Receptor
PDB id Resolution Class Description Source Keywords
1UAK 2.05 Å EC: 2.1.1.228 CRYSTAL STRUCTURE OF TRNA(M1G37)METHYLTRANSFERASE: INSIGHT I RECOGNITION HAEMOPHILUS INFLUENZAE METHYLTRANSFERASE SPOUT CLASS TRMD TRNA(M1G37)METHYLTRANSTRNA MODIFICATION TRANSFERASE
Ref.: CRYSTAL STRUCTURE OF TRNA(M(1)G37)METHYLTRANSFERASE INSIGHTS INTO TRNA RECOGNITION EMBO J. V. 22 2593 2003
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SAM A:301;
Valid;
none;
submit data
398.437 C15 H22 N6 O5 S C[S@@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4MCC 1.95 Å EC: 2.1.1.228 HINTRMD IN COMPLEX WITH N-[4-(AMINOMETHYL)BENZYL]-4-OXO-3,4- DIHYDROTHIENO[2,3-D]PYRIMIDINE-5-CARBOXAMIDE HAEMOPHILUS INFLUENZAE TREFOIL TRMD SAM SAH SINEFUNGIN HMT STRUCTURAL GENOMICTRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: SELECTIVE INHIBITORS OF BACTERIAL T-RNA-(N(1)G37) METHYLTRANSFERASE (TRMD) THAT DEMONSTRATE NOVEL ORD THE LID DOMAIN. J.MED.CHEM. V. 56 7278 2013
Members (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4MCD ic50 = 4.7 uM 22L C12 H8 N2 O S c1ccc(cc1)....
2 3AXZ Kd = 372 uM ADN C10 H13 N5 O4 c1nc(c2c(n....
3 4MCC ic50 = 0.56 uM 21X C15 H14 N4 O2 S c1cc(ccc1C....
4 1UAK - SAM C15 H22 N6 O5 S C[S@@+](CC....
5 4YVH - SFG C15 H23 N7 O5 c1nc(c2c(n....
6 1UAL - SAH C14 H20 N6 O5 S c1nc(c2c(n....
7 1UAM - SAH C14 H20 N6 O5 S c1nc(c2c(n....
8 4YVG - SAM C15 H22 N6 O5 S C[S@@+](CC....
9 4MCB ic50 = 1.5 uM 21W C19 H18 N6 O2 S c1cc(ccc1C....
70% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4MCD ic50 = 4.7 uM 22L C12 H8 N2 O S c1ccc(cc1)....
2 3AXZ Kd = 372 uM ADN C10 H13 N5 O4 c1nc(c2c(n....
3 4MCC ic50 = 0.56 uM 21X C15 H14 N4 O2 S c1cc(ccc1C....
4 1UAK - SAM C15 H22 N6 O5 S C[S@@+](CC....
5 4YVH - SFG C15 H23 N7 O5 c1nc(c2c(n....
6 1UAL - SAH C14 H20 N6 O5 S c1nc(c2c(n....
7 1UAM - SAH C14 H20 N6 O5 S c1nc(c2c(n....
8 4YVG - SAM C15 H22 N6 O5 S C[S@@+](CC....
9 4MCB ic50 = 1.5 uM 21W C19 H18 N6 O2 S c1cc(ccc1C....
10 1P9P Kd = 68 nM SAH C14 H20 N6 O5 S c1nc(c2c(n....
50% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4MCD ic50 = 4.7 uM 22L C12 H8 N2 O S c1ccc(cc1)....
2 3AXZ Kd = 372 uM ADN C10 H13 N5 O4 c1nc(c2c(n....
3 4MCC ic50 = 0.56 uM 21X C15 H14 N4 O2 S c1cc(ccc1C....
4 1UAK - SAM C15 H22 N6 O5 S C[S@@+](CC....
5 4YVH - SFG C15 H23 N7 O5 c1nc(c2c(n....
6 1UAL - SAH C14 H20 N6 O5 S c1nc(c2c(n....
7 1UAM - SAH C14 H20 N6 O5 S c1nc(c2c(n....
8 4YVG - SAM C15 H22 N6 O5 S C[S@@+](CC....
9 4MCB ic50 = 1.5 uM 21W C19 H18 N6 O2 S c1cc(ccc1C....
