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 (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 37 families.
1 3PDN - SFG C15 H23 N7 O5 c1nc(c2c(n....
2 6P7Z - O41 C13 H19 N3 O4 S CS(=O)(=O)....
3 5CCM ic50 = 4 nM 4ZX C28 H34 Cl N5 O4 S c1ccc(cc1)....
4 5CCL - 4ZW C14 H17 N3 O2 c1cc2c(cc1....
5 5EX3 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
6 3RU0 - SFG C15 H23 N7 O5 c1nc(c2c(n....
7 5HI7 Ki = 14 nM 62X C19 H32 N8 O5 CN(C)CCCN(....
8 6P6G Ki = 6 nM LUP C23 H35 F3 N4 O4 S c1c(onc1C(....
9 6P6K - SAM C15 H22 N6 O5 S C[S@@+](CC....
10 6PAF - O6A C19 H24 N4 O4 S c1cc(ccc1C....
11 6IJL - SAM C15 H22 N6 O5 S C[S@@+](CC....
70% Homology Family (11)
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 6P7Z - O41 C13 H19 N3 O4 S CS(=O)(=O)....
3 5CCM ic50 = 4 nM 4ZX C28 H34 Cl N5 O4 S c1ccc(cc1)....
4 5CCL - 4ZW C14 H17 N3 O2 c1cc2c(cc1....
5 5EX3 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
6 3RU0 - SFG C15 H23 N7 O5 c1nc(c2c(n....
7 5HI7 Ki = 14 nM 62X C19 H32 N8 O5 CN(C)CCCN(....
8 6P6G Ki = 6 nM LUP C23 H35 F3 N4 O4 S c1c(onc1C(....
9 6P6K - SAM C15 H22 N6 O5 S C[S@@+](CC....
10 6PAF - O6A C19 H24 N4 O4 S c1cc(ccc1C....
11 6IJL - SAM C15 H22 N6 O5 S C[S@@+](CC....
50% Homology Family (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 21 families.
1 3PDN - SFG C15 H23 N7 O5 c1nc(c2c(n....
2 6P7Z - O41 C13 H19 N3 O4 S CS(=O)(=O)....
3 5CCM ic50 = 4 nM 4ZX C28 H34 Cl N5 O4 S c1ccc(cc1)....
4 5CCL - 4ZW C14 H17 N3 O2 c1cc2c(cc1....
5 5EX3 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
6 3RU0 - SFG C15 H23 N7 O5 c1nc(c2c(n....
7 5HI7 Ki = 14 nM 62X C19 H32 N8 O5 CN(C)CCCN(....
8 6P6G Ki = 6 nM LUP C23 H35 F3 N4 O4 S c1c(onc1C(....
9 6P6K - SAM C15 H22 N6 O5 S C[S@@+](CC....
10 6PAF - O6A C19 H24 N4 O4 S c1cc(ccc1C....
11 6IJL - SAM C15 H22 N6 O5 S C[S@@+](CC....
12 3QWV - SAH C14 H20 N6 O5 S c1nc(c2c(n....
13 3QWW - SFG C15 H23 N7 O5 c1nc(c2c(n....
14 4WUY ic50 < 15 nM 3UJ C36 H42 N6 O Cc1cn(c2c1....
15 5ARF Kd = 540 nM I9H C22 H21 Cl F2 N6 O3 CCN([C@H]1....
16 5KJM ic50 = 0.065 uM 6TM C32 H37 Cl2 N7 O c1ccc(c(c1....
17 3TG4 - SAM C15 H22 N6 O5 S C[S@@+](CC....
18 5ARG ic50 = 27 nM H41 C22 H20 Cl2 F2 N6 O3 CCN([C@H]1....
19 5KJK ic50 = 0.012 uM 6T1 C30 H34 Cl2 N4 O2 c1ccc(c(c1....
