Receptor
PDB id Resolution Class Description Source Keywords
5K8V 2.25 Å EC: 2.1.1.125 CRYSTAL STRUCTURE OF MUS MUSCULUS PROTEIN ARGININE METHYLTRA (CARM1 130-487) WITH CP1 MUS MUSCULUS PROTEIN ARGININE METHYLTRANSFERASE CATALYTIC DOMAIN CHROMAREGULATOR MRNA PROCESSING MRNA SPLICING NUCLEUS S-ADENOMETHIONINE TRANSCRIPTION TRANSCRIPTION REGULATION TRANSF
Ref.: STRUCTURAL STUDIES OF PROTEIN ARGININE METHYLTRANSF REVEAL ITS INTERACTIONS WITH POTENTIAL SUBSTRATES A INHIBITORS. FEBS J. V. 284 77 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO C:503;
C:502;
D:503;
C:504;
A:505;
A:504;
A:503;
B:503;
D:502;
A:506;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
6RE C:501;
B:501;
D:501;
A:501;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
ic50 = 460 nM
323.331 C12 H19 N8 O3 c1nc(...
PEG B:504;
A:507;
Invalid;
Invalid;
none;
none;
submit data
106.12 C4 H10 O3 C(COC...
PG6 B:502;
Invalid;
none;
submit data
266.331 C12 H26 O6 COCCO...
DXE A:502;
Invalid;
none;
submit data
90.121 C4 H10 O2 COCCO...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5K8V 2.25 Å EC: 2.1.1.125 CRYSTAL STRUCTURE OF MUS MUSCULUS PROTEIN ARGININE METHYLTRA (CARM1 130-487) WITH CP1 MUS MUSCULUS PROTEIN ARGININE METHYLTRANSFERASE CATALYTIC DOMAIN CHROMAREGULATOR MRNA PROCESSING MRNA SPLICING NUCLEUS S-ADENOMETHIONINE TRANSCRIPTION TRANSCRIPTION REGULATION TRANSF
Ref.: STRUCTURAL STUDIES OF PROTEIN ARGININE METHYLTRANSF REVEAL ITS INTERACTIONS WITH POTENTIAL SUBSTRATES A INHIBITORS. FEBS J. V. 284 77 2017
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 2Y1X - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 5K8V ic50 = 460 nM 6RE C12 H19 N8 O3 c1nc(c2c(n....
3 2Y1W - SFG C15 H23 N7 O5 c1nc(c2c(n....
4 5DXJ - SFG C15 H23 N7 O5 c1nc(c2c(n....
5 3B3F - SAH C14 H20 N6 O5 S c1nc(c2c(n....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 2Y1X - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 5K8V ic50 = 460 nM 6RE C12 H19 N8 O3 c1nc(c2c(n....
3 2Y1W - SFG C15 H23 N7 O5 c1nc(c2c(n....
4 5DXJ - SFG C15 H23 N7 O5 c1nc(c2c(n....
5 3B3F - SAH C14 H20 N6 O5 S c1nc(c2c(n....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 2Y1X - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 5K8V ic50 = 460 nM 6RE C12 H19 N8 O3 c1nc(c2c(n....
3 2Y1W - SFG C15 H23 N7 O5 c1nc(c2c(n....
4 5DXJ - SFG C15 H23 N7 O5 c1nc(c2c(n....
