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 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: KH3; Similar ligands found: 105
No: Ligand ECFP6 Tc MDL keys Tc
1 KH3 1 1
2 K15 0.791667 0.986486
3 62X 0.693069 0.935065
4 SA8 0.61 0.92
5 KB1 0.605505 0.835443
6 F0P 0.545455 0.894737
7 0UM 0.531532 0.959459
8 S7M 0.522936 0.896104
9 SFG 0.514286 0.851351
10 SAI 0.514019 0.855263
11 EEM 0.504587 0.871795
12 EP4 0.5 0.805195
13 SAH 0.5 0.866667
14 MHZ 0.490566 0.898734
15 5X8 0.485981 0.84
16 GJV 0.466667 0.8
17 6RE 0.466019 0.7875
18 MAO 0.462264 0.807229
19 MYR AMP 0.458333 0.821429
20 J7C 0.457143 0.797468
21 SAM 0.455357 0.871795
22 KAA 0.453782 0.702128
23 5CD 0.453608 0.763158
24 RAB 0.452632 0.776316
25 ADN 0.452632 0.776316
26 XYA 0.452632 0.776316
27 3DH 0.45098 0.826667
28 SXZ 0.45 0.871795
29 1ZZ 0.45 0.821429
30 YLB 0.449612 0.845238
31 YLP 0.448819 0.845238
32 A5A 0.447368 0.638298
33 5SV 0.444444 0.807229
34 SMM 0.443478 0.8625
35 SSA 0.443478 0.652632
36 5N5 0.443299 0.8
37 LAD 0.441667 0.797619
38 A4D 0.438776 0.776316
39 5AL 0.438596 0.72619
40 YLC 0.438462 0.8
41 NVA LMS 0.436975 0.684211
42 AYB 0.43609 0.835294
43 M2T 0.435644 0.7625
44 DTA 0.435644 0.746835
45 XAH 0.435484 0.758621
46 F2R 0.432836 0.741573
47 MTA 0.431373 0.802632
48 5AS 0.431193 0.670213
49 GSU 0.429752 0.670213
50 ZAS 0.428571 0.75
51 DSZ 0.428571 0.652632
52 LSS 0.428571 0.65625
53 54H 0.42735 0.625
54 VMS 0.42735 0.625
55 A3S 0.427273 0.815789
56 S4M 0.425926 0.910256
57 5CA 0.423729 0.652632
58 TSB 0.423729 0.631579
59 53H 0.423729 0.618557
60 CA0 0.423423 0.697674
61 VRT 0.421053 0.868421
62 NEC 0.420561 0.8
63 DSH 0.420561 0.893333
64 GEK 0.420168 0.833333
65 OMR 0.419847 0.811765
66 A3T 0.419643 0.802632
67 SRP 0.418803 0.75
68 WAQ 0.418033 0.77381
69 AMO 0.416667 0.729412
70 A3N 0.416667 0.792208
71 ABM 0.416667 0.714286
72 PRX 0.415929 0.759036
73 52H 0.415254 0.618557
74 LMS 0.415094 0.617021
75 AMP 0.415094 0.690476
76 A 0.415094 0.690476
77 ME8 0.414634 0.77907
78 TXA 0.414634 0.709302
79 SON 0.414414 0.729412
80 ARG AMP 0.414062 0.75
81 7MD 0.414062 0.77907
82 AHX 0.413223 0.704545
83 LEU LMS 0.409836 0.649485
84 BA3 0.409091 0.674419
85 G5A 0.408696 0.670213
86 9ZD 0.408333 0.693182
87 9ZA 0.408333 0.693182
88 8QN 0.408333 0.72619
89 YLA 0.407407 0.781609
90 A3G 0.407407 0.828947
91 AOC 0.407407 0.75641
92 HEJ 0.40708 0.674419
93 ATP 0.40708 0.674419
94 B4P 0.405405 0.674419
95 AP5 0.405405 0.674419
96 NSS 0.404959 0.635417
97 A2D 0.40367 0.674419
98 5FA 0.403509 0.674419
99 0XU 0.403509 0.802632
100 AQP 0.403509 0.674419
101 NB8 0.403226 0.704545
102 A7D 0.401786 0.828947
103 AN2 0.401786 0.666667
104 DAL AMP 0.4 0.72619
105 NVA 2AD 0.4 0.857143
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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