Receptor
PDB id Resolution Class Description Source Keywords
4EK9 2.5 Å EC: 2.1.1.43 CRYSTAL STRUCTURE OF DOT1L IN COMPLEX WITH EPZ000004 HOMO SAPIENS METHYLTRANSFERASE TRANSFERASE TRANSFERASE-TRANSFERASE INHICOMPLEX
Ref.: CONFORMATIONAL ADAPTATION DRIVES POTENT, SELECTIVE DURABLE INHIBITION OF THE HUMAN PROTEIN METHYLTRANS DOT1L. CHEM.BIOL.DRUG DES. V. 80 971 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EP4 A:501;
Valid;
none;
Ki = 38000 nM
294.31 C12 H18 N6 O3 CN(C)...
GOL A:504;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
SO4 A:502;
A:503;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3QOX 2.3 Å EC: 2.1.1.43 DOT1L STRUCTURE IN COMPLEX WITH SAH HOMO SAPIENS H3K79 METHYLATION TRANSFERASE
Ref.: CHEMOGENETIC ANALYSIS OF HUMAN PROTEIN METHYLTRANSF CHEM.BIOL.DRUG DES. V. 78 199 2011
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 40 families.
1 3QOW - SAM C15 H22 N6 O5 S C[S@@+](CC....
2 3QOX Ki = 0.27 uM SAH C14 H20 N6 O5 S c1nc(c2c(n....
3 1NW3 - SAM C15 H22 N6 O5 S C[S@@+](CC....
4 4EK9 Ki = 38000 nM EP4 C12 H18 N6 O3 CN(C)C[C@@....
70% Homology Family (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 29 families.
1 5MVS ic50 = 190 nM 5JJ C20 H17 Cl2 N3 CCC#CCN(c1....
2 5DTR ic50 = 39 uM 5F7 C17 H14 Cl2 N2 O CN(c1ccc2c....
3 5DT2 ic50 = 150 nM 5EV C26 H23 N5 O Cc1cc2ccc(....
4 5DRY ic50 = 20 nM 5EK C24 H18 Cl2 N8 O2 c1ccc(c(c1....
5 3SR4 Ki = 0.29 uM TT8 C15 H22 N6 O5 S CNc1c2c(nc....
6 6TEN ic50 = 0.00017 uM N5K C23 H19 Cl F2 N8 O5 S COc1nc(nc(....
7 6TE6 ic50 = 0.27 uM N4W C23 H20 Cl N5 O2 S CS(=O)(=O)....
8 5DSX ic50 = 10 nM 5EW C26 H24 Cl N7 O Cc1cc2ccc(....
9 5MW3 ic50 = 190 nM 5JJ C20 H17 Cl2 N3 CCC#CCN(c1....
10 5MW4 Ki = 0.002 nM 5JU C32 H36 Cl N9 O2 S Cc1c(cccn1....
11 6TEL ic50 = 0.00011 uM N4Z C28 H27 Cl F2 N8 O5 S COc1nc(nc(....
12 5DTM ic50 = 320 uM 5F4 C13 H10 Cl2 N2 O2 CNC(=O)c1c....
13 4WVL - 3US C33 H51 N9 O5 CC(C)N(CCC....
14 3QOW - SAM C15 H22 N6 O5 S C[S@@+](CC....
15 3QOX Ki = 0.27 uM SAH C14 H20 N6 O5 S c1nc(c2c(n....
16 1NW3 - SAM C15 H22 N6 O5 S C[S@@+](CC....
17 4EK9 Ki = 38000 nM EP4 C12 H18 N6 O3 CN(C)C[C@@....
50% Homology Family (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 23 families.
1 5MVS ic50 = 190 nM 5JJ C20 H17 Cl2 N3 CCC#CCN(c1....
2 5DTR ic50 = 39 uM 5F7 C17 H14 Cl2 N2 O CN(c1ccc2c....
3 5DT2 ic50 = 150 nM 5EV C26 H23 N5 O Cc1cc2ccc(....
4 5DRY ic50 = 20 nM 5EK C24 H18 Cl2 N8 O2 c1ccc(c(c1....
5 3SR4 Ki = 0.29 uM TT8 C15 H22 N6 O5 S CNc1c2c(nc....
6 6TEN ic50 = 0.00017 uM N5K C23 H19 Cl F2 N8 O5 S COc1nc(nc(....
