Receptor
PDB id Resolution Class Description Source Keywords
3VUZ 2.5 Å EC: 2.1.1.43 CRYSTAL STRUCTURE OF HISTONE METHYLTRANSFERASE SET7/9 IN COM AAM-1 HOMO SAPIENS SET DOMAIN TRANSFERASE ADENOSYLMETHIONINE BINDING TRANSFETRANSFERASE INHIBITOR COMPLEX
Ref.: STRUCTURES OF HISTONE METHYLTRANSFERASE SET7/9 IN C WITH ADENOSYLMETHIONINE DERIVATIVES ACTA CRYSTALLOGR.,SECT.D V. 69 595 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
K15 A:401;
Valid;
none;
submit data
451.52 C20 H33 N7 O5 CCCCC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5YLT 1.69 Å EC: 2.1.1.43 CRYSTAL STRUCTURE OF SET7/9 IN COMPLEX WITH A CYPROHEPTADINE DERIVATIVE HOMO SAPIENS SET DOMAIN METHYLTRANSFERASE INHIBITOR TRANSFERASE TRANSTRANSFERASE INHIBITOR COMPLEX
Ref.: DEVELOPMENT OF NOVEL INHIBITORS FOR HISTONE METHYLTRANSFERASE SET7/9 BASED ON CYPROHEPTADINE. CHEMMEDCHEM V. 13 1530 2018
Members (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 40 families.
1 3VUZ - K15 C20 H33 N7 O5 CCCCCCN(CC....
2 3VV0 - KH3 C22 H38 N8 O5 CCCCCCNCCN....
3 3CBO - ILE LYS ARG SER MLZ LYS ASN SER LEU ALA n/a n/a
4 3CBP - ILE LYS ARG SER LYS LYS ASN SER LEU ALA n/a n/a
5 5EG2 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
6 3OS5 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
7 1XQH - SAH C14 H20 N6 O5 S c1nc(c2c(n....
8 1N6A - SAM C15 H22 N6 O5 S C[S@@+](CC....
9 1O9S - SAH C14 H20 N6 O5 S c1nc(c2c(n....
10 5YLT Kd = 0.41 uM C7N C21 H21 N O CN1CCC(=C2....
11 5AYF ic50 = 1 uM C7H C21 H21 N CN1CCC(=C2....
12 3CBM - ILE LYS ARG SER MLZ LYS ASN SER LEU ALA n/a n/a
70% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 29 families.
1 1MT6 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 1N6C - SAM C15 H22 N6 O5 S C[S@@+](CC....
3 3VUZ - K15 C20 H33 N7 O5 CCCCCCN(CC....
4 3VV0 - KH3 C22 H38 N8 O5 CCCCCCNCCN....
5 3CBO - ILE LYS ARG SER MLZ LYS ASN SER LEU ALA n/a n/a
6 3CBP - ILE LYS ARG SER LYS LYS ASN SER LEU ALA n/a n/a
7 5EG2 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
8 3OS5 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
9 1XQH - SAH C14 H20 N6 O5 S c1nc(c2c(n....
10 1N6A - SAM C15 H22 N6 O5 S C[S@@+](CC....
11 1O9S - SAH C14 H20 N6 O5 S c1nc(c2c(n....
12 5YLT Kd = 0.41 uM C7N C21 H21 N O CN1CCC(=C2....
13 5AYF ic50 = 1 uM C7H C21 H21 N CN1CCC(=C2....
14 3CBM - ILE LYS ARG SER MLZ LYS ASN SER LEU ALA n/a n/a
50% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 23 families.
1 1MT6 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 1N6C - SAM C15 H22 N6 O5 S C[S@@+](CC....
3 3VUZ - K15 C20 H33 N7 O5 CCCCCCN(CC....
4 3VV0 - KH3 C22 H38 N8 O5 CCCCCCNCCN....
5 3CBO - ILE LYS ARG SER MLZ LYS ASN SER LEU ALA n/a n/a
6 3CBP - ILE LYS ARG SER LYS LYS ASN SER LEU ALA n/a n/a
7 5EG2 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
8 3OS5 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
9 1XQH - SAH C14 H20 N6 O5 S c1nc(c2c(n....