20 3S7B Kd = 0.5 uM NH5 C29 H38 Cl2 N4 O4 c1cc(c(cc1....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 62X; Similar ligands found: 210
No: Ligand ECFP6 Tc MDL keys Tc
1 62X 1 1
2 K15 0.808989 0.947368
3 KYE 0.757895 0.839506
4 KXW 0.71 0.883117
5 SA8 0.704545 0.933333
6 OZP 0.696078 0.883117
7 KH3 0.693069 0.935065
8 HY8 0.68932 0.860759
9 KB1 0.673469 0.825
10 HZ2 0.669903 0.860759
11 EP4 0.60241 0.866667
12 F0P 0.6 0.883117
13 Q34 0.585586 0.817073
14 Q2M 0.585586 0.8375
15 SFG 0.574468 0.84
16 SAH 0.572917 0.855263
17 Q2V 0.570175 0.871795
18 S7M 0.565657 0.860759
19 EEM 0.561224 0.884615
20 KYB 0.558824 0.814815
21 5X8 0.557895 0.828947
22 SAI 0.556701 0.844156
23 Q2P 0.555556 0.817073
24 KY2 0.554455 0.814815
25 MHZ 0.547368 0.8875
26 SAM 0.535354 0.884615
27 SMM 0.534653 0.898734
28 KY5 0.53271 0.857143
29 MAO 0.531915 0.819277
30 0UM 0.528846 0.896104
31 KY8 0.528302 0.835443
32 XYA 0.511905 0.74359
33 ADN 0.511905 0.74359
34 RAB 0.511905 0.74359
35 5CD 0.511628 0.753247
36 5N5 0.5 0.766234
37 SXZ 0.495413 0.909091
38 A4D 0.494253 0.74359
39 GJV 0.489583 0.768293
40 S4M 0.489583 0.898734
41 6RE 0.489362 0.756098
42 3DH 0.48913 0.792208
43 M2T 0.488889 0.820513
44 DTA 0.488889 0.7375
45 LAD 0.486239 0.767442
46 MTA 0.483516 0.815789
47 SSA 0.47619 0.628866
48 AMP MG 0.473684 0.690476
49 KAA 0.472727 0.677083
50 5AL 0.471154 0.717647
51 CA0 0.47 0.689655
52 DSH 0.46875 0.857143
53 ME8 0.468468 0.790698
54 A5A 0.466667 0.631579
55 KG4 0.465347 0.689655
56 45A 0.463918 0.72619
57 J7C 0.463918 0.765432
58 ABM 0.463918 0.72619
59 LMS 0.463158 0.610526
60 AMP 0.463158 0.682353
61 ZAS 0.463158 0.740741
62 A 0.463158 0.682353
63 GEK 0.462963 0.822785
64 SRP 0.462264 0.72093
65 EU9 0.462185 0.722222
66 NWW 0.460674 0.710526
67 SON 0.46 0.72093
68 A7D 0.46 0.794872
69 GSU 0.459459 0.663158
70 DSZ 0.458716 0.645833
71 LSS 0.458716 0.684211
72 AMO 0.458716 0.72093
73 N37 0.458333 0.797468
74 54H 0.457944 0.652632
75 VMS 0.457944 0.652632
76 TXA 0.455357 0.701149
77 YLC 0.454545 0.770115
78 BA3 0.454545 0.666667
79 YLP 0.453782 0.793103
80 U4Y 0.453782 0.822785
81 5CA 0.453704 0.628866
82 TSB 0.453704 0.625
83 53H 0.453704 0.645833
84 NEC 0.453608 0.74359
85 XAH 0.452174 0.730337
86 HEJ 0.45098 0.666667
87 ATP 0.45098 0.666667
88 AP5 0.45 0.666667
89 5AS 0.45 0.628866
90 B4P 0.45 0.666667
91 8QN 0.449541 0.717647
92 A2D 0.44898 0.666667
93 V47 0.448598 0.779221
94 8LH 0.448598 0.72093
95 F2R 0.448 0.714286
96 AQP 0.446602 0.666667
97 5FA 0.446602 0.666667
98 WAQ 0.446429 0.764706
99 A3S 0.445545 0.782051
100 AN2 0.445545 0.659091
101 52H 0.444444 0.645833
102 FA5 0.443478 0.72093
103 V2G 0.443396 0.715909
104 8LE 0.443396 0.732558
105 SRA 0.443299 0.651685
106 YLB 0.442623 0.793103
107 K2H 0.441441 0.797468
108 NVA LMS 0.441441 0.659794
109 AHX 0.441441 0.677778
110 M33 0.441176 0.697674
111 ADX 0.441176 0.610526
