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 39 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 (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 28 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 5DSX ic50 = 10 nM 5EW C26 H24 Cl N7 O Cc1cc2ccc(....
7 5MW3 ic50 = 190 nM 5JJ C20 H17 Cl2 N3 CCC#CCN(c1....
8 5MW4 Ki = 0.002 nM 5JU C32 H36 Cl N9 O2 S Cc1c(cccn1....
9 5DTM ic50 = 320 uM 5F4 C13 H10 Cl2 N2 O2 CNC(=O)c1c....
10 4WVL - 3US C33 H51 N9 O5 CC(C)N(CCC....
11 3QOW - SAM C15 H22 N6 O5 S C[S@@+](CC....
12 3QOX Ki = 0.27 uM SAH C14 H20 N6 O5 S c1nc(c2c(n....
13 1NW3 - SAM C15 H22 N6 O5 S C[S@@+](CC....
14 4EK9 Ki = 38000 nM EP4 C12 H18 N6 O3 CN(C)C[C@@....
50% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 22 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 5DSX ic50 = 10 nM 5EW C26 H24 Cl N7 O Cc1cc2ccc(....
7 5MW3 ic50 = 190 nM 5JJ C20 H17 Cl2 N3 CCC#CCN(c1....
8 5MW4 Ki = 0.002 nM 5JU C32 H36 Cl N9 O2 S Cc1c(cccn1....
9 5DTM ic50 = 320 uM 5F4 C13 H10 Cl2 N2 O2 CNC(=O)c1c....
10 4WVL - 3US C33 H51 N9 O5 CC(C)N(CCC....
11 3QOW - SAM C15 H22 N6 O5 S C[S@@+](CC....
12 3QOX Ki = 0.27 uM SAH C14 H20 N6 O5 S c1nc(c2c(n....
13 1NW3 - SAM C15 H22 N6 O5 S C[S@@+](CC....
14 4EK9 Ki = 38000 nM EP4 C12 H18 N6 O3 CN(C)C[C@@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: EP4; Similar ligands found: 262
No: Ligand ECFP6 Tc MDL keys Tc
1 EP4 1 1
2 RAB 0.754386 0.852941
3 ADN 0.754386 0.852941
4 XYA 0.754386 0.852941
5 5N5 0.728814 0.880597
6 MAO 0.720588 0.807692
7 5CD 0.716667 0.865672
8 A4D 0.716667 0.852941
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 A 0.623188 0.773333
19 ZAS 0.623188 0.819444
20 AMP 0.623188 0.773333
21 LMS 0.623188 0.682353
22 A2D 0.619718 0.753247
23 J7C 0.619718 0.797297
24 ABM 0.619718 0.8
25 SRA 0.614286 0.734177
26 GJV 0.611111 0.776316
27 AOC 0.605634 0.855072
28 DSH 0.605634 0.821918
29 62X 0.60241 0.866667
30 A3N 0.597222 0.869565
31 5AS 0.594595 0.681818
32 BA3 0.581081 0.753247
33 A12 0.581081 0.725
34 AP2 0.581081 0.725
35 M33 0.578947 0.789474
36 B4P 0.573333 0.753247
37 AP5 0.573333 0.753247
38 ADP 0.573333 0.753247
39 7D7 0.571429 0.771429
40 Y3J 0.569231 0.779412
41 A7D 0.565789 0.830986
42 AT4 0.565789 0.725
43 SON 0.565789 0.725
44 AN2 0.565789 0.74359
45 PRX 0.564103 0.779221
46 APR 0.564103 0.753247
47 AR6 0.564103 0.753247
48 SAM 0.5625 0.826667
49 AU1 0.558442 0.734177
50 ADX 0.558442 0.682353
51 CA0 0.558442 0.734177
52 K15 0.55814 0.815789
53 26A 0.552239 0.897059
54 5X8 0.551282 0.842857
55 HEJ 0.551282 0.753247
56 ACP 0.551282 0.734177
57 ATP 0.551282 0.753247
58 50T 0.551282 0.74359
