Receptor
PDB id Resolution Class Description Source Keywords
4yvh 1.6 Å EC: 2.1.1.228 CRYSTAL STRUCTURE OF H. INFLUENZAE TRMD IN COMPLEX WITH SINE HAEMOPHILUS INFLUENZAE (STRAIN ATCC 5111121 / KW20 / RD) MTASE SPOUT TRANSFERASE
Ref.: STRUCTURAL BASIS FOR METHYL-DONOR-DEPENDENT AND SEQUENCE-SPECIFIC BINDING TO TRNA SUBSTRATES BY KNO METHYLTRANSFERASE TRMD. PROC.NATL.ACAD.SCI.USA V. 112 E4197 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SFG A:301;
 Valid;
 none;
 submit data
381.387 C15 H23 N7 O5 c1nc(...
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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 5 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 (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 6JOE Kd = 0.091 uM BWR C20 H23 N5 O2 S c1cc(ccc1C....
2 4MCD ic50 = 4.7 uM 22L C12 H8 N2 O S c1ccc(cc1)....
3 3AXZ Kd = 372 uM ADN C10 H13 N5 O4 c1nc(c2c(n....
4 4MCC ic50 = 0.56 uM 21X C15 H14 N4 O2 S c1cc(ccc1C....
5 1UAK - SAM C15 H22 N6 O5 S C[S@@+](CC....
6 4YVH - SFG C15 H23 N7 O5 c1nc(c2c(n....
7 1UAL - SAH C14 H20 N6 O5 S c1nc(c2c(n....
8 1UAM - SAH C14 H20 N6 O5 S c1nc(c2c(n....
9 4YVG - SAM C15 H22 N6 O5 S C[S@@+](CC....
10 4MCB ic50 = 1.5 uM 21W C19 H18 N6 O2 S c1cc(ccc1C....
11 1P9P Kd = 68 nM SAH C14 H20 N6 O5 S c1nc(c2c(n....
50% Homology Family (69)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 6QQR - JDN C8 H8 B N O2 B(c1ccc2c(....
2 6QOA - JBN C4 H4 N2 O2 c1cnoc1C(=....
3 6QOF - ADE C5 H5 N5 c1[nH]c2c(....
4 6QQY Kd = 0.5 uM JD2 C18 H14 N6 c1ccnc(c1)....
5 6QRF Kd = 33 uM JF5 C11 H10 N2 O2 c1ccc(cc1)....
6 6QOJ - JBH C8 H8 N2 O c1ccc2c(c1....
7 6QR5 Kd = 0.49 uM JFH C23 H25 N5 c1cc(ccc1C....
8 6QOR - JBK C6 H6 N2 O3 c1cc(c(c(c....
9 6QON - J9W C8 H5 N O3 c1ccc2c(c1....
10 6QOO - JAB C4 H4 N2 O S c1cnoc1C(=....
11 6QOK - J9T C7 H8 N2 O2 COC(=O)c1c....
12 6QR6 Kd = 0.027 uM JCK C24 H24 N6 c1cc(ccc1C....
13 6QQS Kd = 110 uM JCZ C11 H10 N4 c1cc(cc2c1....
14 6QQZ Kd = 0.18 uM JEB C18 H14 N6 c1cc(cnc1)....
15 6QO4 - 97T C9 H7 N O2 c1ccc(c(c1....
16 6QQW Kd = 19 uM JDQ C18 H16 N4 c1ccc(cc1)....
17 6QQT Kd = 59 uM JCH C19 H18 N4 O COc1ccc(cc....
18 6QQQ Kd = 6.7 uM JDE C17 H15 N3 O3 COc1cc(cc(....
19 6QOC - J9Q C9 H8 N2 O c1ccc(c(c1....
20 6NW6 - SAM C15 H22 N6 O5 S C[S@@+](CC....
21 6QO3 - J9N C7 H7 N3 S c1cc(sc1)C....
22 6QR7 Kd = 70 nM JEK C25 H26 N6 c1cc(ccc1C....
23 6QOT Kd = 0.17 mM 6SD C10 H11 N3 O COc1ccc(cc....
