Receptor
PDB id Resolution Class Description Source Keywords
5CCM 2.3 Å EC: 2.1.1.43 CRYSTAL STRUCTURE OF SMYD3 WITH SAM AND EPZ030456 HOMO SAPIENS PROTEIN-INHIBITOR COMPLEX METHYLTRANSFERASE EPIGENETICS DDISCOVERY TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: NOVEL OXINDOLE SULFONAMIDES AND SULFAMIDES: EPZ0316 FIRST ORALLY BIOAVAILABLE SMALL MOLECULE SMYD3 INHI ACS MED.CHEM.LETT. V. 7 134 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SAM A:504;
Valid;
none;
submit data
398.437 C15 H22 N6 O5 S C[S@@...
ZN A:502;
A:501;
A:503;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
4ZX A:505;
Valid;
none;
ic50 = 4 nM
572.119 C28 H34 Cl N5 O4 S c1ccc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5CCM 2.3 Å EC: 2.1.1.43 CRYSTAL STRUCTURE OF SMYD3 WITH SAM AND EPZ030456 HOMO SAPIENS PROTEIN-INHIBITOR COMPLEX METHYLTRANSFERASE EPIGENETICS DDISCOVERY TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: NOVEL OXINDOLE SULFONAMIDES AND SULFAMIDES: EPZ0316 FIRST ORALLY BIOAVAILABLE SMALL MOLECULE SMYD3 INHI ACS MED.CHEM.LETT. V. 7 134 2016
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 36 families.
1 3PDN - SFG C15 H23 N7 O5 c1nc(c2c(n....
2 5CCM ic50 = 4 nM 4ZX C28 H34 Cl N5 O4 S c1ccc(cc1)....
3 5CCL - 4ZW C14 H17 N3 O2 c1cc2c(cc1....
4 5EX3 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
5 3RU0 - SFG C15 H23 N7 O5 c1nc(c2c(n....
6 5HI7 Ki = 14 nM 62X C19 H32 N8 O5 CN(C)CCCN(....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 26 families.
1 3PDN - SFG C15 H23 N7 O5 c1nc(c2c(n....
2 5CCM ic50 = 4 nM 4ZX C28 H34 Cl N5 O4 S c1ccc(cc1)....
3 5CCL - 4ZW C14 H17 N3 O2 c1cc2c(cc1....
4 5EX3 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
5 3RU0 - SFG C15 H23 N7 O5 c1nc(c2c(n....
6 5HI7 Ki = 14 nM 62X C19 H32 N8 O5 CN(C)CCCN(....
50% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 22 families.
1 5CCM ic50 = 4 nM 4ZX C28 H34 Cl N5 O4 S c1ccc(cc1)....
2 5CCL - 4ZW C14 H17 N3 O2 c1cc2c(cc1....
3 5EX3 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
4 3RU0 - SFG C15 H23 N7 O5 c1nc(c2c(n....
5 3QWV - SAH C14 H20 N6 O5 S c1nc(c2c(n....
6 3QWW - SFG C15 H23 N7 O5 c1nc(c2c(n....
7 4WUY ic50 < 15 nM 3UJ C36 H42 N6 O Cc1cn(c2c1....
8 5ARF ic50 = 0.8 uM I9H C22 H21 Cl F2 N6 O3 CCN([C@H]1....
9 5KJM ic50 = 0.065 uM 6TM C32 H37 Cl2 N7 O c1ccc(c(c1....
10 3TG4 - SAM C15 H22 N6 O5 S C[S@@+](CC....
11 5ARG ic50 = 27 nM H41 C22 H20 Cl2 F2 N6 O3 CCN([C@H]1....
12 5KJK ic50 = 0.012 uM 6T1 C30 H34 Cl2 N4 O2 c1ccc(c(c1....