59 SFG 0.551282 0.802817
60 AQP 0.544304 0.753247
61 5FA 0.544304 0.753247
62 APC 0.544304 0.725
63 S7M 0.542169 0.779221
64 SMM 0.542169 0.818182
65 3AM 0.541667 0.736842
66 NEC 0.540541 0.826087
67 AD9 0.5375 0.734177
68 ADV 0.5375 0.725
69 A5D 0.5375 0.816901
70 RBY 0.5375 0.725
71 ADP PO3 0.5375 0.773333
72 AGS 0.5375 0.716049
73 SAP 0.5375 0.716049
74 EEM 0.536585 0.826667
75 5AL 0.536585 0.766234
76 SAH 0.530864 0.819444
77 SAI 0.530864 0.808219
78 G5A 0.530864 0.662921
79 A5A 0.53012 0.686047
80 T99 0.52439 0.725
81 GAP 0.52439 0.75641
82 TAT 0.52439 0.725
83 ACQ 0.52439 0.734177
84 ANP 0.52439 0.734177
85 GEK 0.523256 0.786667
86 KB1 0.522222 0.789474
87 A3G 0.52 0.830986
88 AAT 0.518072 0.776316
89 54H 0.517647 0.709302
90 52H 0.517647 0.701149
91 VMS 0.517647 0.709302
92 3AD 0.514706 0.838235
93 ADP ALF 0.511905 0.716049
94 ATF 0.511905 0.725
95 ALF ADP 0.511905 0.716049
96 53H 0.511628 0.701149
97 DAL AMP 0.511628 0.766234
98 A22 0.511628 0.74359
99 TSB 0.511628 0.678161
100 2AM 0.506849 0.727273
101 ADP VO4 0.505882 0.74359
102 SSA 0.505882 0.644444
103 6YZ 0.505882 0.734177
104 VO4 ADP 0.505882 0.74359
105 SRP 0.505882 0.725
106 9ZD 0.505747 0.772152
107 5SV 0.505747 0.740741
108 8QN 0.505747 0.766234
109 9ZA 0.505747 0.772152
110 9X8 0.505618 0.7375
111 OAD 0.505618 0.75641
112 A3P 0.5 0.75
113 A3R 0.5 0.728395
114 A1R 0.5 0.728395
115 LSS 0.5 0.704545
116 PAJ 0.5 0.775
117 0UM 0.5 0.813333
118 CC5 0.5 0.850746
119 KH3 0.5 0.805195
120 3OD 0.494505 0.75641
121 JB6 0.494505 0.707317
122 NVA LMS 0.494382 0.659341
123 AHX 0.494382 0.698795
124 00A 0.494382 0.707317
125 5CA 0.494253 0.644444
126 8X1 0.494253 0.641304
127 MAP 0.494253 0.716049
128 A3T 0.493827 0.855072
129 N8M 0.493151 0.984848
130 7D5 0.493151 0.696203
131 MTP 0.492754 0.780822
132 LEU LMS 0.488889 0.696629
133 S8M 0.488636 0.786667
134 25A 0.488636 0.753247
135 OOB 0.488636 0.74359
136 A3S 0.4875 0.816901
137 OVE 0.486842 0.7
138 LAD 0.483516 0.710843
139 KAA 0.483516 0.641304
140 4AD 0.483146 0.716049
141 AMO 0.483146 0.725
142 DSZ 0.483146 0.644444
143 NSS 0.483146 0.644444
144 ADQ 0.483146 0.734177
145 QQX 0.48 0.675
146 ME8 0.478261 0.756098
147 9K8 0.478261 0.641304
148 PTJ 0.478261 0.78481
149 BIS 0.478261 0.707317
150 SXZ 0.478261 0.851351
151 TXA 0.478261 0.746835
152 1ZZ 0.478261 0.714286
153 DLL 0.477778 0.74359
154 RP1 0.473684 0.708861
155 QQY 0.473684 0.683544
156 SP1 0.473684 0.708861
157 ACK 0.473684 0.72
158 MYR AMP 0.473118 0.714286
159 3UK 0.472527 0.734177
160 A6D 0.472527 0.725
161 ADP BMA 0.472527 0.734177
162 3D1 0.471429 0.777778
163 3L1 0.471429 0.777778