10 1N6A - SAM C15 H22 N6 O5 S C[S@@+](CC....
11 1O9S - SAH C14 H20 N6 O5 S c1nc(c2c(n....
12 5YLT Kd = 0.41 uM C7N C21 H21 N O CN1CCC(=C2....
13 5AYF ic50 = 1 uM C7H C21 H21 N CN1CCC(=C2....
14 3CBM - ILE LYS ARG SER MLZ LYS ASN SER LEU ALA n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: K15; Similar ligands found: 189
No: Ligand ECFP6 Tc MDL keys Tc
1 K15 1 1
2 62X 0.808989 0.947368
3 KH3 0.791667 0.986486
4 HY8 0.699029 0.883117
5 OZP 0.68932 0.906667
6 SA8 0.677778 0.932432
7 KB1 0.666667 0.846154
8 HZ2 0.663462 0.883117
9 F0P 0.594595 0.906667
10 SAH 0.583333 0.878378
11 5X8 0.568421 0.851351
12 SFG 0.568421 0.863014
13 S7M 0.56 0.907895
14 EP4 0.55814 0.815789
15 EEM 0.555556 0.883117
16 0UM 0.553398 0.945946
17 SAI 0.55102 0.866667
18 3DH 0.516484 0.837838
19 MAO 0.510417 0.817073
20 MHZ 0.510204 0.886076
21 XYA 0.505882 0.763158
22 RAB 0.505882 0.763158
23 ADN 0.505882 0.763158
24 5CD 0.505747 0.773333
25 SXZ 0.504587 0.883117
26 SMM 0.5 0.873418
27 GJV 0.5 0.7875
28 SAM 0.5 0.883117
29 5N5 0.494253 0.786667
30 1ZZ 0.490909 0.831325
31 A4D 0.488636 0.763158
32 MYR AMP 0.486486 0.831325
33 5SV 0.485981 0.817073
34 SSA 0.485714 0.642105
35 6RE 0.484211 0.775
36 DTA 0.483516 0.75641
37 M2T 0.483516 0.772152
38 LAD 0.481818 0.785714
39 KAA 0.481818 0.691489
40 DSH 0.479167 0.88
41 MTA 0.478261 0.813333
42 NVA LMS 0.477064 0.691489
43 A5A 0.47619 0.645161
44 YLB 0.475 0.833333
45 YLP 0.474576 0.833333
46 J7C 0.474227 0.78481
47 A7D 0.47 0.815789
48 S4M 0.469388 0.897436
49 WAQ 0.468468 0.783133
50 GSU 0.468468 0.677419
51 DSZ 0.46789 0.659574
52 LSS 0.46789 0.663158
53 VMS 0.46729 0.631579
54 54H 0.46729 0.631579
55 OMR 0.466667 0.821429
56 5AL 0.466667 0.73494
57 CA0 0.465347 0.705882
58 ME8 0.464286 0.788235
59 NEC 0.463918 0.786667
60 53H 0.462963 0.625
61 5CA 0.462963 0.642105
62 TSB 0.462963 0.638298
63 YLC 0.46281 0.788235
64 KG4 0.460784 0.705882
65 5AS 0.46 0.659574
66 AYB 0.459677 0.823529
67 45A 0.459184 0.722892
68 ABM 0.459184 0.722892
69 GEK 0.458716 0.844156
70 AMP 0.458333 0.698795
71 LMS 0.458333 0.623656
72 ZAS 0.458333 0.759494
73 A 0.458333 0.698795
74 SRP 0.457944 0.738095
75 PRX 0.456311 0.768293
76 F2R 0.456 0.730337
77 SON 0.455446 0.738095
78 N37 0.454545 0.818182
79 AMO 0.454545 0.738095
80 52H 0.453704 0.625
81 BA3 0.45 0.682353
82 AOC 0.44898 0.766234
83 XAH 0.448276 0.747126
84 G5A 0.447619 0.659574
85 VRT 0.447619 0.855263
86 ATP 0.446602 0.682353
87 HEJ 0.446602 0.682353
88 LEU LMS 0.446429 0.65625
89 B4P 0.445545 0.682353
90 AP5 0.445545 0.682353
91 8QN 0.445455 0.73494
92 A2D 0.444444 0.682353
93 8LH 0.444444 0.738095
94 5FA 0.442308 0.682353
95 AQP 0.442308 0.682353
96 NSS 0.441441 0.642105
97 AN2 0.441176 0.674419
98 A3S 0.441176 0.802632
