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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 39 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 28 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 (15)
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 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 3QWV - SAH C14 H20 N6 O5 S c1nc(c2c(n....
8 3QWW - SFG C15 H23 N7 O5 c1nc(c2c(n....
9 4WUY ic50 < 15 nM 3UJ C36 H42 N6 O Cc1cn(c2c1....
10 5ARF ic50 = 0.8 uM I9H C22 H21 Cl F2 N6 O3 CCN([C@H]1....
11 5KJM ic50 = 0.065 uM 6TM C32 H37 Cl2 N7 O c1ccc(c(c1....
12 3TG4 - SAM C15 H22 N6 O5 S C[S@@+](CC....
13 5ARG ic50 = 27 nM H41 C22 H20 Cl2 F2 N6 O3 CCN([C@H]1....
14 5KJK ic50 = 0.012 uM 6T1 C30 H34 Cl2 N4 O2 c1ccc(c(c1....
15 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: 169
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 F0P 0.6 0.883117
8 SFG 0.574468 0.84
9 SAH 0.572917 0.855263
10 S7M 0.565657 0.860759
11 EEM 0.561224 0.884615
12 5X8 0.557895 0.828947
13 SAI 0.556701 0.844156
14 MHZ 0.547368 0.8875
15 SAM 0.535354 0.884615
16 SMM 0.534653 0.898734
17 MAO 0.531915 0.819277
18 0UM 0.528846 0.896104
19 RAB 0.511905 0.74359
20 ADN 0.511905 0.74359
21 XYA 0.511905 0.74359
22 5CD 0.511628 0.753247
23 5N5 0.5 0.766234
24 SXZ 0.495413 0.909091
25 A4D 0.494253 0.74359
26 GJV 0.489583 0.768293
27 S4M 0.489583 0.898734
28 6RE 0.489362 0.756098
29 3DH 0.48913 0.792208
30 M2T 0.488889 0.820513
31 DTA 0.488889 0.7375
32 LAD 0.486239 0.767442
33 MTA 0.483516 0.815789
34 SSA 0.47619 0.628866
35 KAA 0.472727 0.677083
36 5AL 0.471154 0.717647
37 CA0 0.47 0.689655
38 DSH 0.46875 0.857143
39 ME8 0.468468 0.790698
40 A5A 0.466667 0.631579
41 J7C 0.463918 0.765432
42 ABM 0.463918 0.72619
43 LMS 0.463158 0.610526
44 ZAS 0.463158 0.740741
45 A 0.463158 0.682353
46 AMP 0.463158 0.682353
47 GEK 0.462963 0.822785
48 SRP 0.462264 0.72093
49 A7D 0.46 0.794872
50 SON 0.46 0.72093
51 GSU 0.459459 0.663158
52 LSS 0.458716 0.684211
53 DSZ 0.458716 0.645833
54 AMO 0.458716 0.72093
55 54H 0.457944 0.652632
56 VMS 0.457944 0.652632
57 TXA 0.455357 0.701149
58 YLC 0.454545 0.770115
59 BA3 0.454545 0.666667
60 YLP 0.453782 0.793103
61 53H 0.453704 0.645833
62 TSB 0.453704 0.625
63 5CA 0.453704 0.628866
64 NEC 0.453608 0.74359
65 XAH 0.452174 0.730337
66 ATP 0.45098 0.666667
67 HEJ 0.45098 0.666667
68 AP5 0.45 0.666667
69 B4P 0.45 0.666667
70 5AS 0.45 0.628866
71 8QN 0.449541 0.717647
72 A2D 0.44898 0.666667
73 F2R 0.448 0.714286
74 5FA 0.446602 0.666667
75 AQP 0.446602 0.666667
76 WAQ 0.446429 0.764706
77 A3S 0.445545 0.782051
78 AN2 0.445545 0.659091
79 52H 0.444444 0.645833
80 FA5 0.443478 0.72093
81 SRA 0.443299 0.651685