7 6TE6 ic50 = 0.27 uM N4W C23 H20 Cl N5 O2 S CS(=O)(=O)....
8 5DSX ic50 = 10 nM 5EW C26 H24 Cl N7 O Cc1cc2ccc(....
9 5MW3 ic50 = 190 nM 5JJ C20 H17 Cl2 N3 CCC#CCN(c1....
10 5MW4 Ki = 0.002 nM 5JU C32 H36 Cl N9 O2 S Cc1c(cccn1....
11 6TEL ic50 = 0.00011 uM N4Z C28 H27 Cl F2 N8 O5 S COc1nc(nc(....
12 5DTM ic50 = 320 uM 5F4 C13 H10 Cl2 N2 O2 CNC(=O)c1c....
13 4WVL - 3US C33 H51 N9 O5 CC(C)N(CCC....
14 3QOW - SAM C15 H22 N6 O5 S C[S@@+](CC....
15 3QOX Ki = 0.27 uM SAH C14 H20 N6 O5 S c1nc(c2c(n....
16 1NW3 - SAM C15 H22 N6 O5 S C[S@@+](CC....
17 4EK9 Ki = 38000 nM EP4 C12 H18 N6 O3 CN(C)C[C@@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: EP4; Similar ligands found: 284
No: Ligand ECFP6 Tc MDL keys Tc
1 EP4 1 1
2 XYA 0.754386 0.852941
3 RAB 0.754386 0.852941
4 ADN 0.754386 0.852941
5 5N5 0.728814 0.880597
6 MAO 0.720588 0.807692
7 A4D 0.716667 0.852941
8 5CD 0.716667 0.865672
9 M2T 0.698413 0.941176
10 MHZ 0.690141 0.807692
11 MTA 0.6875 0.939394
12 DTA 0.671875 0.816901
13 3DH 0.666667 0.882353
14 SA8 0.662162 0.875
15 6RE 0.637681 0.786667
16 S4M 0.633803 0.818182
17 5AD 0.633333 0.830769
18 AMP 0.623188 0.773333
19 ZAS 0.623188 0.819444
20 A 0.623188 0.773333
21 LMS 0.623188 0.682353
22 ABM 0.619718 0.8
23 J7C 0.619718 0.797297
24 45A 0.619718 0.8
25 A2D 0.619718 0.753247
26 SRA 0.614286 0.734177
27 GJV 0.611111 0.776316
28 AOC 0.605634 0.855072
29 DSH 0.605634 0.821918
30 62X 0.60241 0.866667
31 A3N 0.597222 0.869565
32 5AS 0.594595 0.681818
33 AP2 0.581081 0.725
34 A12 0.581081 0.725
35 BA3 0.581081 0.753247
36 M33 0.578947 0.789474
37 ADP 0.573333 0.753247
38 B4P 0.573333 0.753247
39 AP5 0.573333 0.753247
40 7D7 0.571429 0.771429
41 Y3J 0.569231 0.779412
42 AN2 0.565789 0.74359
43 SON 0.565789 0.725
44 A7D 0.565789 0.830986
45 ADP MG 0.565789 0.773333
46 AT4 0.565789 0.725
47 AR6 0.564103 0.753247
48 PRX 0.564103 0.779221
49 APR 0.564103 0.753247
50 SAM 0.5625 0.826667
51 ADX 0.558442 0.682353
52 AU1 0.558442 0.734177
53 CA0 0.558442 0.734177
54 K15 0.55814 0.815789
55 26A 0.552239 0.897059
56 SFG 0.551282 0.802817
57 H1Q 0.551282 0.763158
58 50T 0.551282 0.74359
59 ATP 0.551282 0.753247
60 KG4 0.551282 0.734177
61 HEJ 0.551282 0.753247
62 ACP 0.551282 0.734177
63 5X8 0.551282 0.842857
64 5FA 0.544304 0.753247
65 APC 0.544304 0.725
66 AQP 0.544304 0.753247
67 S7M 0.542169 0.779221
68 SMM 0.542169 0.818182
69 3AM 0.541667 0.736842
70 NEC 0.540541 0.826087
71 AD9 0.5375 0.734177
72 SAP 0.5375 0.716049
73 RBY 0.5375 0.725
74 APC MG 0.5375 0.753247
75 ADP PO3 0.5375 0.773333
76 ATP MG 0.5375 0.773333
77 ADV 0.5375 0.725
78 AGS 0.5375 0.716049
79 A5D 0.5375 0.816901
80 5AL 0.536585 0.766234
81 EEM 0.536585 0.826667
