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...
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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 39 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 28 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 22 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: 172
No: Ligand ECFP6 Tc MDL keys Tc
1 K15 1 1
2 62X 0.808989 0.947368
3 KH3 0.791667 0.986486
4 SA8 0.677778 0.932432
5 KB1 0.666667 0.846154
6 F0P 0.594595 0.906667
7 SAH 0.583333 0.878378
8 SFG 0.568421 0.863014
9 5X8 0.568421 0.851351
10 S7M 0.56 0.907895
11 EP4 0.55814 0.815789
12 EEM 0.555556 0.883117
13 0UM 0.553398 0.945946
14 SAI 0.55102 0.866667
15 3DH 0.516484 0.837838
16 MAO 0.510417 0.817073
17 MHZ 0.510204 0.886076
18 RAB 0.505882 0.763158
19 ADN 0.505882 0.763158
20 XYA 0.505882 0.763158
21 5CD 0.505747 0.773333
22 SXZ 0.504587 0.883117
23 GJV 0.5 0.7875
24 SAM 0.5 0.883117
25 SMM 0.5 0.873418
26 5N5 0.494253 0.786667
27 1ZZ 0.490909 0.831325
28 A4D 0.488636 0.763158
29 MYR AMP 0.486486 0.831325
30 5SV 0.485981 0.817073
31 SSA 0.485714 0.642105
32 6RE 0.484211 0.775
33 M2T 0.483516 0.772152
34 DTA 0.483516 0.75641
35 KAA 0.481818 0.691489
36 LAD 0.481818 0.785714
37 DSH 0.479167 0.88
38 MTA 0.478261 0.813333
39 NVA LMS 0.477064 0.691489
40 A5A 0.47619 0.645161
41 YLB 0.475 0.833333
42 YLP 0.474576 0.833333
43 J7C 0.474227 0.78481
44 A7D 0.47 0.815789
45 S4M 0.469388 0.897436
46 GSU 0.468468 0.677419
47 WAQ 0.468468 0.783133
48 LSS 0.46789 0.663158
49 DSZ 0.46789 0.659574
50 VMS 0.46729 0.631579
51 54H 0.46729 0.631579
52 OMR 0.466667 0.821429
53 5AL 0.466667 0.73494
54 CA0 0.465347 0.705882
55 ME8 0.464286 0.788235
56 NEC 0.463918 0.786667
57 53H 0.462963 0.625
58 5CA 0.462963 0.642105
59 TSB 0.462963 0.638298
60 YLC 0.46281 0.788235
61 5AS 0.46 0.659574
62 AYB 0.459677 0.823529
63 ABM 0.459184 0.722892
64 GEK 0.458716 0.844156
65 A 0.458333 0.698795
66 LMS 0.458333 0.623656
67 ZAS 0.458333 0.759494
68 AMP 0.458333 0.698795
69 SRP 0.457944 0.738095
70 PRX 0.456311 0.768293
71 F2R 0.456 0.730337
72 SON 0.455446 0.738095
73 AMO 0.454545 0.738095
74 52H 0.453704 0.625
75 BA3 0.45 0.682353
76 AOC 0.44898 0.766234
77 XAH 0.448276 0.747126
78 VRT 0.447619 0.855263
79 G5A 0.447619 0.659574
80 HEJ 0.446602 0.682353
81 ATP 0.446602 0.682353
82 LEU LMS 0.446429 0.65625
83 B4P 0.445545 0.682353
84 AP5 0.445545 0.682353
85 8QN 0.445455 0.73494
86 A2D 0.444444 0.682353
87 5FA 0.442308 0.682353
88 AQP 0.442308 0.682353
89 NSS 0.441441 0.642105
90 AN2 0.441176 0.674419
91 A3S 0.441176 0.802632
92 TT8 0.440367 0.88
93 SRA 0.438776 0.666667
94 TXA 0.438596 0.717647
95 AHX 0.4375 0.693182
96 7MD 0.436975 0.767442
97 ARG AMP 0.436975 0.738636
98 ADX 0.436893 0.623656
99 M33 0.436893 0.694118
100 DAL AMP 0.436364 0.73494
101 A12 0.435644 0.697674
102 AP2 0.435644 0.697674
103 50T 0.432692 0.674419
104 A3T 0.432692 0.789474
105 9ZD 0.432432 0.701149
106 S8M 0.432432 0.797468
107 9ZA 0.432432 0.701149
108 5AD 0.431818 0.739726
109 ADP 0.431373 0.682353
110 A3N 0.43 0.779221
111 GAP 0.429907 0.72619
112 PAJ 0.428571 0.704545
113 Y3J 0.428571 0.697368
114 0XU 0.428571 0.813333
115 YLA 0.428571 0.770115
116 4AD 0.428571 0.729412
117 FA5 0.42735 0.738095
118 AT4 0.427184 0.659091
119 7D7 0.426966 0.714286
120 NB8 0.426087 0.712644
121 PTJ 0.426087 0.712644
122 AAT 0.425926 0.833333
123 SAP 0.424528 0.651685
124 AGS 0.424528 0.651685
125 NVA 2AD 0.424528 0.844156
126 YSA 0.423729 0.642105
127 8X1 0.423423 0.65625
128 AU1 0.423077 0.666667
129 SO8 0.420561 0.805195
130 A3G 0.42 0.815789
131 ACP 0.419048 0.686047
132 3AM 0.418367 0.666667
133 T99 0.416667 0.659091
134 TAT 0.416667 0.659091
135 ANP 0.416667 0.666667
136 8PZ 0.415254 0.642105
137 YAP 0.415254 0.729412
138 AR6 0.415094 0.702381
139 APR 0.415094 0.702381
140 APC 0.415094 0.697674
141 9K8 0.413793 0.639175
142 YLY 0.413534 0.845238
143 00A 0.412281 0.681818
144 ADP PO3 0.411215 0.698795
145 AD9 0.411215 0.666667
146 A5D 0.411215 0.75641
147 RBY 0.411215 0.717647
148 ADV 0.411215 0.717647
149 A22 0.410714 0.674419
150 4YB 0.409836 0.663158
151 IOT 0.409449 0.761364
152 ALF ADP 0.409091 0.651685
153 ADP ALF 0.409091 0.651685
154 3UK 0.408696 0.705882
155 OAD 0.408696 0.72619
156 2AM 0.408163 0.658824
157 OOB 0.40708 0.714286
158 9SN 0.40678 0.674157
159 2VA 0.40566 0.769231
160 6YZ 0.405405 0.686047
161 P5A 0.405172 0.702128
162 B5V 0.405172 0.697674
163 7MC 0.404762 0.790698
164 N0B 0.404412 0.770115
165 ACQ 0.40367 0.686047
166 A1R 0.403509 0.741176
167 B5Y 0.403361 0.709302
168 48N 0.403226 0.732558
169 BIS 0.401709 0.681818
170 3OD 0.401709 0.72619
171 80F 0.401515 0.673913
172 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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