Receptor
PDB id Resolution Class Description Source Keywords
5HI7 2.15 Å EC: 2.1.1.43 CO-CRYSTAL STRUCTURE OF HUMAN SMYD3 WITH AN AZA-SAH COMPOUND HOMO SAPIENS SMYD3 METHYLTRANSFERASE ONCOLOGY INHIBITOR TRANSFERASE-ICOMPLEX
Ref.: STRUCTURE-BASED DESIGN OF A NOVEL SMYD3 INHIBITOR T BRIDGES THE SAM-AND MEKK2-BINDING POCKETS. STRUCTURE V. 24 774 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
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...
62X A:507;
Valid;
none;
Ki = 14 nM
452.508 C19 H32 N8 O5 CN(C)...
MG A:505;
A:504;
Part of Protein;
Invalid;
none;
none;
submit data
24.305 Mg [Mg+2...
DMS A:506;
Invalid;
none;
submit data
78.133 C2 H6 O S CS(=O...
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 (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 40 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(....
7 6IJL - SAM C15 H22 N6 O5 S C[S@@+](CC....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 29 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(....
7 6IJL - SAM C15 H22 N6 O5 S C[S@@+](CC....
50% Homology Family (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 23 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(....
7 6IJL - SAM C15 H22 N6 O5 S C[S@@+](CC....
8 3QWV - SAH C14 H20 N6 O5 S c1nc(c2c(n....
9 3QWW - SFG C15 H23 N7 O5 c1nc(c2c(n....
10 4WUY ic50 < 15 nM 3UJ C36 H42 N6 O Cc1cn(c2c1....
11 5ARF ic50 = 0.8 uM I9H C22 H21 Cl F2 N6 O3 CCN([C@H]1....
12 5KJM ic50 = 0.065 uM 6TM C32 H37 Cl2 N7 O c1ccc(c(c1....
13 3TG4 - SAM C15 H22 N6 O5 S C[S@@+](CC....
14 5ARG ic50 = 27 nM H41 C22 H20 Cl2 F2 N6 O3 CCN([C@H]1....
15 5KJK ic50 = 0.012 uM 6T1 C30 H34 Cl2 N4 O2 c1ccc(c(c1....
16 3S7B ic50 = 0.12 uM NH5 C29 H38 Cl2 N4 O4 c1cc(c(cc1....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 62X; Similar ligands found: 186
No: Ligand ECFP6 Tc MDL keys Tc
1 62X 1 1
2 K15 0.808989 0.947368
3 SA8 0.704545 0.933333
4 OZP 0.696078 0.883117
5 KH3 0.693069 0.935065
6 HY8 0.68932 0.860759
7 KB1 0.673469 0.825
8 HZ2 0.669903 0.860759
9 EP4 0.60241 0.866667
10 F0P 0.6 0.883117
11 SFG 0.574468 0.84
12 SAH 0.572917 0.855263
13 S7M 0.565657 0.860759
14 EEM 0.561224 0.884615
15 5X8 0.557895 0.828947
16 SAI 0.556701 0.844156
17 MHZ 0.547368 0.8875
18 SAM 0.535354 0.884615
19 SMM 0.534653 0.898734
20 MAO 0.531915 0.819277
21 0UM 0.528846 0.896104
22 RAB 0.511905 0.74359
23 XYA 0.511905 0.74359
24 ADN 0.511905 0.74359
25 5CD 0.511628 0.753247
26 5N5 0.5 0.766234
27 SXZ 0.495413 0.909091
28 A4D 0.494253 0.74359
29 S4M 0.489583 0.898734
30 GJV 0.489583 0.768293
31 6RE 0.489362 0.756098
32 3DH 0.48913 0.792208
33 M2T 0.488889 0.820513
34 DTA 0.488889 0.7375
35 LAD 0.486239 0.767442
36 MTA 0.483516 0.815789
37 SSA 0.47619 0.628866
38 KAA 0.472727 0.677083
39 5AL 0.471154 0.717647
40 CA0 0.47 0.689655
41 DSH 0.46875 0.857143
42 ME8 0.468468 0.790698
43 A5A 0.466667 0.631579
44 KG4 0.465347 0.689655
45 ABM 0.463918 0.72619
46 45A 0.463918 0.72619
47 J7C 0.463918 0.765432
48 ZAS 0.463158 0.740741
49 A 0.463158 0.682353
50 LMS 0.463158 0.610526
51 AMP 0.463158 0.682353
52 GEK 0.462963 0.822785
53 SRP 0.462264 0.72093
54 SON 0.46 0.72093
55 A7D 0.46 0.794872
56 GSU 0.459459 0.663158
57 DSZ 0.458716 0.645833
58 AMO 0.458716 0.72093
59 LSS 0.458716 0.684211
60 N37 0.458333 0.797468
61 54H 0.457944 0.652632
62 VMS 0.457944 0.652632
63 TXA 0.455357 0.701149
64 BA3 0.454545 0.666667
65 YLC 0.454545 0.770115
66 YLP 0.453782 0.793103
