 1TZD ADP 0.01665 0.41148 4.88889
62 3I53 SAH 0.004819 0.41087 4.88889
63 4ZOM 4Q3 0.04552 0.40644 4.88889
64 1ZQ9 SAM 0.001251 0.4323 4.91228
65 1TVP CBI 0.01207 0.40238 5.15759
66 4CS9 AMP 0.00768 0.44173 5.29101
67 2BZG SAH 0.000253 0.4621 5.33333
68 3LKZ SFG 0.0002224 0.45659 5.33333
69 3BGD SAH 0.0001497 0.44326 5.33333
70 3BXO SAM 0.001804 0.41209 5.33333
71 2ZWA SAH 0.001896 0.40995 5.33333
72 5MPT SAH 0.00201 0.42345 5.44413
73 4LWP SAH 0.00206 0.42299 5.44413
74 5JAQ NAI 0.02017 0.40443 5.44413
75 1AE1 NAP 0.01856 0.4 5.49451
76 5XVK SAH 0.006637 0.40816 5.6338
77 2WA2 SAM 0.0001711 0.46315 5.73066
78 2UYQ SAM 0.000061 0.54025 5.77778
79 3VSE SAH 0.0001282 0.4512 5.77778
80 3DUW SAH 0.002996 0.41797 5.8296
81 4OBW SAM 0.001882 0.42468 5.83658
82 3FUU ADN 0.0007112 0.44496 5.90406
83 2A14 SAH 0.00832 0.40222 6.08365
84 1XSE NDP 0.02283 0.4028 6.1017
85 1G55 SAH 0.00003177 0.50326 6.12245
86 1IM8 SAI 0.0002154 0.46954 6.14754
87 5FA8 SAM 0.002446 0.42724 6.21118
88 2VDV SAM 0.001864 0.43746 6.22222
89 5THQ NDP 0.01511 0.4006 6.22222
90 2HNK SAH 0.001031 0.4249 6.27615
91 1RJD SAM 0.000798 0.44483 6.30372
92 2ZFU SAH 0.007401 0.40097 6.51163
93 2WPB ZZI 0.01429 0.41299 6.57895
94 5THZ SAH 0.0008605 0.44718 6.59026
95 5THY SAH 0.001114 0.43853 6.59026
96 3S1S SAH 0.001744 0.43371 6.59026
97 1G60 SAM 0.000007898 0.52937 6.66667
98 3PT9 SAH 0.0001002 0.47937 6.66667
99 1KYZ SAH 0.001947 0.42802 6.66667
100 1BC5 SAH 0.005282 0.41253 6.66667
101 2AE2 NAP 0.01653 0.40943 6.66667
102 2AE2 PTO 0.01653 0.40943 6.66667
103 5FTW SAH 0.002805 0.40706 6.66667
104 5BW4 SAM 0.005352 0.41061 6.74157
105 3GRU AMP 0.0006362 0.45294 6.77966
106 1NV8 SAM 0.0008012 0.45684 6.87679
107 1NV8 MEQ 0.0008608 0.4539 6.87679
108 4AZW SAM 0.001799 0.42755 6.87679
109 4AZT SAM 0.00193 0.42421 6.87679
110 3G2O SAM 0.002453 0.41974 6.87679
111 1YC5 NCA 0.01073 0.40476 6.91057
112 2XVM SAH 0.001155 0.4209 7.03518
113 5N5D SAM 0.002766 0.41947 7.07965
114 1NW5 SAM 0.00001792 0.514 7.11111
115 3GDH SAH 0.00003215 0.46212 7.11111
116 2JJQ SAH 0.0006759 0.42984 7.11111
117 1VE3 SAM 0.001582 0.42792 7.11111
118 5JGL SAM 0.002771 0.41372 7.11111
119 3ML1 MGD 0.03439 0.41262 7.11111
120 1XCL SAH 0.01695 0.40069 7.11111
121 5DWQ SFG 0.007063 0.40854 7.16332
122 5DX0 SFG 0.008395 0.40671 7.16332
123 5E72 SAM 0.002131 0.42812 7.22543
124 3D3W NAP 0.00683 0.41996 7.37705
125 1PR9 NAP 0.008002 0.41681 7.37705
126 2PX8 SAH 0.0003056 0.45857 7.43494
127 4KRI SAH 0.002613 0.40682 7.44986
128 4POO SAM 0.009621 0.40259 7.5
129 2DPM SAM 0.0004745 0.43409 7.55556
130 4NMC 2OP 0.01877 0.40296 7.55556
131 4NMC FAD 0.01972 0.40296 7.55556
