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 37 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 ic50 = 0.41 uM C7N C21 H21 N O CN1CCC(=C2....
11 5AYF Ki = 15 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 26 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 ic50 = 0.41 uM C7N C21 H21 N O CN1CCC(=C2....
13 5AYF Ki = 15 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 21 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 ic50 = 0.41 uM C7N C21 H21 N O CN1CCC(=C2....
13 5AYF Ki = 15 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 (2D)
Ligand no: 1; Ligand: K15; Similar ligands found: 212
No: Ligand ECFP6 Tc MDL keys Tc
1 K15 1 1
2 62X 0.808989 0.947368
3 KH3 0.791667 0.986486
4 KYE 0.787234 0.860759
5 KXW 0.737374 0.906667
6 HY8 0.699029 0.883117
7 OZP 0.68932 0.906667
8 SA8 0.677778 0.932432
9 KB1 0.666667 0.846154
10 HZ2 0.663462 0.883117
11 F0P 0.594595 0.906667
12 KYB 0.584158 0.835443
13 SAH 0.583333 0.878378
14 Q2M 0.580357 0.858974
15 Q34 0.580357 0.8375
16 KY2 0.58 0.835443
17 5X8 0.568421 0.851351
18 SFG 0.568421 0.863014
19 Q2V 0.565217 0.894737
20 Q2P 0.564103 0.8375
21 S7M 0.56 0.907895
22 EP4 0.55814 0.815789
23 KY5 0.556604 0.88
24 EEM 0.555556 0.883117
25 0UM 0.553398 0.945946
26 KY8 0.552381 0.857143
27 SAI 0.55102 0.866667
28 3DH 0.516484 0.837838
29 MAO 0.510417 0.817073
30 MHZ 0.510204 0.886076
31 XYA 0.505882 0.763158
32 ADN 0.505882 0.763158
33 RAB 0.505882 0.763158
34 5CD 0.505747 0.773333
35 SXZ 0.504587 0.883117
36 SAM 0.5 0.883117
37 SMM 0.5 0.873418
38 GJV 0.5 0.7875
39 5N5 0.494253 0.786667
40 1ZZ 0.490909 0.831325
41 A4D 0.488636 0.763158
42 MYR AMP 0.486486 0.831325
43 5SV 0.485981 0.817073
44 SSA 0.485714 0.642105
45 6RE 0.484211 0.775
46 M2T 0.483516 0.772152
47 DTA 0.483516 0.75641
48 KAA 0.481818 0.691489
49 LAD 0.481818 0.785714
50 DSH 0.479167 0.88
51 MTA 0.478261 0.813333
52 NVA LMS 0.477064 0.691489
53 A5A 0.47619 0.645161
54 YLB 0.475 0.833333
55 YLP 0.474576 0.833333
56 J7C 0.474227 0.78481
57 A7D 0.47 0.815789
58 S4M 0.469388 0.897436
59 AMP MG 0.46875 0.707317
60 WAQ 0.468468 0.783133
61 GSU 0.468468 0.677419
62 DSZ 0.46789 0.659574
63 LSS 0.46789 0.663158
64 54H 0.46729 0.631579
65 VMS 0.46729 0.631579
66 OMR 0.466667 0.821429
67 5AL 0.466667 0.73494
68 CA0 0.465347 0.705882
69 ME8 0.464286 0.788235
70 NEC 0.463918 0.786667
71 53H 0.462963 0.625
72 TSB 0.462963 0.638298
73 5CA 0.462963 0.642105
74 YLC 0.46281 0.788235
75 U4Y 0.462185 0.844156
76 KG4 0.460784 0.705882
77 5AS 0.46 0.659574
78 AYB 0.459677 0.823529
79 ABM 0.459184 0.722892
80 45A 0.459184 0.722892
81 GEK 0.458716 0.844156
82 A 0.458333 0.698795
83 ZAS 0.458333 0.759494
84 AMP 0.458333 0.698795
85 LMS 0.458333 0.623656
86 SRP 0.457944 0.738095
87 V47 0.457944 0.8
88 PRX 0.456311 0.768293
89 F2R 0.456 0.730337
90 NWW 0.455556 0.72973
91 SON 0.455446 0.738095
92 AMO 0.454545 0.738095
93 N37 0.454545 0.818182
94 52H 0.453704 0.625
95 BA3 0.45 0.682353
96 QA7 0.449541 0.729412
97 AOC 0.44898 0.766234
98 XAH 0.448276 0.747126
99 VRT 0.447619 0.855263
100 G5A 0.447619 0.659574
101 HEJ 0.446602 0.682353
