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...
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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 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: KH3; Similar ligands found: 133
No: Ligand ECFP6 Tc MDL keys Tc
1 KH3 1 1
2 K15 0.791667 0.986486
3 KYE 0.695238 0.873418
4 62X 0.693069 0.935065
5 HZ2 0.663636 0.896104
6 KXW 0.654545 0.92
7 HY8 0.637168 0.896104
8 SA8 0.61 0.92
9 KB1 0.605505 0.835443
10 OZP 0.6 0.894737
11 F0P 0.545455 0.894737
12 Q34 0.545455 0.82716
13 Q2M 0.532787 0.848101
14 0UM 0.531532 0.959459
15 KYB 0.531532 0.848101
16 KY2 0.527273 0.848101
17 S7M 0.522936 0.896104
18 Q2V 0.52 0.883117
19 SFG 0.514286 0.851351
20 SAI 0.514019 0.855263
21 KY5 0.508621 0.893333
22 Q2P 0.507812 0.82716
23 EEM 0.504587 0.871795
24 KY8 0.504348 0.87013
25 SAH 0.5 0.866667
26 EP4 0.5 0.805195
27 MHZ 0.490566 0.898734
28 5X8 0.485981 0.84
29 GJV 0.466667 0.8
30 6RE 0.466019 0.7875
31 MAO 0.462264 0.807229
32 MYR AMP 0.458333 0.821429
33 J7C 0.457143 0.797468
34 SAM 0.455357 0.871795
35 KAA 0.453782 0.702128
36 5CD 0.453608 0.763158
37 ADN 0.452632 0.776316
38 RAB 0.452632 0.776316
39 XYA 0.452632 0.776316
40 3DH 0.45098 0.826667
41 SXZ 0.45 0.871795
42 1ZZ 0.45 0.821429
43 YLB 0.449612 0.845238
44 YLP 0.448819 0.845238
45 A5A 0.447368 0.638298
46 5SV 0.444444 0.807229
47 SMM 0.443478 0.8625
48 SSA 0.443478 0.652632
49 5N5 0.443299 0.8
50 LAD 0.441667 0.797619
51 A4D 0.438776 0.776316
52 5AL 0.438596 0.72619
53 YLC 0.438462 0.8
54 NVA LMS 0.436975 0.684211
55 AYB 0.43609 0.835294
56 M2T 0.435644 0.7625
57 DTA 0.435644 0.746835
58 XAH 0.435484 0.758621
59 F2R 0.432836 0.741573
60 KG4 0.432432 0.697674
61 MTA 0.431373 0.802632
62 5AS 0.431193 0.670213
63 GSU 0.429752 0.670213
64 ZAS 0.428571 0.75
65 DSZ 0.428571 0.652632
66 LSS 0.428571 0.65625
67 VMS 0.42735 0.625
68 54H 0.42735 0.625
69 A3S 0.427273 0.815789
70 V2G 0.426087 0.744186
71 S4M 0.425926 0.910256
72 AMP MG 0.424528 0.698795
73 53H 0.423729 0.618557
74 QA7 0.423729 0.72093
75 5CA 0.423729 0.652632
76 TSB 0.423729 0.631579
77 CA0 0.423423 0.697674
78 EU9 0.423077 0.730337
79 VRT 0.421053 0.868421
80 NEC 0.420561 0.8
81 DSH 0.420561 0.893333
82 GEK 0.420168 0.833333
83 N37 0.419847 0.807692
84 OMR 0.419847 0.811765
85 A3T 0.419643 0.802632
86 8LH 0.418803 0.75
87 V47 0.418803 0.789474
88 SRP 0.418803 0.75
89 WAQ 0.418033 0.77381
90 ABM 0.416667 0.714286
91 AMO 0.416667 0.729412
92 45A 0.416667 0.714286
93 A3N 0.416667 0.792208
94 PRX 0.415929 0.759036
95 U4Y 0.415385 0.833333
96 52H 0.415254 0.618557
97 AMP 0.415094 0.690476
98 LMS 0.415094 0.617021
99 A 0.415094 0.690476
100 ME8 0.414634 0.77907
101 TXA 0.414634 0.709302
102 SON 0.414414 0.729412
103 ARG AMP 0.414062 0.75
104 7MD 0.414062 0.77907
105 AHX 0.413223 0.704545
106 NWW 0.41 0.72
107 LEU LMS 0.409836 0.680851
108 BA3 0.409091 0.674419
109 G5A 0.408696 0.670213
110 9ZA 0.408333 0.693182
111 8QN 0.408333 0.72619
112 9ZD 0.408333 0.693182
113 YLA 0.407407 0.781609
114 AOC 0.407407 0.75641
115 A3G 0.407407 0.828947
116 ATP 0.40708 0.674419
117 HEJ 0.40708 0.674419
118 J4G 0.406504 0.741176
119 B4P 0.405405 0.674419
120 AP5 0.405405 0.674419
121 NSS 0.404959 0.635417
122 A2D 0.40367 0.674419
123 0XU 0.403509 0.802632
124 5FA 0.403509 0.674419
125 AQP 0.403509 0.674419
126 NB8 0.403226 0.704545
127 AN2 0.401786 0.666667
128 A7D 0.401786 0.828947
129 8LE 0.401709 0.701149
130 K2H 0.401639 0.78481
131 DAL AMP 0.4 0.72619
132 8LQ 0.4 0.75
133 NVA 2AD 0.4 0.857143
Similar Ligands (3D)
Ligand no: 1; Ligand: KH3; 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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