132 4M73 SAH 0.00281 0.44121 7.71513
133 4M73 M72 0.004446 0.43309 7.71513
134 5LOG SAH 0.0004683 0.4528 7.72532
135 5KOK S9T 0.0007383 0.46549 7.73639
136 5KOK R9T 0.002516 0.43982 7.73639
137 5KOK SAH 0.001359 0.4328 7.73639
138 5F8F SFG 0.0009811 0.44556 8
139 2PT9 2MH 0.003458 0.43471 8
140 2PT9 S4M 0.001969 0.43471 8
141 2JHP SAH 0.003106 0.41911 8
142 1SQF SAM 0.000513 0.44892 8.02292
143 3Q87 SAM 0.0001103 0.48638 8.23529
144 2WSB NAD 0.007242 0.42628 8.26772
145 4YMH SAH 0.001103 0.42262 8.33333
146 3GCZ SAM 0.0002635 0.46134 8.44444
147 1WG8 SAM 0.007782 0.40668 8.77193
148 2YX1 SFG 0.000405 0.43446 8.88889
149 4DCM SAM 0.0001054 0.46617 9.33333
150 1EJ0 SAM 0.00009112 0.48113 9.44444
151 3QOX SAH 0.001916 0.4319 9.77778
152 5MW4 5JU 0.006798 0.42757 9.77778
153 4QTU SAM 0.004453 0.4032 10.0962
154 1O97 AMP 0.007643 0.4369 10.2222
155 1O97 FAD 0.007643 0.4369 10.2222
156 3H8V ATP 0.004276 0.40936 10.2222
157 4C4A SAH 0.006348 0.40386 10.3152
158 4XUC 43G 0.002547 0.44081 10.5505
159 4XUC SAM 0.002547 0.44081 10.5505
160 2P41 SAH 0.0001446 0.47253 10.6667
161 4DMG SAM 0.0005642 0.46655 10.6667
162 4ITU 1HS 0.008007 0.42613 10.6667
163 4ITU NAI 0.005009 0.42613 10.6667
164 5ITV NAI 0.005389 0.42221 10.6667
165 3ABI NAD 0.005463 0.42065 10.6667
166 4BWL MN9 0.01212 0.42019 10.6667
167 5L95 AMP 0.002841 0.41897 10.6667
168 5FA5 MTA 0.0009243 0.42863 10.8883
169 1I9G SAM 0.003063 0.41943 11.0714
170 1LSS NAD 0.001658 0.41358 11.4286
171 3DXY SAM 0.001442 0.44738 11.5556
172 2BD0 NAP 0.01142 0.40856 11.5556
173 1EFV FAD 0.0075 0.43802 11.7479
174 1EFV AMP 0.009062 0.43401 11.7479
175 4RPL 3UC 0.03677 0.40953 11.7479
176 4RPL FAD 0.04491 0.40347 11.7479
177 3OU2 SAH 0.0013 0.40268 11.9266
178 3HVJ 705 0.002033 0.44886 12.2172
179 5E1M PRO PRO LYS ARG ILE ALA 0.005456 0.42561 12.4481
180 5E1M SAH 0.005456 0.42561 12.4481
181 2PXX SAH 0.000322 0.45002 13.0233
182 1Q0S SAH 0.000557 0.4573 13.3333
183 2AG5 NAD 0.007278 0.415 13.4146
184 3A4T SFG 0.00008251 0.45916 13.7778
185 3EVG SAH 0.0002384 0.4632 14.2222
186 3NUG NAD 0.003117 0.43301 14.2222
187 4YAG NAI 0.0249 0.40278 14.2222
188 4NBU NAI 0.006376 0.41889 14.6667
189 1I1N SAH 0.007778 0.41104 15.1111
190 1WY7 SAH 0.00009612 0.45857 15.4589
191 1YXM ADE 0.001678 0.478 15.5556
192 1IY8 NAD 0.003154 0.43278 15.5556
193 1QAN SAH 0.00003459 0.47367 16.4444
194 2XYQ SAH 0.0009239 0.43795 16.4444
195 1JG3 ADN 0.009574 0.40831 16.4444
196 5DX1 SFG 0.005312 0.41556 21.0526
197 2F5Z FAD 0.02711 0.40186 23.4375
198 1UWK URO 0.004169 0.4423 24
199 1UWK NAD 0.004169 0.4423 24
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