164 WAQ 0.467391 0.707317
165 GSU 0.467391 0.644444
166 P5A 0.467391 0.634409
167 PR8 0.467391 0.702381
168 A A 0.467391 0.753247
169 B5V 0.467391 0.725
170 6MD 0.464789 0.867647
171 2FA 0.464789 0.794521
172 PAP 0.464286 0.74026
173 B5Y 0.463158 0.7375
174 B5M 0.463158 0.7375
175 CMP 0.4625 0.756757
176 A2P 0.4625 0.736842
177 2BA 0.4625 0.746667
178 FYA 0.462366 0.74359
179 NB8 0.462366 0.698795
180 F0P 0.460784 0.8
181 5F1 0.458333 0.760563
182 XAH 0.458333 0.694118
183 2VA 0.457831 0.884058
184 25L 0.457447 0.74359
185 V3L 0.453488 0.753247
186 9SN 0.452632 0.698795
187 7D3 0.45 0.679012
188 G3A 0.44898 0.698795
189 PPS 0.448276 0.662791
190 8PZ 0.447917 0.644444
191 FA5 0.447917 0.725
192 YAP 0.447917 0.716049
193 ATP A A A 0.447917 0.763158
194 NVA 2AD 0.447059 0.810811
195 YLP 0.445545 0.697674
196 48N 0.445545 0.719512
197 AR6 AR6 0.444444 0.753247
198 1DA 0.444444 0.852941
199 GA7 0.444444 0.769231
200 G5P 0.444444 0.698795
201 YSA 0.443299 0.644444
202 NOC 0.442857 0.768116
203 VRT 0.44186 0.821918
204 SO8 0.44186 0.871429
205 DQV 0.44 0.74359
206 GTA 0.44 0.714286
207 AMP DBH 0.438776 0.734177
208 TYR AMP 0.438776 0.716049
209 4UV 0.438776 0.716049
210 OMR 0.436893 0.705882
211 3NZ 0.43617 0.810811
212 AHZ 0.435644 0.694118
213 2A5 0.435294 0.691358
214 7C5 0.434343 0.753247
215 A2R 0.433333 0.74359
216 AP0 0.432692 0.719512
217 YLB 0.432692 0.717647
218 YLC 0.432692 0.714286
219 ATR 0.430233 0.727273
220 4UU 0.43 0.716049
221 AFH 0.43 0.690476
222 ARG AMP 0.43 0.686047
223 7MD 0.43 0.694118
224 7D4 0.428571 0.679012
225 D3Y 0.428571 0.794521
226 6V0 0.427184 0.719512
227 DND 0.427184 0.725
228 4UW 0.427184 0.731707
229 NAX 0.427184 0.682353
230 TXD 0.427184 0.75
231 NAI 0.427184 0.707317
232 NXX 0.427184 0.725
233 TAD 0.425743 0.690476
234 4YB 0.425743 0.630435
235 ARJ 0.424658 0.753623
236 TXE 0.423077 0.728395
237 LAQ 0.421569 0.674419
238 7MC 0.419048 0.697674
239 LPA AMP 0.417476 0.674419
240 CNA 0.416667 0.725
241 AYB 0.416667 0.709302
242 UP5 0.413462 0.716049
243 6CR 0.413333 0.783784
244 F2R 0.412844 0.678161
245 101 0.4125 0.696203
246 AV2 0.411111 0.6875
247 A A A 0.410526 0.74359
248 WSA 0.409524 0.651685
249 TYM 0.409524 0.725
250 649 0.409524 0.617021
251 AF3 ADP 3PG 0.409524 0.690476
252 COD 0.409091 0.732558
253 T5A 0.407407 0.678161
254 ADJ 0.407407 0.705882
255 YLA 0.407407 0.678161
256 UPA 0.40566 0.707317
257 4TC 0.40566 0.698795
258 8Q2 0.40566 0.623656
259 AFX 0.405405 0.68
260 IVH 0.404762 0.769231
261 BS5 0.40367 0.62766
262 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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