13 3S7B ic50 = 0.12 uM NH5 C29 H38 Cl2 N4 O4 c1cc(c(cc1....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SAM; Similar ligands found: 192
No: Ligand ECFP6 Tc MDL keys Tc
1 SAM 1 1
2 SMM 0.792683 0.96
3 S4M 0.6875 0.909091
4 S7M 0.670455 0.945946
5 M2T 0.636364 0.878378
6 GEK 0.612903 0.931507
7 SAI 0.571429 0.878378
8 XYA 0.565789 0.773333
9 ADN 0.565789 0.773333
10 RAB 0.565789 0.773333
11 5CD 0.564103 0.783784
12 EP4 0.5625 0.826667
13 SA8 0.56044 0.945205
14 SFG 0.555556 0.875
15 5X8 0.555556 0.888889
16 5N5 0.551282 0.773333
17 A4D 0.544304 0.797297
18 EEM 0.542553 0.945946
19 SAH 0.537634 0.916667
20 DTA 0.536585 0.789474
21 62X 0.535354 0.884615
22 MTA 0.53012 0.875
23 3DH 0.517647 0.849315
24 AMP MG 0.511364 0.710843
25 5AL 0.510417 0.743902
26 VMS 0.510204 0.673913
27 54H 0.510204 0.673913
28 0UM 0.51 0.857143
29 A 0.505747 0.707317
30 AMP 0.505747 0.707317
31 ABM 0.505618 0.753086
32 A5A 0.505155 0.688889
33 DAL AMP 0.50505 0.765432
34 NVA LMS 0.504951 0.725275
35 K15 0.5 0.883117
36 6RE 0.5 0.78481
37 5AD 0.5 0.75
38 SSA 0.5 0.684783
39 SON 0.5 0.746988
40 SRP 0.5 0.746988
41 LSS 0.49505 0.706522
42 CA0 0.494624 0.714286
43 A12 0.494505 0.705882
44 AP2 0.494505 0.705882
45 ME8 0.490385 0.841463
46 5CA 0.49 0.684783
47 TSB 0.49 0.681319
48 53H 0.49 0.666667
49 ACP 0.489362 0.694118
50 5AS 0.48913 0.648936
51 ADP 0.48913 0.690476
52 A2D 0.488889 0.690476
53 J7C 0.488889 0.772152
54 ZAS 0.488636 0.769231
55 8QN 0.485149 0.743902
56 GAP 0.484536 0.73494
57 AN2 0.483871 0.682353
58 A3S 0.483871 0.813333
59 A7D 0.483871 0.851351
60 GJV 0.483516 0.775
61 SRA 0.483146 0.694118
62 LAD 0.480769 0.752941
63 KAA 0.480769 0.698925
64 GSU 0.480769 0.722222
65 AMO 0.480392 0.746988
66 DSZ 0.480392 0.703297
67 52H 0.48 0.666667
68 ADP MG 0.478723 0.702381
69 M33 0.478723 0.722892
70 MAO 0.478261 0.82716
71 BA3 0.478261 0.690476
72 AOC 0.477778 0.776316
73 DSH 0.477778 0.842105
74 NEC 0.477778 0.75
75 SXZ 0.47619 0.894737
76 AHX 0.475728 0.701149
77 Y3J 0.47561 0.706667
78 G5A 0.474227 0.684783
79 A3T 0.473684 0.8
80 ADP BEF 0.473684 0.686047
81 BEF ADP 0.473684 0.686047
82 B4P 0.473118 0.690476
83 AP5 0.473118 0.690476
84 A3N 0.472527 0.766234
85 KB1 0.471698 0.833333
86 LEU LMS 0.471154 0.706522
87 APC 0.46875 0.705882
88 PRX 0.46875 0.73494
89 PAJ 0.466019 0.712644
90 4AD 0.466019 0.759036
91 RBY 0.463918 0.72619
92 ADP PO3 0.463918 0.728395
93 ADV 0.463918 0.72619
94 ADX 0.463158 0.666667
95 MHZ 0.463158 0.82716
96 AU1 0.463158 0.674419
97 YAP 0.462963 0.738095
98 TXA 0.462264 0.72619
99 NB8 0.462264 0.72093
100 A3G 0.461538 0.802632
101 VRT 0.459184 0.842105
102 ATP MG 0.459184 0.702381
103 YSA 0.458716 0.684783
104 XAH 0.458716 0.715909