82 8LE 0.536585 0.782051
83 SAI 0.530864 0.808219
84 SAH 0.530864 0.819444
85 G5A 0.530864 0.662921
86 A5A 0.53012 0.686047
87 TAT 0.52439 0.725
88 GAP 0.52439 0.75641
89 T99 0.52439 0.725
90 ANP 0.52439 0.734177
91 ACQ 0.52439 0.734177
92 8LH 0.52381 0.769231
93 GEK 0.523256 0.786667
94 KB1 0.522222 0.789474
95 A3G 0.52 0.830986
96 AAT 0.518072 0.776316
97 HQG 0.517647 0.74359
98 54H 0.517647 0.709302
99 VMS 0.517647 0.709302
100 52H 0.517647 0.701149
101 3AD 0.514706 0.838235
102 ALF ADP 0.511905 0.716049
103 ATF 0.511905 0.725
104 ADP ALF 0.511905 0.716049
105 TSB 0.511628 0.678161
106 8LQ 0.511628 0.769231
107 A22 0.511628 0.74359
108 53H 0.511628 0.701149
109 DAL AMP 0.511628 0.766234
110 2AM 0.506849 0.727273
111 6YZ 0.505882 0.734177
112 ADP VO4 0.505882 0.74359
113 SSA 0.505882 0.644444
114 SRP 0.505882 0.725
115 VO4 ADP 0.505882 0.74359
116 5SV 0.505747 0.740741
117 9ZD 0.505747 0.772152
118 9ZA 0.505747 0.772152
119 8QN 0.505747 0.766234
120 9X8 0.505618 0.7375
121 OAD 0.505618 0.75641
122 A3R 0.5 0.728395
123 A3P 0.5 0.75
124 KH3 0.5 0.805195
125 CC5 0.5 0.850746
126 A1R 0.5 0.728395
127 N5O 0.5 0.791667
128 LSS 0.5 0.704545
129 PAJ 0.5 0.775
130 0UM 0.5 0.813333
131 JB6 0.494505 0.707317
132 3OD 0.494505 0.75641
133 AHX 0.494382 0.698795
134 NVA LMS 0.494382 0.659341
135 00A 0.494382 0.707317
136 MAP 0.494253 0.716049
137 8X1 0.494253 0.641304
138 5CA 0.494253 0.644444
139 A3T 0.493827 0.855072
140 N8M 0.493151 0.984848
141 7D5 0.493151 0.696203
142 MTP 0.492754 0.780822
143 LEU LMS 0.488889 0.696629
144 S8M 0.488636 0.786667
145 OZV 0.488636 0.753247
146 OOB 0.488636 0.74359
147 25A 0.488636 0.753247
148 A3S 0.4875 0.816901
149 N5A 0.487179 0.788732
150 OVE 0.486842 0.7
151 KAA 0.483516 0.641304
152 LAD 0.483516 0.710843
153 AMO 0.483146 0.725
154 4AD 0.483146 0.716049
155 ADQ 0.483146 0.734177
156 DSZ 0.483146 0.644444
157 NSS 0.483146 0.644444
158 QQX 0.48 0.675
159 HZ2 0.479592 0.779221
160 1ZZ 0.478261 0.714286
161 SXZ 0.478261 0.851351
162 PTJ 0.478261 0.78481
163 9K8 0.478261 0.641304
164 ME8 0.478261 0.756098
165 BIS 0.478261 0.707317
166 TXA 0.478261 0.746835
167 DLL 0.477778 0.74359
168 OZP 0.474747 0.8
169 QQY 0.473684 0.683544
170 RP1 0.473684 0.708861
171 SP1 0.473684 0.708861
172 ACK 0.473684 0.72
173 MYR AMP 0.473118 0.714286
174 ADP BMA 0.472527 0.734177
175 3UK 0.472527 0.734177
176 A6D 0.472527 0.725
177 3L1 0.471429 0.777778
178 3D1 0.471429 0.777778
179 HY8 0.47 0.779221
180 WAQ 0.467391 0.707317
181 P5A 0.467391 0.634409
182 PR8 0.467391 0.702381
183 GSU 0.467391 0.644444
184 A A 0.467391 0.753247
185 B5V 0.467391 0.725
186 2FA 0.464789 0.794521
187 6MD 0.464789 0.867647
188 PAP 0.464286 0.74026