24 6QR0 Kd = 0.12 uM JFB C18 H14 N6 c1cc(cc2c1....
25 6QR9 Kd = 190 nM JEE C24 H24 N6 O c1cc(ccc1C....
26 6QOQ - JAE C7 H6 N2 S c1cc2c(cc1....
27 6QOD - FBB C7 H5 F N2 S c1cc2c(cc1....
28 6QOV - JAH C12 H12 N2 c1ccc(cc1)....
29 6QR1 Kd = 8.5 uM JFT C18 H13 Cl N6 c1cc(cnc1)....
30 6QOI - ABV C7 H6 N2 S c1ccc2c(c1....
31 6QRC Kd = 13 uM JFE C19 H18 N4 O COc1cccc(c....
32 6QOW - JBZ C9 H7 N O3 S COc1ccc2c(....
33 6QRE Kd = 14 uM JCQ C12 H12 N2 O3 COc1cccc(c....
34 6QOX - JA5 C9 H9 N O3 S COC(=O)c1c....
35 6QOG - JA8 C7 H5 Br N2 S c1cc2c(cc1....
36 6QR2 Kd = 3.2 uM JQB C18 H14 N6 O c1cc(c(nc1....
37 6QQV Kd = 12 uM JEW C19 H15 N5 c1ccc(c(c1....
38 6NW7 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
39 6QRA Kd = 710 nM JDK C24 H27 N5 c1cc(ccc1C....
40 6QOS - GOJ C6 H8 N2 O2 CCOC(=O)c1....
41 6QRB Kd = 27 nM JEQ C25 H26 N6 c1ccc(cc1)....
42 6QR8 Kd = 0.073 uM JDH C25 H27 N7 CN1CCN(CC1....
43 6QO6 - 5OB C8 H8 N2 O COc1ccc2c(....
44 6QRD Kd = 100 nM JEH C27 H31 N7 CC(C)N1CCN....
45 6QOH - 6GU C5 H4 Cl N5 c1[nH]c2c(....
46 6QOP - JBQ C8 H7 F N2 O c1cc2c(c(c....
47 6QR3 Kd = 0.36 uM JE8 C19 H22 N6 CN1CCC[C@@....
48 6QOL - JB5 C8 H7 N3 c1cc2c(cc1....
49 6QQU Kd = 5 uM JF8 C12 H9 N5 c1cc(cc2c1....
50 6QOM - JBE C5 H5 N3 O2 c1cc(c(nc1....
51 6QRG Kd = 10 uM JET C14 H14 N2 O5 COC(=O)COc....
52 6QR4 Kd = 0.59 uM JD8 C19 H22 N6 CN1CCCC[C@....
53 6QO2 - JAW C9 H8 N2 O c1cc2c(cc[....
54 6QOU Kd = 0.26 mM JB8 C8 H8 B N O2 B(c1ccc2cc....
55 6JOE Kd = 0.091 uM BWR C20 H23 N5 O2 S c1cc(ccc1C....
56 4MCD ic50 = 4.7 uM 22L C12 H8 N2 O S c1ccc(cc1)....
57 3AXZ Kd = 372 uM ADN C10 H13 N5 O4 c1nc(c2c(n....
58 4MCC ic50 = 0.56 uM 21X C15 H14 N4 O2 S c1cc(ccc1C....
59 1UAK - SAM C15 H22 N6 O5 S C[S@@+](CC....
60 4YVH - SFG C15 H23 N7 O5 c1nc(c2c(n....
61 1UAL - SAH C14 H20 N6 O5 S c1nc(c2c(n....
62 1UAM - SAH C14 H20 N6 O5 S c1nc(c2c(n....
63 4YVG - SAM C15 H22 N6 O5 S C[S@@+](CC....
64 4MCB ic50 = 1.5 uM 21W C19 H18 N6 O2 S c1cc(ccc1C....
65 5ZHJ Kd = 10.1 uM SAH C14 H20 N6 O5 S c1nc(c2c(n....
66 5ZHL Kd = 0.19 uM 9D0 C23 H30 N4 O2 S CCCCCCCCNC....
