Receptor
PDB id Resolution Class Description Source Keywords
1UAL 1.8 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
SAH A:301;
Valid;
none;
submit data
384.411 C14 H20 N6 O5 S c1nc(...
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: SAH; Similar ligands found: 197
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 SXZ 0.692308 0.916667
6 DSH 0.692308 0.914286
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 RAB 0.573333 0.84058
19 ADN 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 SSA 0.536842 0.712644
28 SMM 0.536842 0.88
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 AMP 0.529412 0.763158
36 A 0.529412 0.763158
37 5CA 0.525773 0.712644
38 ME8 0.524752 0.8125
39 M2T 0.52439 0.821918
40 6RE 0.523256 0.824324
41 GJV 0.522727 0.813333
42 AAT 0.515789 0.863014
43 LSS 0.515152 0.696629
44 KAA 0.514852 0.727273
45 J7C 0.511364 0.835616
46 A5A 0.510417 0.697674
47 SON 0.505495 0.805195
48 SRP 0.505155 0.805195
49 5AL 0.5 0.779221
50 VMS 0.5 0.681818
51 KH3 0.5 0.866667
52 ADX 0.5 0.694118
53 CA0 0.5 0.769231
54 AMP MG 0.5 0.74359
55 AMO 0.5 0.805195
56 54H 0.5 0.681818
57 AHX 0.49505 0.753086
58 TSB 0.494949 0.689655
59 53H 0.494949 0.674157
60 G5A 0.494737 0.712644
61 A2D 0.494382 0.74359
62 ABM 0.494382 0.74359
63 ZAS 0.494253 0.808219
64 A6D 0.490196 0.759494
65 8QN 0.49 0.779221
66 GEK 0.49 0.956522
67 GAP 0.489583 0.769231
68 A3S 0.48913 0.884058
69 AN2 0.48913 0.734177
70 S4M 0.488889 0.831169
71 SRA 0.488636 0.746835
72 LAD 0.485437 0.810127
73 52H 0.484848 0.674157
74 A12 0.483516 0.759494
75 BA3 0.483516 0.74359
76 AP2 0.483516 0.759494
77 AOC 0.483146 0.842857
78 NEC 0.483146 0.788732
79 Y3J 0.481481 0.768116
80 NVA LMS 0.480392 0.696629
81 VRT 0.479167 0.861111
82 50T 0.478723 0.734177
83 5AS 0.478261 0.655556
84 B4P 0.478261 0.74359
85 ADP 0.478261 0.74359
86 AP5 0.478261 0.74359
87 A3N 0.477778 0.830986
88 YSA 0.476636 0.712644
89 XAH 0.476636 0.768293
90 0XU 0.473684 0.897059
91 WAQ 0.471154 0.807692
92 NSS 0.470588 0.712644
93 5AD 0.468354 0.791045
94 ADP MG 0.468085 0.734177
95 AU1 0.468085 0.725
96 M33 0.468085 0.734177
97 MAO 0.467391 0.797468
98 TXA 0.466667 0.759494
99 A3G 0.466667 0.871429
100 NB8 0.466667 0.775
101 3AM 0.465909 0.727273
102 DAL AMP 0.465347 0.779221
103 ATP 0.463158 0.74359
104 ADP BEF 0.463158 0.716049
105 A3T 0.463158 0.842857
106 BEF ADP 0.463158 0.716049
107 ACP 0.463158 0.746835
108 7D7 0.4625 0.785714
109 LEU LMS 0.461538 0.677778
110 APC 0.458333 0.759494
111 AQP 0.458333 0.74359
112 APR 0.458333 0.766234
113 PRX 0.458333 0.746835
114 AR6 0.458333 0.766234
115 5FA 0.458333 0.74359
116 IOT 0.456897 0.761905
117 4AD 0.456311 0.794872
118 PAJ 0.456311 0.722892
119 WSA 0.45614 0.72093
120 FA5 0.453704 0.805195
121 YAP 0.453704 0.794872
122 RBY 0.453608 0.782051
123 ADV 0.453608 0.782051
124 ADP PO3 0.453608 0.763158
125 AD9 0.453608 0.725
126 SAP 0.453608 0.728395
127 AGS 0.453608 0.728395
128 PTJ 0.45283 0.731707
129 MHZ 0.452632 0.797468
130 00A 0.451923 0.740741
131 A3P 0.451613 0.74026
132 YLP 0.451327 0.771084
133 7MD 0.45045 0.768293
134 ALF ADP 0.45 0.707317
135 ADP ALF 0.45 0.707317
136 ATP MG 0.44898 0.734177
137 2VA 0.447917 0.819444
138 OOB 0.446602 0.779221
139 ANP 0.444444 0.725
140 ACQ 0.444444 0.746835
141 TAT 0.444444 0.7375
142 P5A 0.443396 0.719101
143 7D5 0.443182 0.708861
144 ARG AMP 0.442478 0.759036
145 A1R 0.442308 0.7625
146 YLC 0.439655 0.790123
147 2AM 0.438202 0.717949
148 DLL 0.438095 0.779221
149 A22 0.436893 0.734177
150 D3Y 0.436893 0.859155
151 TYR AMP 0.436364 0.782051
152 ATF 0.435644 0.716049
153 MYR AMP 0.435185 0.746988
154 SO8 0.434343 0.808219
155 3UK 0.433962 0.769231
156 OAD 0.433962 0.769231
157 TAD 0.433628 0.765432
158 25A 0.432692 0.74359
159 ANP MG 0.431373 0.707317
160 VO4 ADP 0.431373 0.734177
161 ADP VO4 0.431373 0.734177
162 9SN 0.431193 0.731707
163 TYM 0.431034 0.805195
164 PR8 0.429907 0.8
165 ADQ 0.428571 0.746835
166 YLB 0.42735 0.771084
167 3OD 0.425926 0.769231
168 FYA 0.425926 0.779221
169 1ZZ 0.425926 0.746988
170 PPS 0.425743 0.674419
171 NVA 2AD 0.424242 0.808219
172 MAP 0.423077 0.707317
173 A2P 0.421053 0.727273
174 4YB 0.421053 0.735632
175 ADP BMA 0.420561 0.746835
176 5SV 0.419048 0.731707
177 3NZ 0.416667 0.824324
178 YLA 0.416667 0.771084
179 48N 0.413793 0.753086
180 LPA AMP 0.413793 0.768293
181 AYB 0.413223 0.761905
182 QQY 0.413043 0.696203
183 ACK 0.413043 0.710526
184 JB6 0.412844 0.7625
185 BIS 0.412844 0.719512
186 PAP 0.41 0.730769
187 OVE 0.408602 0.7125
188 4UV 0.40708 0.75
189 AMP DBH 0.40708 0.746835
190 3AD 0.406977 0.852941
191 AF3 ADP 3PG 0.40678 0.743902
192 OMR 0.40678 0.738095
193 LAQ 0.405172 0.768293
194 A A 0.40367 0.74359
195 7C5 0.403509 0.789474
196 7MC 0.403361 0.75
197 4UU 0.4 0.75
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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