5 3B3F - SAH C14 H20 N6 O5 S c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 6RE; Similar ligands found: 245
No: Ligand ECFP6 Tc MDL keys Tc
1 6RE 1 1
2 J7C 0.820895 0.985507
3 GJV 0.782609 0.985714
4 ADN 0.671875 0.830986
5 XYA 0.671875 0.830986
6 RAB 0.671875 0.830986
7 5N5 0.651515 0.857143
8 5CD 0.641791 0.816901
9 A4D 0.641791 0.830986
10 EP4 0.637681 0.786667
11 M2T 0.605634 0.766234
12 DTA 0.605634 0.773333
13 3DH 0.60274 0.783784
14 MTA 0.597222 0.783784
15 A 0.586667 0.779221
16 AMP 0.586667 0.779221
17 A3N 0.584416 0.821918
18 SRA 0.578947 0.740741
19 AMP MG 0.571429 0.759494
20 MHZ 0.567901 0.768293
21 ZAS 0.565789 0.849315
22 ABM 0.564103 0.7375
23 A2D 0.564103 0.7375
24 SFG 0.560976 0.833333
25 A3G 0.551282 0.861111
26 AOC 0.551282 0.783784
27 DSH 0.551282 0.851351
28 A12 0.55 0.753086
29 MAO 0.55 0.746988
30 AP2 0.55 0.753086
31 BA3 0.55 0.7375
32 CA0 0.548781 0.719512
33 AU1 0.548781 0.740741
34 SA8 0.547619 0.805195
35 5AD 0.544118 0.757143
36 5AS 0.54321 0.67033
37 AP5 0.54321 0.7375
38 B4P 0.54321 0.7375
39 ADP 0.54321 0.759494
40 5X8 0.542169 0.821918
41 S4M 0.5375 0.8
42 SON 0.536585 0.753086
43 AN2 0.536585 0.75
44 A3S 0.536585 0.847222
45 PRX 0.535714 0.740741
46 NEC 0.531646 0.780822
47 M33 0.53012 0.728395
48 ADP MG 0.53012 0.75
49 ADX 0.53012 0.670455
50 0UM 0.527473 0.818182
51 A3T 0.52381 0.808219
52 ADP BEF 0.52381 0.731707
53 ACP 0.52381 0.7625
54 50T 0.52381 0.75
55 ATP 0.52381 0.759494
56 BEF ADP 0.52381 0.731707
57 SAI 0.523256 0.813333
58 SAH 0.523256 0.824324
59 G5A 0.523256 0.707865
60 ATF 0.522727 0.731707
61 A7D 0.518072 0.835616
62 AR6 0.517647 0.7375
63 APC 0.517647 0.753086
64 APR 0.517647 0.7375
65 AQP 0.517647 0.759494
66 5FA 0.517647 0.759494
67 ANP 0.517241 0.740741
68 GAP 0.517241 0.78481
69 S7M 0.516854 0.78481
70 7D7 0.514286 0.753425
71 Y3J 0.513889 0.736111
72 3AM 0.512821 0.766234
73 ADV 0.511628 0.731707
74 AD9 0.511628 0.740741
75 AGS 0.511628 0.722892
76 RBY 0.511628 0.731707
77 ADP PO3 0.511628 0.779221
78 SAP 0.511628 0.722892
79 5AL 0.511364 0.728395
80 EEM 0.511364 0.78481
81 ATP MG 0.505747 0.75
82 A5A 0.505618 0.655556
83 JB6 0.505263 0.73494
84 TAT 0.5 0.731707
85 SMM 0.5 0.756098
86 ACQ 0.5 0.7625
87 SAM 0.5 0.78481
88 ANP MG 0.5 0.722892
89 SSA 0.5 0.688889
90 SRP 0.5 0.775
91 4AD 0.494624 0.765432
92 LSS 0.494624 0.655914
93 52H 0.494505 0.634409
94 54H 0.494505 0.641304
95 VMS 0.494505 0.641304
96 AAT 0.494382 0.828947
97 A5D 0.494253 0.773333
98 A3P 0.493976 0.75641
99 TXA 0.489583 0.710843
100 DLL 0.489362 0.728395
101 AHX 0.489362 0.746988
102 62X 0.489362 0.756098
103 DAL AMP 0.48913 0.75
104 TSB 0.48913 0.648352
105 53H 0.48913 0.634409
106 A22 0.48913 0.75
107 5CA 0.48913 0.688889
108 MAP 0.48913 0.722892
109 ALF ADP 0.488889 0.722892
110 ADP ALF 0.488889 0.722892
111 3AD 0.486486 0.842857
112 YLP 0.485437 0.744186
113 KB1 0.484536 0.794872
114 K15 0.484211 0.775
115 OOB 0.483871 0.728395
116 8QN 0.483871 0.728395
117 5SV 0.483871 0.705882
118 ADP VO4 0.483516 0.75
119 VO4 ADP 0.483516 0.75