67 5ZHK - 9D6 C23 H28 N4 O2 S CCN(Cc1ccc....
68 6JOF Kd = 10.4 uM BWR C20 H23 N5 O2 S c1cc(ccc1C....
69 1P9P Kd = 68 nM SAH C14 H20 N6 O5 S c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: SFG; Similar ligands found: 281
No: Ligand ECFP6 Tc MDL keys Tc
1 SFG 1 1
2 0UM 0.689655 0.887324
3 SAI 0.654762 0.940298
4 SA8 0.642857 0.9
5 SAH 0.635294 0.954545
6 EEM 0.62069 0.875
7 5X8 0.619048 0.924242
8 S7M 0.606742 0.875
9 ADN 0.597222 0.850746
10 RAB 0.597222 0.850746
11 XYA 0.597222 0.850746
12 5CD 0.594595 0.863636
13 N37 0.582524 0.940298
14 5N5 0.581081 0.850746
15 62X 0.574468 0.84
16 A4D 0.573333 0.850746
17 K15 0.568421 0.863014
18 DTA 0.564103 0.84058
19 6RE 0.560976 0.833333
20 SAM 0.555556 0.875
21 EP4 0.551282 0.802817
22 KB1 0.55102 0.887324
23 M2T 0.544304 0.780822
24 SMM 0.537634 0.84
25 MTA 0.5375 0.826087
26 KYE 0.534653 0.851351
27 NWW 0.532468 0.84375
28 LMS 0.53012 0.678571
29 ZAS 0.53012 0.816901
30 A 0.53012 0.77027
31 AMP 0.53012 0.77027
32 J7C 0.529412 0.84507
33 KG4 0.52809 0.776316
34 3DH 0.52439 0.826087
35 AMP MG 0.52381 0.780822
36 HZ2 0.52381 0.875
37 GJV 0.523256 0.821918
38 SON 0.522727 0.813333
39 0XU 0.522222 0.938462
40 SSA 0.521277 0.697674
41 SRP 0.521277 0.813333
42 AOC 0.517647 0.826087
43 CA0 0.516854 0.776316
44 5AL 0.516129 0.786667
45 AMO 0.515464 0.813333
46 DSZ 0.515464 0.717647
47 GSU 0.515152 0.738095
48 KXW 0.514286 0.9
49 KH3 0.514286 0.851351
50 45A 0.511628 0.75
51 A2D 0.511628 0.75
52 A3N 0.511628 0.814286
53 ABM 0.511628 0.75
54 A5A 0.510638 0.682353
55 5CA 0.510417 0.697674
56 SRA 0.505882 0.730769
57 S4M 0.505747 0.792208
58 AN2 0.505618 0.74026
59 A3S 0.505618 0.895522
60 A7D 0.505618 0.882353
61 GAP 0.505376 0.776316
62 OZP 0.504673 0.9
63 A12 0.5 0.766234
64 EU9 0.5 0.7875
65 M33 0.5 0.74026
66 AP2 0.5 0.766234
67 BA3 0.5 0.75
68 Y3J 0.5 0.80303
69 KAA 0.5 0.712644
70 LSS 0.5 0.681818
71 DSH 0.5 0.871429
72 V2G 0.5 0.759494
73 LAD 0.5 0.818182
74 54H 0.5 0.666667
75 ADX 0.5 0.678571
76 HY8 0.5 0.875
77 VMS 0.5 0.666667
78 ME8 0.49505 0.775
79 SXZ 0.49505 0.875
80 AHX 0.494949 0.759494
81 53H 0.494845 0.659091
82 DAL AMP 0.494845 0.786667
83 TSB 0.494845 0.674419
84 G5A 0.494624 0.697674
85 50T 0.494505 0.74026
86 ADP 0.494382 0.75
87 B4P 0.494382 0.75
88 5AS 0.494382 0.640449
89 AP5 0.494382 0.75
90 Q2M 0.490909 0.875
91 Q34 0.490909 0.851351
92 F0P 0.490909 0.9
93 GEK 0.489796 0.913043
94 8QN 0.489796 0.786667
95 8LH 0.489583 0.766234
96 V47 0.489583 0.923077
97 ADP BEF 0.488889 0.77027
98 AT4 0.488889 0.721519
99 ADP MG 0.488889 0.77027
100 5AD 0.486842 0.828125