102 ATP 0.446602 0.682353
103 EU9 0.446281 0.738636
104 AP5 0.445545 0.682353
105 B4P 0.445545 0.682353
106 QXP 0.445455 0.645161
107 8QN 0.445455 0.73494
108 8LH 0.444444 0.738095
109 A2D 0.444444 0.682353
110 AQP 0.442308 0.682353
111 5FA 0.442308 0.682353
112 NSS 0.441441 0.642105
113 AN2 0.441176 0.674419
114 A3S 0.441176 0.802632
115 TT8 0.440367 0.88
116 V2G 0.439252 0.732558
117 8LE 0.439252 0.709302
118 SRA 0.438776 0.666667
119 TXA 0.438596 0.717647
120 AHX 0.4375 0.693182
121 K2H 0.4375 0.794872
122 ARG AMP 0.436975 0.738636
123 7MD 0.436975 0.767442
124 M33 0.436893 0.694118
125 ADX 0.436893 0.623656
126 DAL AMP 0.436364 0.73494
127 8LQ 0.436364 0.759036
128 A12 0.435644 0.697674
129 AP2 0.435644 0.697674
130 LEU LMS 0.433628 0.688172
131 QXG 0.433628 0.638298
132 50T 0.432692 0.674419
133 A3T 0.432692 0.789474
134 9ZA 0.432432 0.701149
135 9ZD 0.432432 0.701149
136 S8M 0.432432 0.797468
137 5AD 0.431818 0.739726
138 ADP 0.431373 0.682353
139 A3N 0.43 0.779221
140 GAP 0.429907 0.72619
141 0XU 0.428571 0.813333
142 4AD 0.428571 0.729412
143 YLA 0.428571 0.770115
144 PAJ 0.428571 0.704545
145 Y3J 0.428571 0.697368
146 FA5 0.42735 0.738095
147 AT4 0.427184 0.659091
148 ADP MG 0.427184 0.698795
149 ADP BEF 0.427184 0.698795
150 7D7 0.426966 0.714286
151 PTJ 0.426087 0.712644
152 NB8 0.426087 0.712644
153 AAT 0.425926 0.833333
154 AGS 0.424528 0.651685
155 NVA 2AD 0.424528 0.844156
156 YSA 0.423729 0.642105
157 K3H 0.423729 0.765432
158 8X1 0.423423 0.65625
159 AU1 0.423077 0.666667
160 NWQ 0.42268 0.733333
161 SO8 0.420561 0.805195
162 A3G 0.42 0.815789
163 N5O 0.42 0.802632
164 ACP 0.419048 0.686047
165 3AM 0.418367 0.666667
166 J4G 0.417391 0.75
167 R2V 0.417391 0.645161
168 T99 0.416667 0.659091
169 TAT 0.416667 0.659091
170 ANP 0.416667 0.666667
171 8PZ 0.415254 0.642105
172 AR6 0.415094 0.702381
173 APR 0.415094 0.702381
174 APC 0.415094 0.697674
175 9K8 0.413793 0.639175
176 YLY 0.413534 0.845238
177 00A 0.412281 0.681818
178 N5A 0.411765 0.8
179 ADP PO3 0.411215 0.698795
180 ADV 0.411215 0.717647
181 AD9 0.411215 0.666667
182 A5D 0.411215 0.75641
183 ATP MG 0.411215 0.698795
184 APC MG 0.411215 0.702381
185 RBY 0.411215 0.717647
186 A22 0.410714 0.674419
187 4YB 0.409836 0.663158
188 IOT 0.409449 0.761364
189 ANP MG 0.409091 0.674419
190 ALF ADP 0.409091 0.651685
191 OAD 0.408696 0.72619
192 3UK 0.408696 0.705882
193 2AM 0.408163 0.658824
194 BEF ADP 0.407407 0.682353
195 OOB 0.40708 0.714286
196 9SN 0.40678 0.674157
197 2VA 0.40566 0.769231
198 H1Q 0.40566 0.690476
199 6YZ 0.405405 0.686047
200 P5A 0.405172 0.702128
201 B5V 0.405172 0.697674
202 7MC 0.404762 0.790698
203 N0B 0.404412 0.770115
204 ACQ 0.40367 0.686047
205 A1R 0.403509 0.741176
206 B5Y 0.403361 0.709302
207 48N 0.403226 0.732558
208 HQG 0.401786 0.694118
209 BIS 0.401709 0.681818
210 3OD 0.401709 0.72619
211 80F 0.401515 0.673913
212 DLL 0.4 0.714286
Similar Ligands (3D)
Ligand no: 1; Ligand: K15; 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 : 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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