120 2AM 0.481013 0.75641
121 KAA 0.479167 0.703297
122 LAD 0.479167 0.780488
123 ADQ 0.478723 0.740741
124 PAJ 0.478723 0.697674
125 AMO 0.478723 0.753086
126 NSS 0.478723 0.688889
127 DSZ 0.478723 0.67033
128 QQX 0.475 0.682927
129 PTJ 0.474227 0.705882
130 SXZ 0.474227 0.7625
131 NB8 0.474227 0.72619
132 00A 0.473684 0.694118
133 NVA LMS 0.473684 0.673913
134 D3Y 0.473118 0.824324
135 YLC 0.471698 0.761905
136 YLB 0.471698 0.744186
137 2VA 0.471264 0.786667
138 XAH 0.47 0.761905
139 ADP BMA 0.46875 0.7625
140 3UK 0.46875 0.719512
141 LEU LMS 0.46875 0.655914
142 OAD 0.46875 0.719512
143 7D5 0.468354 0.725
144 GEK 0.468085 0.815789
145 25A 0.468085 0.759494
146 S8M 0.468085 0.792208
147 KH3 0.466019 0.7875
148 9SN 0.464646 0.686047
149 PR8 0.463918 0.771084
150 WAQ 0.463918 0.73494
151 P5A 0.463918 0.695652
152 GSU 0.463918 0.688889
153 OVE 0.463415 0.728395
154 A1R 0.463158 0.777778
155 IOT 0.462963 0.819277
156 ARG AMP 0.461538 0.8625
157 PAP 0.460674 0.746835
158 FYA 0.459184 0.772152
159 1ZZ 0.459184 0.681818
160 3OD 0.459184 0.719512
161 BIS 0.459184 0.73494
162 ME8 0.459184 0.72093
163 A2P 0.458824 0.74359
164 YLA 0.458716 0.744186
165 VRT 0.455556 0.826667
166 SO8 0.455556 0.776316
167 YSA 0.455446 0.67033
168 MYR AMP 0.454545 0.701149
169 AYB 0.454545 0.735632
170 A6D 0.453608 0.731707
171 CC5 0.452055 0.828571
172 QQY 0.451219 0.691358
173 ACK 0.451219 0.727273
174 2A5 0.449438 0.7625
175 3NZ 0.44898 0.792208
176 A A 0.44898 0.782051
177 PPS 0.445652 0.670455
178 YAP 0.445545 0.743902
179 FA5 0.445545 0.753086
180 7MD 0.442308 0.761905
181 4UU 0.442308 0.702381
182 TYR AMP 0.441176 0.753086
183 25L 0.44 0.75
184 4UV 0.436893 0.702381
185 AMP DBH 0.436893 0.740741
186 V3L 0.434783 0.759494
187 LAQ 0.433962 0.681818
188 SP1 0.433735 0.695122
189 RP1 0.433735 0.695122
190 ATP A A A 0.431373 0.769231
191 7D3 0.430233 0.707317
192 48N 0.429907 0.746988
193 LPA AMP 0.429907 0.701149
194 3D1 0.428571 0.808219
195 AFH 0.428571 0.717647
196 ATR 0.428571 0.734177
197 AR6 AR6 0.428571 0.759494
198 MTP 0.428571 0.717949
199 3L1 0.428571 0.808219
200 YLY 0.42735 0.735632
201 NAI 0.425926 0.694118
202 4UW 0.425926 0.678161
203 6V0 0.425926 0.705882
204 CMP 0.425287 0.74026
205 2BA 0.425287 0.730769
206 TAD 0.424528 0.697674
207 4YB 0.424528 0.673913
208 26A 0.423077 0.75
209 2FA 0.423077 0.8
210 6MD 0.423077 0.794521
211 LA8 ALF 3PG 0.422018 0.717647
212 ALF ADP 3PG 0.422018 0.717647
213 OMR 0.422018 0.674157
214 WSA 0.422018 0.677778
215 COD 0.421053 0.719101
216 AHZ 0.420561 0.701149
217 G3A 0.419048 0.768293
218 7C5 0.419048 0.828947
219 AP0 0.418182 0.686047
220 7MC 0.418182 0.744186
221 5F1 0.417722 0.767123
222 N0B 0.416667 0.744186
223 A2R 0.416667 0.75
224 G5P 0.415094 0.768293
225 NVA 2AD 0.413043 0.8
226 TXD 0.412844 0.714286
227 NXX 0.412844 0.731707
228 NAX 0.412844 0.729412
229 DND 0.412844 0.731707
230 GTA 0.411215 0.761905
231 7D4 0.411111 0.707317
232 A A A 0.41 0.772152
233 V1N 0.409524 0.759494
234 AF3 ADP 3PG 0.409091 0.717647
235 TXE 0.409091 0.714286