112 AU1 0.441176 0.651685
113 7MD 0.440678 0.75
114 8LQ 0.440367 0.741176
115 DAL AMP 0.440367 0.717647
116 QA7 0.440367 0.752941
117 AP2 0.44 0.681818
118 A12 0.44 0.681818
119 K3H 0.439655 0.768293
120 AOC 0.438776 0.746835
121 G5A 0.438095 0.645833
122 ACP 0.436893 0.670455
123 50T 0.436893 0.659091
124 A3T 0.436893 0.769231
125 5AD 0.436782 0.72
126 9ZA 0.436364 0.724138
127 9ZD 0.436364 0.724138
128 QXP 0.436364 0.631579
129 ADP 0.435644 0.666667
130 A3N 0.434343 0.759494
131 GAP 0.433962 0.709302
132 Y3J 0.433333 0.679487
133 0XU 0.432692 0.792208
134 PRX 0.432692 0.729412
135 PAJ 0.432432 0.727273
136 ADP BEF 0.431373 0.682353
137 AT4 0.431373 0.644444
138 ADP MG 0.431373 0.682353
139 NB8 0.429825 0.696629
140 PTJ 0.429825 0.735632
141 AYB 0.428571 0.784091
142 AGS 0.428571 0.637363
143 NWQ 0.427083 0.736842
144 QXG 0.424779 0.625
145 LEU LMS 0.424779 0.709677
146 VRT 0.424528 0.810127
147 BEF ADP 0.424528 0.666667
148 A3G 0.424242 0.794872
149 N5O 0.424242 0.782051
150 5SV 0.423423 0.776471
151 S8M 0.423423 0.777778
152 3AM 0.42268 0.651163
153 YLA 0.420635 0.752809
154 T99 0.420561 0.644444
155 TAT 0.420561 0.644444
156 NSS 0.419643 0.628866
157 4AD 0.419643 0.712644
158 APR 0.419048 0.686047
159 AR6 0.419048 0.686047
160 APC 0.419048 0.681818
161 TT8 0.418182 0.881579
162 JB6 0.417391 0.685393
163 1ZZ 0.417391 0.790698
164 AAT 0.416667 0.8125
165 ARG AMP 0.416667 0.722222
166 00A 0.415929 0.666667
167 N5A 0.415842 0.779221
168 7D7 0.41573 0.696203
169 YSA 0.415254 0.628866
170 ATP MG 0.415094 0.682353
171 RBY 0.415094 0.701149
172 A5D 0.415094 0.7375
173 AD9 0.415094 0.651685
174 ADV 0.415094 0.701149
175 ADP PO3 0.415094 0.682353
176 APC MG 0.415094 0.686047
177 8X1 0.414414 0.642857
178 MYR AMP 0.413793 0.790698
179 OAD 0.412281 0.709302
180 3UK 0.412281 0.689655
181 SO8 0.411215 0.78481
182 OOB 0.410714 0.697674
183 2VA 0.409524 0.794872
184 H1Q 0.409524 0.674419
185 6YZ 0.409091 0.670455
186 B5V 0.408696 0.681818
187 R2V 0.408696 0.631579
188 J4G 0.408696 0.732558
189 7MC 0.408 0.772727
190 ANP 0.407407 0.651685
191 ACQ 0.407407 0.670455
192 8PZ 0.40678 0.628866
193 B5Y 0.40678 0.693182
194 48N 0.406504 0.715909
195 YLY 0.406015 0.825581
196 HQG 0.405405 0.678161
197 3OD 0.405172 0.709302
198 9K8 0.405172 0.61
199 DLL 0.403509 0.697674
200 NVA 2AD 0.401869 0.8
201 A22 0.401786 0.659091
202 D3Y 0.401786 0.7625
203 IOT 0.401575 0.744444
204 ANP MG 0.4 0.659091
205 VO4 ADP 0.4 0.651685
206 ATF 0.4 0.644444
207 ALF ADP 0.4 0.637363
208 OMR 0.4 0.781609
209 9X8 0.4 0.674157
210 TYM 0.4 0.72093
Similar Ligands (3D)
Ligand no: 1; Ligand: 62X; Similar ligands found: 0
No: Ligand Similarity coefficient
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 46 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 45 residues
No: Leader PDB Ligand Sequence Similarity
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