105 50T 0.458333 0.682353
106 ATP 0.458333 0.690476
107 7D7 0.45679 0.723684
108 ANP MG 0.455446 0.678161
109 KH3 0.455357 0.871795
110 ACQ 0.454545 0.694118
111 AQP 0.453608 0.690476
112 5FA 0.453608 0.690476
113 AR6 0.453608 0.710843
114 APR 0.453608 0.710843
115 NSS 0.451923 0.703297
116 FA5 0.449541 0.746988
117 AGS 0.44898 0.678161
118 SAP 0.44898 0.678161
119 A5D 0.44898 0.789474
120 AD9 0.44898 0.674419
121 PTJ 0.448598 0.72093
122 YLB 0.448276 0.758621
123 YLP 0.447368 0.738636
124 D3Y 0.446602 0.792208
125 ADP ALF 0.445545 0.678161
126 ALF ADP 0.445545 0.678161
127 TYR AMP 0.445455 0.746988
128 MYR AMP 0.444444 0.776471
129 3AM 0.444444 0.674699
130 OAD 0.443396 0.73494
131 2VA 0.443299 0.779221
132 OOB 0.442308 0.722892
133 S8M 0.442308 0.831169
134 ADP VO4 0.441176 0.702381
135 VO4 ADP 0.441176 0.702381
136 ANP 0.44 0.674419
137 TAT 0.44 0.686047
138 WAQ 0.439252 0.75
139 ARG AMP 0.438596 0.727273
140 YLC 0.435897 0.755814
141 AAT 0.435644 0.797468
142 3OD 0.435185 0.73494
143 1ZZ 0.435185 0.755814
144 NVA 2AD 0.434343 0.815789
145 DLL 0.433962 0.722892
146 00A 0.433962 0.689655
147 7MD 0.433628 0.715909
148 ATF 0.431373 0.666667
149 SO8 0.43 0.792208
150 3UK 0.429907 0.714286
151 A6D 0.429907 0.72619
152 5SV 0.428571 0.741176
153 AMP DBH 0.428571 0.714286
154 WSA 0.42735 0.692308
155 TYM 0.42735 0.746988
156 9SN 0.427273 0.681818
157 AHZ 0.426087 0.755814
158 A A 0.425926 0.710843
159 3NZ 0.425926 0.807692
160 P5A 0.425926 0.691489
161 PR8 0.425926 0.744186
162 A1R 0.424528 0.709302
163 2A5 0.424242 0.674419
164 7MC 0.423729 0.719101
165 7D5 0.422222 0.658824
166 FYA 0.422018 0.722892
167 JB6 0.422018 0.709302
168 AYB 0.421488 0.75
169 PLP AAD 0.419355 0.764045
170 A22 0.419048 0.682353
171 MAP 0.419048 0.659091
172 2AM 0.417582 0.666667
173 TAD 0.417391 0.712644
174 A3P 0.416667 0.686747
175 ADP BMA 0.416667 0.714286
176 25A 0.415094 0.690476
177 YLA 0.413223 0.719101
178 ADQ 0.411215 0.694118
179 48N 0.410256 0.72093
180 0XU 0.41 0.824324
181 NAD IBO 0.406504 0.717647
182 7D3 0.40625 0.643678
183 PAP 0.405941 0.678571
184 OVE 0.404255 0.662791
185 4UV 0.403509 0.697674
186 ALF ADP 3PG 0.403361 0.712644
187 AF3 ADP 3PG 0.403361 0.712644
188 LA8 ALF 3PG 0.403361 0.712644
189 3AD 0.402299 0.783784
190 CMP 0.402062 0.691358
191 2BA 0.402062 0.682927
192 7C5 0.4 0.731707
Ligand no: 2; Ligand: 4ZX; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 4ZX 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5CCM; Ligand: 4ZX; Similar sites found: 27
This union binding pocket(no: 1) in the query (biounit: 5ccm.bio1) has 50 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1TZD ADP 0.04608 0.41866 1.45455
2 4RHS SIA SIA GAL 0.01851 0.43781 2.45902
