Receptor
PDB id Resolution Class Description Source Keywords
3VV0 2 Å EC: 2.1.1.43 CRYSTAL STRUCTURE OF HISTONE METHYLTRANSFERASE SET7/9 IN COM DAAM-3 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
KH3 A:401;
Valid;
none;
submit data
494.588 C22 H38 N8 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: KH3; Similar ligands found: 115
No: Ligand ECFP6 Tc MDL keys Tc
1 KH3 1 1
2 K15 0.791667 0.986486
3 62X 0.693069 0.935065
4 HZ2 0.663636 0.896104
5 HY8 0.637168 0.896104
6 SA8 0.61 0.92
7 KB1 0.605505 0.835443
8 OZP 0.6 0.894737
9 F0P 0.545455 0.894737
10 0UM 0.531532 0.959459
11 S7M 0.522936 0.896104
12 SFG 0.514286 0.851351
13 SAI 0.514019 0.855263
14 EEM 0.504587 0.871795
15 EP4 0.5 0.805195
16 SAH 0.5 0.866667
17 MHZ 0.490566 0.898734
18 5X8 0.485981 0.84
19 GJV 0.466667 0.8
20 6RE 0.466019 0.7875
21 MAO 0.462264 0.807229
22 MYR AMP 0.458333 0.821429
23 J7C 0.457143 0.797468
24 SAM 0.455357 0.871795
25 KAA 0.453782 0.702128
26 5CD 0.453608 0.763158
27 XYA 0.452632 0.776316
28 RAB 0.452632 0.776316
29 ADN 0.452632 0.776316
30 3DH 0.45098 0.826667
31 SXZ 0.45 0.871795
32 1ZZ 0.45 0.821429
33 YLB 0.449612 0.845238
34 YLP 0.448819 0.845238
35 A5A 0.447368 0.638298
36 5SV 0.444444 0.807229
37 SMM 0.443478 0.8625
38 SSA 0.443478 0.652632
39 5N5 0.443299 0.8
40 LAD 0.441667 0.797619
41 A4D 0.438776 0.776316
42 5AL 0.438596 0.72619
43 YLC 0.438462 0.8
44 NVA LMS 0.436975 0.684211
45 AYB 0.43609 0.835294
46 DTA 0.435644 0.746835
47 M2T 0.435644 0.7625
48 XAH 0.435484 0.758621
49 F2R 0.432836 0.741573
50 KG4 0.432432 0.697674
51 MTA 0.431373 0.802632
52 5AS 0.431193 0.670213
53 GSU 0.429752 0.670213
54 DSZ 0.428571 0.652632
55 ZAS 0.428571 0.75
56 LSS 0.428571 0.65625
57 54H 0.42735 0.625
58 VMS 0.42735 0.625
59 A3S 0.427273 0.815789
60 S4M 0.425926 0.910256
61 TSB 0.423729 0.631579
62 5CA 0.423729 0.652632
63 53H 0.423729 0.618557
64 CA0 0.423423 0.697674
65 VRT 0.421053 0.868421
66 DSH 0.420561 0.893333
67 NEC 0.420561 0.8
68 GEK 0.420168 0.833333
69 N37 0.419847 0.807692
70 OMR 0.419847 0.811765
71 A3T 0.419643 0.802632
72 SRP 0.418803 0.75
73 8LH 0.418803 0.75
74 WAQ 0.418033 0.77381
75 AMO 0.416667 0.729412
76 A3N 0.416667 0.792208
77 45A 0.416667 0.714286
78 ABM 0.416667 0.714286
79 PRX 0.415929 0.759036
80 52H 0.415254 0.618557
81 A 0.415094 0.690476
82 LMS 0.415094 0.617021
83 AMP 0.415094 0.690476
84 TXA 0.414634 0.709302
85 ME8 0.414634 0.77907
86 SON 0.414414 0.729412
87 ARG AMP 0.414062 0.75
88 7MD 0.414062 0.77907
89 AHX 0.413223 0.704545
90 LEU LMS 0.409836 0.649485
91 BA3 0.409091 0.674419
92 G5A 0.408696 0.670213
93 8QN 0.408333 0.72619
94 9ZD 0.408333 0.693182
95 9ZA 0.408333 0.693182
96 YLA 0.407407 0.781609
97 AOC 0.407407 0.75641
98 A3G 0.407407 0.828947
99 ATP 0.40708 0.674419
100 HEJ 0.40708 0.674419
101 J4G 0.406504 0.741176
102 AP5 0.405405 0.674419
103 B4P 0.405405 0.674419
104 NSS 0.404959 0.635417
105 A2D 0.40367 0.674419
106 0XU 0.403509 0.802632
107 AQP 0.403509 0.674419
108 5FA 0.403509 0.674419
109 NB8 0.403226 0.704545
110 AN2 0.401786 0.666667
111 A7D 0.401786 0.828947
112 8LE 0.401709 0.701149
113 NVA 2AD 0.4 0.857143
114 8LQ 0.4 0.75
115 DAL AMP 0.4 0.72619
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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