101 PAJ 0.484848 0.728395
102 52H 0.484536 0.659091
103 8LE 0.484211 0.75641
104 APC MG 0.483871 0.773333
105 AU1 0.483516 0.730769
106 MAO 0.483146 0.782051
107 NEC 0.482759 0.797101
108 A3G 0.482759 0.882353
109 3AM 0.482353 0.733333
110 7D7 0.480519 0.794118
111 TXA 0.480392 0.766234
112 NB8 0.480392 0.782051
113 NVA LMS 0.48 0.693182
114 QA7 0.479592 0.75641
115 8LQ 0.479592 0.789474
116 ATF 0.479167 0.721519
117 ACP 0.478261 0.753247
118 HEJ 0.478261 0.75
119 H1Q 0.478261 0.76
120 ATP 0.478261 0.75
121 A3T 0.478261 0.852941
122 Q2P 0.478261 0.851351
123 Q2V 0.477876 0.887324
124 U4Y 0.477064 0.913043
125 7MD 0.476636 0.775
126 YSA 0.47619 0.697674
127 XAH 0.47619 0.775
128 9ZA 0.474747 0.746835
129 9ZD 0.474747 0.746835
130 PRX 0.473118 0.753247
131 APR 0.473118 0.773333
132 AQP 0.473118 0.75
133 5FA 0.473118 0.75
134 AR6 0.473118 0.773333
135 APC 0.473118 0.766234
136 NWQ 0.470588 0.818182
137 WAQ 0.470588 0.815789
138 4AD 0.47 0.802632
139 NSS 0.47 0.697674
140 F2R 0.469565 0.756098
141 RBY 0.468085 0.789474
142 A5D 0.468085 0.84058
143 AD9 0.468085 0.730769
144 ADV 0.468085 0.789474
145 ATP MG 0.468085 0.77027
146 ADP PO3 0.468085 0.77027
147 AGS 0.468085 0.7125
148 MHZ 0.467391 0.782051
149 FA5 0.466667 0.813333
150 PTJ 0.466019 0.7375
151 N5O 0.465909 0.867647
152 00A 0.465347 0.746835
153 D3Y 0.464646 0.869565
154 8X1 0.464646 0.693182
155 BEF ADP 0.463158 0.75
156 VRT 0.463158 0.871429
157 GA7 0.462963 0.74359
158 LEU LMS 0.460784 0.709302
159 S8M 0.46 0.859155
160 OOB 0.46 0.786667
161 QXP 0.46 0.682353
162 ACQ 0.458333 0.753247
163 T99 0.458333 0.721519
164 TAT 0.458333 0.721519
165 ANP 0.458333 0.730769
166 J4G 0.456311 0.826667
167 B5V 0.456311 0.766234
168 N5A 0.455556 0.865672
169 HQG 0.454545 0.763158
170 AAT 0.453608 0.847222
171 2AM 0.453488 0.723684
172 8PZ 0.45283 0.697674
173 FYA 0.451923 0.786667
174 YLC 0.451327 0.797468
175 DLL 0.45098 0.786667
176 A3P 0.450549 0.746667
177 YLP 0.45045 0.777778
178 A22 0.45 0.74026
179 ARG AMP 0.449541 0.765432
180 ANP MG 0.44898 0.74026
181 VO4 ADP 0.44898 0.730769
182 ALF ADP 0.44898 0.7125
183 2VA 0.446809 0.828571
184 QXG 0.446602 0.674419
185 3UK 0.446602 0.776316
186 OAD 0.446602 0.776316
187 OZV 0.445545 0.75
188 80F 0.445378 0.73494
189 6YZ 0.444444 0.753247
190 IOT 0.443478 0.768293
191 9SN 0.443396 0.7375
192 P5A 0.442308 0.704545
193 R2V 0.442308 0.682353
194 PR8 0.442308 0.807692
195 7D5 0.44186 0.714286
196 A1R 0.441176 0.769231
197 7C5 0.440367 0.797297
198 TT8 0.44 0.926471
199 YLA 0.439655 0.777778
200 YLB 0.438596 0.777778
201 9K8 0.438095 0.655556
202 1ZZ 0.438095 0.753086