10 1P9P Kd = 68 nM 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 : 4MCC; Ligand: 21X; Similar sites found: 76
This union binding pocket(no: 1) in the query (biounit: 4mcc.bio1) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5FUI APY 0.01058 0.45296 None
2 5W3Y ACO 0.03067 0.40077 1.21951
3 4RRG A3T 0.002148 0.43303 1.41844
4 4IF4 BEF 0.04339 0.40332 1.44231
5 3OII SAH 0.00001744 0.52016 2.03252
6 1KGZ PRP 0.009924 0.41778 2.03252
7 3WH2 FLC 0.008868 0.44356 2.04082
8 1CT9 AMP 0.005375 0.43985 2.43902
9 2POC UD1 0.009744 0.42666 2.43902
10 1SBR VIB 0.02019 0.4147 2.5
11 1OSS BEN 0.02946 0.40603 2.69058
12 5APG EEM 0.0004882 0.45313 2.7027
13 5UDS ATP 0.006211 0.43203 2.84553
14 3S6X SIA GAL BGC 0.01464 0.41831 2.84553
15 4C2C ALA ALA ALA 0.03018 0.40595 2.84553
16 1RTF BEN 0.01087 0.42911 3.25203
17 3VSE SAH 0.0167 0.4106 3.25203
18 1J1R ADE 0.02854 0.40713 3.25203
19 4BHL ARG 0.02318 0.40328 3.25203
20 3GYQ SAM 0.0001763 0.48122 3.65854
21 2Z9I GLY ALA THR VAL 0.02081 0.41026 3.65854
22 3OF1 CMP 0.02153 0.40507 3.65854
23 5H5F SAM 0.00008883 0.48009 3.84615
24 3BBH SFG 0.000005837 0.55323 3.90244
25 3BBD SAH 0.0001341 0.49156 3.90244
26 1UYY BGC BGC 0.03623 0.40127 4.06504
27 5TVA AMP 0.01723 0.40991 4.16667
28 4JAL SAH 0.0001683 0.42846 4.19162
29 3OCP CMP 0.01977 0.40693 4.31655
30 1KQR MNA 0.0009352 0.4557 4.46927
31 4AU8 Z3R 0.02077 0.40586 4.47154
32 3JUC PCA 0.04392 0.40569 4.47154
33 4I5I 4I5 0.02442 0.40232 4.47154
34 5T52 A2G 0.02852 0.40273 4.54545
35 1GPM AMP 0.007999 0.43095 4.87805
36 3B6O TMP 0.02375 0.41098 4.87805
37 2P3I MNA 0.000278 0.48767 4.96894
38 3RK1 ATP 0.0106 0.41255 5.06329
39 4CNG SAH 0.0007452 0.43262 5.28455
40 5A7Y SAH 0.0002537 0.50736 5.69106
41 2D2F ADP 0.03617 0.40463 5.69106
42 2YY8 MTA 0.00000133 0.60551 5.97015
43 2YY8 SAM 0.0000006884 0.58117 5.97015
44 3U3Z SEP GLN GLU PTR 0.02767 0.40958 6.03015
45 4CNE SAH 0.0003187 0.46981 6.09756
46 4R78 AMP 0.01888 0.41195 6.09756
47 3NK7 SAM 0.0002219 0.47215 6.50407
48 1NE6 SP1 0.009395 0.41136 6.50407
49 1NFU RRP 0.01398 0.41053 6.50407
50 4FXQ G9L 0.03243 0.40557 6.50407
51 2GUC MAN 0.0323 0.40956 6.55738
52 3O7J 2AL 0.0214 0.4052 6.87831
53 4FK7 P34 0.008055 0.436 6.9869
54 2Y7I ARG 0.02447 0.40228 7.86026
55 1TE2 PGA 0.01318 0.4273 7.9646
56 1PVC ILE SER GLU VAL 0.02832 0.42662 7.98319
57 3IWD M2T 0.02023 0.41833 8.06452
58 4JWH SAH 0.000007602 0.51445 8.13008
59 4JWF SAH 0.0000174 0.50473 8.13008
60 3LRE ADP 0.01791 0.41787 8.53659
61 3LE7 ADE 0.03089 0.4041 8.94309
62 2FKA BEF 0.003725 0.45948 9.30233
63 4AUA 4AU 0.01538 0.40139 9.34959
64 3FGZ BEF 0.02476 0.42434 9.375
65 1L7N ALF 0.02288 0.40987 9.47867
66 5AHW CMP 0.005772 0.41748 9.7561
67 3PTG 932 0.003424 0.44984 10.9756
68 3AIA SAM 0.00001557 0.54019 11.3744
69 5TWJ SAM 0.00002178 0.5056 11.7886
70 2IDO TMP 0.02422 0.41334 12.3656
71 1VKF CIT 0.03277 0.40599 12.766
72 2BOS GLA GAL GLC 0.004388 0.45644 16.1765
73 2BOS GLA GAL GLC NBU 0.01282 0.42451 16.1765
74 4XZ3 ACP 0.03291 0.40349 16.2602
75 4JWJ SAH 0.0000177 0.50443 16.3366
76 3HP8 SUC 0.02124 0.41397 25.4545
Pocket No.: 2; Query (leader) PDB : 4MCC; Ligand: 21X; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4mcc.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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