67 53H 0.453704 0.645833
68 TSB 0.453704 0.625
69 5CA 0.453704 0.628866
70 NEC 0.453608 0.74359
71 XAH 0.452174 0.730337
72 HEJ 0.45098 0.666667
73 ATP 0.45098 0.666667
74 AP5 0.45 0.666667
75 B4P 0.45 0.666667
76 5AS 0.45 0.628866
77 8QN 0.449541 0.717647
78 A2D 0.44898 0.666667
79 8LH 0.448598 0.72093
80 F2R 0.448 0.714286
81 5FA 0.446602 0.666667
82 AQP 0.446602 0.666667
83 WAQ 0.446429 0.764706
84 AN2 0.445545 0.659091
85 A3S 0.445545 0.782051
86 52H 0.444444 0.645833
87 FA5 0.443478 0.72093
88 8LE 0.443396 0.732558
89 SRA 0.443299 0.651685
90 YLB 0.442623 0.793103
91 NVA LMS 0.441441 0.659794
92 AHX 0.441441 0.677778
93 AU1 0.441176 0.651685
94 ADX 0.441176 0.610526
95 M33 0.441176 0.697674
96 7MD 0.440678 0.75
97 DAL AMP 0.440367 0.717647
98 8LQ 0.440367 0.741176
99 AP2 0.44 0.681818
100 A12 0.44 0.681818
101 AOC 0.438776 0.746835
102 G5A 0.438095 0.645833
103 50T 0.436893 0.659091
104 ACP 0.436893 0.670455
105 A3T 0.436893 0.769231
106 5AD 0.436782 0.72
107 9ZD 0.436364 0.724138
108 9ZA 0.436364 0.724138
109 ADP 0.435644 0.666667
110 A3N 0.434343 0.759494
111 GAP 0.433962 0.709302
112 Y3J 0.433333 0.679487
113 0XU 0.432692 0.792208
114 PRX 0.432692 0.729412
115 PAJ 0.432432 0.727273
116 AT4 0.431373 0.644444
117 ADP MG 0.431373 0.682353
118 YAP 0.431034 0.712644
119 PTJ 0.429825 0.735632
120 NB8 0.429825 0.696629
121 AYB 0.428571 0.784091
122 AGS 0.428571 0.637363
123 SAP 0.428571 0.637363
124 LEU LMS 0.424779 0.677083
125 VRT 0.424528 0.810127
126 A3G 0.424242 0.794872
127 N5O 0.424242 0.782051
128 S8M 0.423423 0.777778
129 5SV 0.423423 0.776471
130 3AM 0.42268 0.651163
131 YLA 0.420635 0.752809
132 T99 0.420561 0.644444
133 TAT 0.420561 0.644444
134 4AD 0.419643 0.712644
135 NSS 0.419643 0.628866
136 AR6 0.419048 0.686047
137 APC 0.419048 0.681818
138 APR 0.419048 0.686047
139 TT8 0.418182 0.881579
140 1ZZ 0.417391 0.790698
141 JB6 0.417391 0.685393
142 AAT 0.416667 0.8125
143 ARG AMP 0.416667 0.722222
144 00A 0.415929 0.666667
145 N5A 0.415842 0.779221
146 7D7 0.41573 0.696203
147 YSA 0.415254 0.628866
148 RBY 0.415094 0.701149
149 ATP MG 0.415094 0.682353
150 ADV 0.415094 0.701149
151 A5D 0.415094 0.7375
152 APC MG 0.415094 0.686047
153 AD9 0.415094 0.651685
154 ADP PO3 0.415094 0.682353
155 8X1 0.414414 0.642857
156 MYR AMP 0.413793 0.790698
157 3UK 0.412281 0.689655
158 OAD 0.412281 0.709302
159 SO8 0.411215 0.78481
160 OOB 0.410714 0.697674
161 2VA 0.409524 0.794872
162 H1Q 0.409524 0.674419
163 6YZ 0.409091 0.670455
164 J4G 0.408696 0.732558
165 B5V 0.408696 0.681818
166 7MC 0.408 0.772727
167 ACQ 0.407407 0.670455
168 ANP 0.407407 0.651685
169 B5Y 0.40678 0.693182
170 8PZ 0.40678 0.628866
171 48N 0.406504 0.715909
172 YLY 0.406015 0.825581
173 HQG 0.405405 0.678161
174 9K8 0.405172 0.61
175 3OD 0.405172 0.709302
176 DLL 0.403509 0.697674
177 NVA 2AD 0.401869 0.8
178 A22 0.401786 0.659091
179 D3Y 0.401786 0.7625
180 IOT 0.401575 0.744444
181 ATF 0.4 0.644444
182 OMR 0.4 0.781609
183 TYM 0.4 0.72093
184 ALF ADP 0.4 0.637363
185 ADP ALF 0.4 0.637363
186 9X8 0.4 0.674157
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5CCM; Ligand: 4ZX; 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: 5ccm.bio1) has 52 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5CCM; Ligand: SAM; 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: 5ccm.bio1) has 47 residues
No: Leader PDB Ligand Sequence Similarity
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