99 TT8 0.440367 0.88
100 8LE 0.439252 0.709302
101 SRA 0.438776 0.666667
102 TXA 0.438596 0.717647
103 AHX 0.4375 0.693182
104 ARG AMP 0.436975 0.738636
105 7MD 0.436975 0.767442
106 M33 0.436893 0.694118
107 ADX 0.436893 0.623656
108 DAL AMP 0.436364 0.73494
109 8LQ 0.436364 0.759036
110 A12 0.435644 0.697674
111 AP2 0.435644 0.697674
112 50T 0.432692 0.674419
113 A3T 0.432692 0.789474
114 9ZD 0.432432 0.701149
115 9ZA 0.432432 0.701149
116 S8M 0.432432 0.797468
117 5AD 0.431818 0.739726
118 ADP 0.431373 0.682353
119 A3N 0.43 0.779221
120 GAP 0.429907 0.72619
121 YLA 0.428571 0.770115
122 0XU 0.428571 0.813333
123 Y3J 0.428571 0.697368
124 4AD 0.428571 0.729412
125 PAJ 0.428571 0.704545
126 FA5 0.42735 0.738095
127 ADP MG 0.427184 0.698795
128 AT4 0.427184 0.659091
129 7D7 0.426966 0.714286
130 NB8 0.426087 0.712644
131 PTJ 0.426087 0.712644
132 AAT 0.425926 0.833333
133 SAP 0.424528 0.651685
134 AGS 0.424528 0.651685
135 NVA 2AD 0.424528 0.844156
136 YSA 0.423729 0.642105
137 8X1 0.423423 0.65625
138 AU1 0.423077 0.666667
139 SO8 0.420561 0.805195
140 A3G 0.42 0.815789
141 N5O 0.42 0.802632
142 ACP 0.419048 0.686047
143 3AM 0.418367 0.666667
144 J4G 0.417391 0.75
145 T99 0.416667 0.659091
146 ANP 0.416667 0.666667
147 TAT 0.416667 0.659091
148 8PZ 0.415254 0.642105
149 YAP 0.415254 0.729412
150 AR6 0.415094 0.702381
151 APC 0.415094 0.697674
152 APR 0.415094 0.702381
153 9K8 0.413793 0.639175
154 YLY 0.413534 0.845238
155 00A 0.412281 0.681818
156 N5A 0.411765 0.8
157 ADP PO3 0.411215 0.698795
158 AD9 0.411215 0.666667
159 RBY 0.411215 0.717647
160 A5D 0.411215 0.75641
161 APC MG 0.411215 0.702381
162 ATP MG 0.411215 0.698795
163 ADV 0.411215 0.717647
164 A22 0.410714 0.674419
165 4YB 0.409836 0.663158
166 IOT 0.409449 0.761364
167 ADP ALF 0.409091 0.651685
168 ALF ADP 0.409091 0.651685
169 OAD 0.408696 0.72619
170 3UK 0.408696 0.705882
171 2AM 0.408163 0.658824
172 OOB 0.40708 0.714286
173 9SN 0.40678 0.674157
174 H1Q 0.40566 0.690476
175 2VA 0.40566 0.769231
176 6YZ 0.405405 0.686047
177 P5A 0.405172 0.702128
178 B5V 0.405172 0.697674
179 7MC 0.404762 0.790698
180 N0B 0.404412 0.770115
181 ACQ 0.40367 0.686047
182 A1R 0.403509 0.741176
183 B5Y 0.403361 0.709302
184 48N 0.403226 0.732558
185 HQG 0.401786 0.694118
186 3OD 0.401709 0.72619
187 BIS 0.401709 0.681818
188 80F 0.401515 0.673913
189 DLL 0.4 0.714286
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5YLT; Ligand: SFG; 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: 5ylt.bio1) has 41 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5YLT; Ligand: C7N; 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: 5ylt.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
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