3 4N9Z V3L 0.02756 0.43856 2.80374
4 4X1Z FUC GAL NDG 0.04266 0.40473 3.61446
5 1EXF GLY 0.006791 0.43947 3.71901
6 5MX4 HPA 0.0333 0.42141 3.86266
7 5N1X 8HH 0.009672 0.44178 4.23729
8 2HFP NSI 0.009522 0.4125 4.25532
9 2PIE GLU LEU LYS TPO GLU ARG TYR 0.0198 0.42545 4.34783
10 1YZG GDP 0.03104 0.41213 4.46927
11 4DG8 AMP 0.03417 0.40358 5.14019
12 3F5A SIA GAL NAG 0.01103 0.41926 5.28455
13 1ZJ6 G3D 0.03794 0.40757 5.34759
14 3QXY SAM 0.000001741 0.62291 5.37383
15 4OKD GLC GLC GLC 0.03051 0.42245 5.37383
16 2BVE PH5 0.01374 0.44147 5.88235
17 5LFV SIA GAL NAG 0.04032 0.40764 5.99369
18 2H21 SAM 0.00000005037 0.64438 7.94393
19 1TLG GAL 0.0223 0.40341 8
20 5M5G SAH 0.0006378 0.47999 8.64486
21 5M5G VAL MET LEU PRO GLY ARG GLY VAL PRO 0.00002086 0.47936 8.64486
22 1R1Q ACE ARG GLU PTR VAL ASN VAL 0.01944 0.43933 10
23 3DWQ NGC GAL NGA POL AZI 0.04804 0.4137 12.6984
24 2VOH CIT 0.03017 0.43872 12.7389
25 5T0K SAM 0.00005007 0.53774 12.8114
26 5JIY SAM 0.00004438 0.54607 13.1387
27 3KMT SAH 0.00003682 0.55627 26.8908
Pocket No.: 2; Query (leader) PDB : 5CCM; Ligand: SAM; Similar sites found: 35
This union binding pocket(no: 2) in the query (biounit: 5ccm.bio1) has 45 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1NE7 16G 0.04767 0.40876 1.38408
2 1TZD ADP 0.03933 0.41866 1.45455
3 1XS5 MET 0.04829 0.40845 1.65975
4 1JI0 ATP 0.04401 0.4107 2.08333
5 3VSV XYS 0.03779 0.41159 2.1028
6 4RHS SIA SIA GAL 0.01576 0.43781 2.45902
7 4N9Z V3L 0.02371 0.43856 2.80374
8 4X1Z FUC GAL NDG 0.03654 0.40473 3.61446
9 1EXF GLY 0.005787 0.43947 3.71901
10 5MX4 HPA 0.02815 0.42141 3.86266
11 5N1X 8HH 0.008327 0.44178 4.23729
12 2HFP NSI 0.007449 0.4125 4.25532
13 2PIE GLU LEU LYS TPO GLU ARG TYR 0.0167 0.42545 4.34783
14 4DXG NDG FUC SIA GAL 0.04404 0.41084 4.41176
15 1YZG GDP 0.02562 0.41213 4.46927
16 4DG8 AMP 0.02802 0.40358 5.14019
17 3F5A SIA GAL NAG 0.009386 0.41926 5.28455
18 1ZJ6 G3D 0.03143 0.40757 5.34759
19 3QXY SAM 0.000001248 0.62291 5.37383
20 4OKD GLC GLC GLC 0.02575 0.42245 5.37383
21 2BVE PH5 0.01205 0.44073 5.88235
22 5LFV SIA GAL NAG 0.03717 0.40572 5.99369
23 4B1L FRU 0.04413 0.40789 7.87879
24 2H21 SAM 0.00000003253 0.64438 7.94393
25 1TLG GAL 0.01914 0.40341 8
26 5M5G SAH 0.0004879 0.47999 8.64486
27 5M5G VAL MET LEU PRO GLY ARG GLY VAL PRO 0.00001518 0.47778 8.64486
28 1R1Q ACE ARG GLU PTR VAL ASN VAL 0.01554 0.4404 10
29 3DWQ NGC GAL NGA POL AZI 0.04065 0.4137 12.6984
30 2VOH CIT 0.02599 0.43872 12.7389
31 5T0K SAM 0.00003713 0.53774 12.8114
32 5GJH SER ASP PTR MET ASN MET THR PRO 0.04521 0.40273 13
33 5JIY SAM 0.00003306 0.54607 13.1387
34 3IWD M2T 0.04681 0.40355 16.129
35 3KMT SAH 0.00002752 0.55627 26.8908
Feedback