203 3OD 0.438095 0.776316
204 BIS 0.438095 0.725
205 NVA 2AD 0.4375 0.859155
206 JNT 0.436893 0.753247
207 MAP 0.435644 0.7125
208 KY2 0.435644 0.824324
209 MYR AMP 0.433962 0.753086
210 NAI 0.433628 0.725
211 SO8 0.43299 0.816901
212 A6D 0.432692 0.74359
213 9X8 0.432692 0.734177
214 5SV 0.431373 0.7375
215 25A 0.431373 0.75
216 WSA 0.429825 0.705882
217 TYM 0.429825 0.813333
218 3NZ 0.428571 0.833333
219 LAQ 0.428571 0.753086
220 A3R 0.427184 0.769231
221 ADQ 0.427184 0.753247
222 KYB 0.427184 0.824324
223 7MC 0.426087 0.756098
224 8Q2 0.426087 0.674157
225 B5M 0.425926 0.75641
226 B5Y 0.425926 0.75641
227 48N 0.424779 0.759494
228 LPA AMP 0.424779 0.753086
229 JB6 0.424528 0.746835
230 PPS 0.424242 0.658824
231 AYB 0.423729 0.768293
232 K2H 0.423077 0.780822
233 PAP 0.42268 0.736842
234 OVE 0.422222 0.696203
235 B1U 0.422018 0.623656
236 3AD 0.421687 0.863636
237 KY5 0.420561 0.871429
238 4YB 0.419643 0.72093
239 CMP 0.419355 0.753425
240 2BA 0.419355 0.743243
241 A2P 0.419355 0.733333
242 ADP BMA 0.419048 0.753247
243 4UV 0.418182 0.75641
244 ALF ADP 3PG 0.417391 0.75
245 AHZ 0.415929 0.731707
246 QQX 0.41573 0.670886
247 K2K 0.415094 0.859155
248 NX8 0.414141 0.859155
249 AP0 0.413793 0.695122
250 KL2 0.413793 0.697368
251 L3W 0.413793 0.74359
252 K3K 0.412844 0.780822
253 ATP A 0.412844 0.76
254 ATP A A A 0.412844 0.76
255 NWZ 0.412371 0.84507
256 KOY 0.412281 0.857143
257 RP1 0.411111 0.705128
258 QQY 0.411111 0.679487
259 ACK 0.411111 0.716216
260 SP1 0.411111 0.705128
261 4UU 0.410714 0.75641
262 AFH 0.410714 0.728395
263 TXD 0.408696 0.725
264 DND 0.408696 0.766234
265 7D3 0.408602 0.696203
266 CC5 0.407407 0.876923
267 25L 0.407407 0.74026
268 TAD 0.40708 0.75
269 DQV 0.40708 0.763158
270 K3E 0.405405 0.77027
271 AMP DBH 0.405405 0.753247
272 OMR 0.405172 0.743902
273 TXE 0.405172 0.725
274 AF3 ADP 3PG 0.405172 0.75
275 MTP 0.404762 0.72973
276 K38 0.40367 0.780822
277 KY8 0.401869 0.847222
278 N0B 0.401575 0.777778
279 V3L 0.4 0.773333
280 YLY 0.4 0.768293
281 KMQ 0.4 0.74359
Similar Ligands (3D)
Ligand no: 1; Ligand: SFG; Similar ligands found: 4
No: Ligand Similarity coefficient
1 GDP 0.8795
2 CUU 0.8758
3 GTP 0.8645
4 CTP 0.8566
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4MCC; Ligand: 21X; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4mcc.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4MCC; Ligand: 21X; Similar sites found with APoc: 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 31 residues
No: Leader PDB Ligand Sequence Similarity
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