236 TYM 0.409091 0.753086
237 649 0.409091 0.659574
238 BTX 0.408696 0.724138
239 UPA 0.405405 0.714286
240 BT5 0.405172 0.715909
241 J1D 0.405172 0.708333
242 1DA 0.405063 0.830986
243 BS5 0.403509 0.706522
244 NOC 0.402597 0.774648
245 UP5 0.4 0.702381
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5K8V; Ligand: 6RE; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5k8v.bio1) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5K8V; Ligand: 6RE; Similar sites found: 54
This union binding pocket(no: 2) in the query (biounit: 5k8v.bio1) has 54 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2IVD FAD 0.005711 0.40132 1.38504
2 2G30 ALA ALA PHE 0.02076 0.40242 1.93798
3 2EG5 SAH 0.000201 0.52814 1.93906
4 3WQD PLP 999 0.04745 0.40005 1.93906
5 5DX9 T6P 0.02575 0.40007 2.21519
6 3VYW SAM 0.0004844 0.4857 2.27273
7 4RVG SAM 0.0009338 0.41967 2.49307
8 1T9D PYD 0.0418 0.41185 2.49307
9 4RVG TYD 0.001376 0.40986 2.49307
10 2WBP SIN 0.01414 0.41454 2.51397
11 2WBP ZZU 0.01414 0.41454 2.51397
12 2CBZ ATP 0.002252 0.48953 2.53165
13 3IA4 MTX 0.01611 0.43022 3.08642
14 3IX9 MTX 0.04023 0.40653 3.15789
15 4OBW SAM 0.003271 0.45403 3.50195
16 2I7C AAT 0.001288 0.43026 3.53357
17 5N53 8NB 0.02267 0.43853 3.58974
18 2VDV SAM 0.00002701 0.57288 3.65854
19 2GUE NAG 0.02013 0.41101 4.09836
20 3OU2 SAH 0.00005217 0.51286 4.12844
21 4RL4 PPV 0.03454 0.4138 4.24528
22 5JE8 NAD 0.01271 0.414 4.30464
23 1Y8Q ATP 0.0003038 0.48325 5.20231
24 5XVQ SAH 0.004561 0.43409 5.6338
25 4ELG 52J 0.01674 0.41115 6.0241
26 4ELG 52I 0.02155 0.40119 6.0241
27 3HVJ 705 0.00001746 0.41331 6.78733
28 5WGR PM7 0.03512 0.40385 6.92521
29 4RHY 3QG 0.03637 0.40047 6.96517
30 5MW4 5JU 0.00001665 0.41986 7.18563
31 5HJM MTA 0.000009246 0.57142 7.67045
32 4RDH AMP 0.002305 0.4694 7.98611
33 3EZ2 ADP 0.03451 0.42345 9.41828
34 5JJR SAH 0.00006315 0.53696 9.69529
35 3OFK SAH 0.0004344 0.48391 10.1852
36 4DMG SAM 0.0004666 0.5147 10.2493
37 3EGV SAH 0.000002561 0.61096 11.0236
38 3TLJ SAH 0.00003301 0.53041 11.6343
39 1XDS SAM 0.0003821 0.51382 12.2995
40 3IVV ASP GLU VAL THR SER THR THR SER SER SER 0.03935 0.42413 13.1034
41 4QTU SAM 0.00003943 0.54153 14.8148
42 4M73 SAH 0.00003961 0.4004 14.8368
43 1OBB NAD 0.0167 0.40614 15.2355
44 3GDH SAH 0.00002825 0.52886 15.3527
45 1HGX 5GP 0.03358 0.42411 15.847
46 3EGI ADP 0.00008657 0.57395 17.9612
47 4C4A SAH 0.00000000265 0.42674 20.4986
48 3X0D SAH 0.0000000006509 0.44358 21.3296
49 4X60 SFG 0.0000002083 0.55499 33.241
50 4X60 3XV 0.0000002695 0.54713 33.241
51 4M38 SAH 0.00000002751 0.41756 35.5685
52 4LWP SAH 0.00000000003125 0.45784 44.3213
53 4Y2H SAH 0.000000000000009992 0.65979 48.0114
54 4Y2H 49K 0.0000000000001128 0.63544 48.0114
Pocket No.: 3; Query (leader) PDB : 5K8V; Ligand: 6RE; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5k8v.bio1) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5K8V; Ligand: 6RE; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5k8v.bio1) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Feedback