189 B5M 0.463158 0.7375
190 B5Y 0.463158 0.7375
191 A2P 0.4625 0.736842
192 CMP 0.4625 0.756757
193 2BA 0.4625 0.746667
194 NB8 0.462366 0.698795
195 FYA 0.462366 0.74359
196 F0P 0.460784 0.8
197 XAH 0.458333 0.694118
198 5F1 0.458333 0.760563
199 2VA 0.457831 0.884058
200 25L 0.457447 0.74359
201 V3L 0.453488 0.753247
202 9SN 0.452632 0.698795
203 7D3 0.45 0.679012
204 G3A 0.44898 0.698795
205 PPS 0.448276 0.662791
206 FA5 0.447917 0.725
207 8PZ 0.447917 0.644444
208 YAP 0.447917 0.716049
209 ATP A 0.447917 0.763158
210 ATP A A A 0.447917 0.763158
211 NVA 2AD 0.447059 0.810811
212 YLP 0.445545 0.697674
213 48N 0.445545 0.719512
214 GA7 0.444444 0.769231
215 AR6 AR6 0.444444 0.753247
216 G5P 0.444444 0.698795
217 1DA 0.444444 0.852941
218 B1U 0.443299 0.610526
219 YSA 0.443299 0.644444
220 NOC 0.442857 0.768116
221 SO8 0.44186 0.871429
222 VRT 0.44186 0.821918
223 DQV 0.44 0.74359
224 GTA 0.44 0.714286
225 AMP DBH 0.438776 0.734177
226 TYR AMP 0.438776 0.716049
227 4UV 0.438776 0.716049
228 OMR 0.436893 0.705882
229 3NZ 0.43617 0.810811
230 AHZ 0.435644 0.694118
231 2A5 0.435294 0.691358
232 7C5 0.434343 0.753247
233 A2R 0.433333 0.74359
234 AP0 0.432692 0.719512
235 YLB 0.432692 0.717647
236 YLC 0.432692 0.714286
237 ATR 0.430233 0.727273
238 7MD 0.43 0.694118
239 ARG AMP 0.43 0.686047
240 4UU 0.43 0.716049
241 AFH 0.43 0.690476
242 D3Y 0.428571 0.794521
243 7D4 0.428571 0.679012
244 NXX 0.427184 0.725
245 TXD 0.427184 0.75
246 NAI 0.427184 0.707317
247 NAX 0.427184 0.682353
248 4UW 0.427184 0.731707
249 DND 0.427184 0.725
250 6V0 0.427184 0.719512
251 TAD 0.425743 0.690476
252 4YB 0.425743 0.630435
253 ARJ 0.424658 0.753623
254 TXE 0.423077 0.728395
255 N37 0.423077 0.76
256 LAQ 0.421569 0.674419
257 7MC 0.419048 0.697674
258 ERJ 0.417722 0.785714
259 KOY 0.417476 0.783784
260 LPA AMP 0.417476 0.674419
261 CNA 0.416667 0.725
262 AYB 0.416667 0.709302
263 UP5 0.413462 0.716049
264 6CR 0.413333 0.783784
265 F2R 0.412844 0.678161
266 101 0.4125 0.696203
267 AV2 0.411111 0.6875
268 A A A 0.410526 0.74359
269 AF3 ADP 3PG 0.409524 0.690476
270 WSA 0.409524 0.651685
271 649 0.409524 0.617021
272 TYM 0.409524 0.725
273 COD 0.409091 0.732558
274 YLA 0.407407 0.678161
275 T5A 0.407407 0.678161
276 ADJ 0.407407 0.705882
277 J4G 0.40625 0.716049
278 UPA 0.40566 0.707317
279 8Q2 0.40566 0.623656
280 4TC 0.40566 0.698795
281 AFX 0.405405 0.68
282 IVH 0.404762 0.769231
283 BS5 0.40367 0.62766
284 A4P 0.401869 0.662921
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3QOX; Ligand: SAH; 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: 3qox.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
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