82 YLB 0.442623 0.793103
83 AHX 0.441441 0.677778
84 NVA LMS 0.441441 0.659794
85 AU1 0.441176 0.651685
86 M33 0.441176 0.697674
87 ADX 0.441176 0.610526
88 7MD 0.440678 0.75
89 DAL AMP 0.440367 0.717647
90 AP2 0.44 0.681818
91 A12 0.44 0.681818
92 AOC 0.438776 0.746835
93 G5A 0.438095 0.645833
94 A3T 0.436893 0.769231
95 50T 0.436893 0.659091
96 ACP 0.436893 0.670455
97 5AD 0.436782 0.72
98 9ZA 0.436364 0.724138
99 9ZD 0.436364 0.724138
100 ADP 0.435644 0.666667
101 A3N 0.434343 0.759494
102 GAP 0.433962 0.709302
103 Y3J 0.433333 0.679487
104 PRX 0.432692 0.729412
105 0XU 0.432692 0.792208
106 PAJ 0.432432 0.727273
107 AT4 0.431373 0.644444
108 YAP 0.431034 0.712644
109 PTJ 0.429825 0.735632
110 NB8 0.429825 0.696629
111 AYB 0.428571 0.784091
112 AGS 0.428571 0.637363
113 SAP 0.428571 0.637363
114 LEU LMS 0.424779 0.677083
115 VRT 0.424528 0.810127
116 A3G 0.424242 0.794872
117 5SV 0.423423 0.776471
118 S8M 0.423423 0.777778
119 3AM 0.42268 0.651163
120 YLA 0.420635 0.752809
121 TAT 0.420561 0.644444
122 T99 0.420561 0.644444
123 4AD 0.419643 0.712644
124 NSS 0.419643 0.628866
125 APR 0.419048 0.686047
126 AR6 0.419048 0.686047
127 APC 0.419048 0.681818
128 TT8 0.418182 0.881579
129 JB6 0.417391 0.685393
130 1ZZ 0.417391 0.790698
131 ARG AMP 0.416667 0.722222
132 AAT 0.416667 0.8125
133 00A 0.415929 0.666667
134 7D7 0.41573 0.696203
135 YSA 0.415254 0.628866
136 A5D 0.415094 0.7375
137 ADV 0.415094 0.701149
138 ADP PO3 0.415094 0.682353
139 AD9 0.415094 0.651685
140 RBY 0.415094 0.701149
141 8X1 0.414414 0.642857
142 MYR AMP 0.413793 0.790698
143 OAD 0.412281 0.709302
144 3UK 0.412281 0.689655
145 SO8 0.411215 0.78481
146 OOB 0.410714 0.697674
147 2VA 0.409524 0.794872
148 6YZ 0.409091 0.670455
149 B5V 0.408696 0.681818
150 7MC 0.408 0.772727
151 ACQ 0.407407 0.670455
152 ANP 0.407407 0.651685
153 B5Y 0.40678 0.693182
154 8PZ 0.40678 0.628866
155 48N 0.406504 0.715909
156 YLY 0.406015 0.825581
157 9K8 0.405172 0.61
158 3OD 0.405172 0.709302
159 DLL 0.403509 0.697674
160 NVA 2AD 0.401869 0.8
161 D3Y 0.401786 0.7625
162 A22 0.401786 0.659091
163 IOT 0.401575 0.744444
164 ADP ALF 0.4 0.637363
165 TYM 0.4 0.72093
166 OMR 0.4 0.781609
167 ALF ADP 0.4 0.637363
168 9X8 0.4 0.674157
169 ATF 0.4 0.644444
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: 51
This union binding pocket(no: 1) in the query (biounit: 5ccm.bio1) has 50 residues
No: Leader PDB Ligand Sequence Similarity
1 1TZD ADP 1.45455
2 3ZOK GLY 1.85185
3 4U8P UDP 2.1028
4 1XF1 CIT 2.1028
5 5WHT SIA GAL GLC 2.17391
6 5WHT SIA GAL 2.17391
7 5WHT SIA 2.17391
8 1M26 GAL A2G 2.25564
9 2CHT TSA 2.3622
10 4RHS SIA SIA GAL 2.45902
11 5CZY SAM 2.57009
