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 (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 (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 22 families.
1 3PDN - SFG C15 H23 N7 O5 c1nc(c2c(n....
2 5HI7 Ki = 14 nM 62X C19 H32 N8 O5 CN(C)CCCN(....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 62X; Similar ligands found: 159
No: Ligand ECFP6 Tc MDL keys Tc
1 62X 1 1
2 K15 0.808989 0.947368
3 SA8 0.704545 0.933333
4 KH3 0.693069 0.935065
5 KB1 0.673469 0.825
6 EP4 0.60241 0.866667
7 SFG 0.574468 0.84
8 SAH 0.572917 0.855263
9 S7M 0.565657 0.860759
10 EEM 0.561224 0.884615
11 5X8 0.557895 0.828947
12 SAI 0.556701 0.844156
13 MHZ 0.547368 0.8875
14 SAM 0.535354 0.884615
15 SMM 0.534653 0.898734
16 MAO 0.531915 0.819277
17 0UM 0.528846 0.896104
18 ADN 0.511905 0.74359
19 XYA 0.511905 0.74359
20 RAB 0.511905 0.74359
21 5CD 0.511628 0.753247
22 5N5 0.5 0.766234
23 SXZ 0.495413 0.909091
24 A4D 0.494253 0.74359
25 S4M 0.489583 0.898734
26 GJV 0.489583 0.768293
27 6RE 0.489362 0.756098
28 3DH 0.48913 0.792208
29 M2T 0.488889 0.820513
30 DTA 0.488889 0.7375
31 LAD 0.486239 0.767442
32 MTA 0.483516 0.815789
33 SSA 0.47619 0.628866
34 KAA 0.472727 0.677083
35 5AL 0.471154 0.717647
36 CA0 0.47 0.689655
37 DSH 0.46875 0.857143
38 AMP MG 0.46875 0.666667
39 ME8 0.468468 0.790698
40 A5A 0.466667 0.631579
41 ABM 0.463918 0.72619
42 J7C 0.463918 0.765432
43 AMP 0.463158 0.682353
44 ZAS 0.463158 0.740741
45 A 0.463158 0.682353
46 GEK 0.462963 0.822785
47 SRP 0.462264 0.72093
48 SON 0.46 0.72093
49 A7D 0.46 0.794872
50 GSU 0.459459 0.663158
51 AMO 0.458716 0.72093
52 DSZ 0.458716 0.645833
53 LSS 0.458716 0.684211
54 54H 0.457944 0.652632
55 VMS 0.457944 0.652632
56 TXA 0.455357 0.701149
57 BA3 0.454545 0.666667
58 YLC 0.454545 0.770115
59 YLP 0.453782 0.793103
60 5CA 0.453704 0.628866
61 TSB 0.453704 0.625
62 53H 0.453704 0.645833
63 NEC 0.453608 0.74359
64 XAH 0.452174 0.730337
65 ATP 0.45098 0.666667
66 5AS 0.45 0.628866
67 B4P 0.45 0.666667
68 AP5 0.45 0.666667
69 8QN 0.449541 0.717647
70 A2D 0.44898 0.666667
71 5FA 0.446602 0.666667
72 AQP 0.446602 0.666667
73 WAQ 0.446429 0.764706
74 A3S 0.445545 0.782051
75 AN2 0.445545 0.659091
76 52H 0.444444 0.645833
77 FA5 0.443478 0.72093
78 SRA 0.443299 0.651685
79 YLB 0.442623 0.793103
80 AHX 0.441441 0.677778
81 NVA LMS 0.441441 0.649485
82 M33 0.441176 0.697674
83 ADX 0.441176 0.610526
84 AU1 0.441176 0.651685
85 7MD 0.440678 0.75
86 DAL AMP 0.440367 0.717647
87 AP2 0.44 0.681818
88 A12 0.44 0.681818
89 AOC 0.438776 0.746835
90 G5A 0.438095 0.645833
91 ACP 0.436893 0.670455
92 A3T 0.436893 0.769231
93 50T 0.436893 0.659091
94 5AD 0.436782 0.72
95 ADP 0.435644 0.666667
96 A3N 0.434343 0.759494
97 GAP 0.433962 0.709302
98 Y3J 0.433333 0.679487
99 0XU 0.432692 0.792208
100 PRX 0.432692 0.729412
101 PAJ 0.432432 0.727273
102 YAP 0.431034 0.712644
103 PTJ 0.429825 0.735632
104 NB8 0.429825 0.696629
105 AYB 0.428571 0.784091
106 SAP 0.428571 0.637363
107 AGS 0.428571 0.637363
108 ADP MG 0.427184 0.659091
109 LEU LMS 0.424779 0.666667
110 VRT 0.424528 0.810127
111 A3G 0.424242 0.794872
112 S8M 0.423423 0.777778
113 5SV 0.423423 0.776471
114 ADP BEF 0.423077 0.644444
115 BEF ADP 0.423077 0.644444
116 3AM 0.42268 0.651163
117 YLA 0.420635 0.752809
118 TAT 0.420561 0.644444
119 4AD 0.419643 0.712644
120 NSS 0.419643 0.628866
121 APC 0.419048 0.681818
122 APR 0.419048 0.686047
123 AR6 0.419048 0.686047
124 TT8 0.418182 0.881579
125 JB6 0.417391 0.685393
126 1ZZ 0.417391 0.790698
127 AAT 0.416667 0.8125
128 00A 0.415929 0.666667
129 7D7 0.41573 0.696203
130 YSA 0.415254 0.628866
131 A5D 0.415094 0.7375
132 AD9 0.415094 0.651685
133 ADP PO3 0.415094 0.682353
134 ADV 0.415094 0.701149
135 RBY 0.415094 0.701149
136 MYR AMP 0.413793 0.790698
137 OAD 0.412281 0.709302
138 3UK 0.412281 0.689655
139 SO8 0.411215 0.78481
140 ATP MG 0.411215 0.659091
141 OOB 0.410714 0.697674
142 2VA 0.409524 0.794872
143 7MC 0.408 0.772727
144 ANP 0.407407 0.651685
145 ACQ 0.407407 0.670455
146 48N 0.406504 0.715909
147 YLY 0.406015 0.825581
148 3OD 0.405172 0.709302
149 DLL 0.403509 0.697674
150 TYR AMP 0.403361 0.701149
151 NVA 2AD 0.401869 0.7625
152 A22 0.401786 0.659091
153 D3Y 0.401786 0.7625
154 IOT 0.401575 0.744444
155 ADP ALF 0.4 0.637363
156 ATF 0.4 0.644444
157 ALF ADP 0.4 0.637363
158 OMR 0.4 0.781609
159 TYM 0.4 0.72093
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
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