12 5GZ9 MAN 2.62295
13 5D63 FUC GAL GLA 2.73038
14 5N6N SUC 3.27103
15 5YW5 ADE 3.35196
16 4X1Z FUC GAL NDG 3.61446
17 1Q3P GLU ALA GLN THR ARG LEU 3.66972
18 1EXF GLY 3.71901
19 5N1X 8HH 4.23729
20 1TL2 NDG 4.23729
21 2HFP NSI 4.25532
22 2PIE GLU LEU LYS TPO GLU ARG TYR 4.34783
23 1F76 ORO 4.46429
24 1YZG GDP 4.46927
25 2NU8 COA 5.14019
26 4DG8 AMP 5.14019
27 3F5A SIA GAL NAG 5.28455
28 1ZJ6 G3D 5.34759
29 3QXY SAM 5.37383
30 4OKD GLC GLC GLC 5.37383
31 2BVE PH5 5.88235
32 5LFV SIA GAL NAG 5.99369
33 1MR3 G3D 7.18232
34 2H21 SAM 7.94393
35 1TLG GAL 8
36 5WJ6 B4A 8.17757
37 3KIF GDL 8.49057
38 4CNK MEU 8.69565
39 5GG9 8GM 9.64912
40 1R1Q ACE ARG GLU PTR VAL ASN VAL 10
41 5FIT AP2 11.5646
42 3DWQ NGC GAL NGA POL AZI 12.6984
43 2VOH CIT 12.7389
44 5T0K SAM 12.8114
45 5JIY SAM 13.1387
46 2RDG NDG FUC SIA GAL 14.7959
47 4GNC ASO 21.0702
48 6FHQ DE5 24.1379
49 3KIH GDL 24.7423
50 4EHQ GBL 25
51 3KMT SAH 26.8908
Pocket No.: 2; Query (leader) PDB : 5CCM; Ligand: SAM; Similar sites found with APoc: 66
This union binding pocket(no: 2) in the query (biounit: 5ccm.bio1) has 45 residues
No: Leader PDB Ligand Sequence Similarity
1 1NE7 16G 1.38408
2 1TZD ADP 1.45455
3 1XS5 MET 1.65975
4 5H20 GLC 1.8018
5 3ZOK GLY 1.85185
6 1JI0 ATP 2.08333
7 4U8P UDP 2.1028
8 1XF1 CIT 2.1028
9 3VSV XYS 2.1028
10 6EKZ SNP 2.13415
11 5WHT SIA GAL GLC 2.17391
12 5WHT SIA GAL 2.17391
13 5WHT SIA 2.17391
14 1M26 GAL A2G 2.25564
15 2CHT TSA 2.3622
16 4RHS SIA SIA GAL 2.45902
17 5CZY SAM 2.57009
18 5GZ9 MAN 2.62295
19 5TZO 7V7 2.65957
20 5D63 FUC GAL GLA 2.73038
21 5N6N SUC 3.27103
22 5XLS URA 3.27103
23 5YW5 ADE 3.35196
24 1SQL GUN 3.42466
25 4X1Z FUC GAL NDG 3.61446
26 1Q3P GLU ALA GLN THR ARG LEU 3.66972
27 1EXF GLY 3.71901
28 5X20 AOT 3.84615
29 5N1X 8HH 4.23729
30 1TL2 NDG 4.23729
31 2HFP NSI 4.25532
32 2PIE GLU LEU LYS TPO GLU ARG TYR 4.34783
33 4DXG NDG FUC SIA GAL 4.41176
34 1F76 ORO 4.46429
35 1YZG GDP 4.46927
36 2NU8 COA 5.14019
37 4DG8 AMP 5.14019
38 3F5A SIA GAL NAG 5.28455
39 1ZJ6 G3D 5.34759
40 4OKD GLC GLC GLC 5.37383
41 3QXY SAM 5.37383
42 2BVE PH5 5.88235
43 5LFV SIA GAL NAG 5.99369
44 5C2N NAG 6.25
45 1MR3 G3D 7.18232
46 4B1L FRU 7.87879
47 2H21 SAM 7.94393
48 1TLG GAL 8
49 5WJ6 B4A 8.17757
50 3KIF GDL 8.49057
51 4CNK MEU 8.69565
52 5GG9 8GM 9.64912
53 1R1Q ACE ARG GLU PTR VAL ASN VAL 10
54 5FIT AP2 11.5646
55 3DWQ NGC GAL NGA POL AZI 12.6984
56 2VOH CIT 12.7389
57 5T0K SAM 12.8114
58 5GJH SER ASP PTR MET ASN MET THR PRO 13
59 5JIY SAM 13.1387
60 2RDG NDG FUC SIA GAL 14.7959
61 3IWD M2T 16.129
62 4GNC ASO 21.0702
63 6FHQ DE5 24.1379
64 3KIH GDL 24.7423
65 4EHQ GBL 25
66 3KMT SAH 26.8908
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