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
5AYF 2.01 Å EC: 2.1.1.43 CRYSTAL STRUCTURE OF SET7/9 IN COMPLEX WITH CYPROHEPTADINE HOMO SAPIENS SET DOMAIN METHYLTRANSFERASE INHIBITOR TRANSFERASE-TRANSFINHIBITOR COMPLEX
Ref.: IDENTIFICATION OF CYPROHEPTADINE AS AN INHIBITOR OF DOMAIN CONTAINING LYSINE METHYLTRANSFERASE 7/9 (SET REGULATES ESTROGEN-DEPENDENT TRANSCRIPTION J.MED.CHEM. V. 59 3650 2016
Members (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 36 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 5AYF ic50 = 1 uM C7H C21 H21 N CN1CCC(=C2....
11 3CBM - ILE LYS ARG SER MLZ LYS ASN SER LEU ALA n/a n/a
70% Homology Family (13)
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 5AYF ic50 = 1 uM C7H C21 H21 N CN1CCC(=C2....
13 3CBM - ILE LYS ARG SER MLZ LYS ASN SER LEU ALA n/a n/a
50% Homology Family (13)
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 5AYF ic50 = 1 uM C7H C21 H21 N CN1CCC(=C2....
13 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: 99
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 0UM 0.531532 0.959459
7 S7M 0.522936 0.896104
8 SFG 0.514286 0.851351
9 SAI 0.514019 0.855263
10 EEM 0.504587 0.871795
11 EP4 0.5 0.805195
12 SAH 0.5 0.866667
13 MHZ 0.490566 0.898734
14 5X8 0.485981 0.84
15 GJV 0.466667 0.8
16 6RE 0.466019 0.7875
17 MAO 0.462264 0.807229
18 MYR AMP 0.458333 0.821429
19 J7C 0.457143 0.797468
20 SAM 0.455357 0.871795
21 KAA 0.453782 0.702128
22 5CD 0.453608 0.763158
23 ADN 0.452632 0.776316
24 XYA 0.452632 0.776316
25 RAB 0.452632 0.776316
26 3DH 0.45098 0.826667
27 1ZZ 0.45 0.821429
28 SXZ 0.45 0.871795
29 YLB 0.449612 0.845238
30 NVA LMS 0.449153 0.673684
31 YLP 0.448819 0.845238
32 A5A 0.447368 0.638298
33 5SV 0.444444 0.807229
34 SSA 0.443478 0.652632
35 SMM 0.443478 0.8625
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 AYB 0.43609 0.835294
42 DTA 0.435644 0.746835
43 M2T 0.435644 0.7625
44 XAH 0.435484 0.758621
45 MTA 0.431373 0.802632
46 5AS 0.431193 0.670213
47 GSU 0.429752 0.670213
48 LSS 0.428571 0.65625
49 ZAS 0.428571 0.75
50 DSZ 0.428571 0.652632
51 54H 0.42735 0.625
52 VMS 0.42735 0.625
53 A3S 0.427273 0.815789
54 S4M 0.425926 0.910256
55 53H 0.423729 0.618557
56 5CA 0.423729 0.652632
57 TSB 0.423729 0.631579
58 CA0 0.423423 0.697674
59 VRT 0.421053 0.868421
60 DSH 0.420561 0.893333
61 NEC 0.420561 0.8
62 AMP MG 0.420561 0.674419
63 GEK 0.420168 0.833333
64 OMR 0.419847 0.811765
65 A3T 0.419643 0.802632
66 SRP 0.418803 0.75
67 WAQ 0.418033 0.77381
68 A3N 0.416667 0.792208
69 AMO 0.416667 0.729412
70 ABM 0.416667 0.714286
71 PRX 0.415929 0.759036
72 52H 0.415254 0.618557
73 A 0.415094 0.690476
74 AMP 0.415094 0.690476
75 ME8 0.414634 0.77907
76 TXA 0.414634 0.709302
77 SON 0.414414 0.729412
78 7MD 0.414062 0.77907
79 AHX 0.413223 0.704545
80 NVA 2AD 0.412281 0.818182
81 LEU LMS 0.409836 0.639175
82 BA3 0.409091 0.674419
83 G5A 0.408696 0.670213
84 8QN 0.408333 0.72619
85 YLA 0.407407 0.781609
86 A3G 0.407407 0.828947
87 AOC 0.407407 0.75641
88 ATP 0.40708 0.674419
89 B4P 0.405405 0.674419
90 AP5 0.405405 0.674419
91 NSS 0.404959 0.635417
92 A2D 0.40367 0.674419
93 AQP 0.403509 0.674419
94 0XU 0.403509 0.802632
95 5FA 0.403509 0.674419
96 NB8 0.403226 0.704545
97 AN2 0.401786 0.666667
98 A7D 0.401786 0.828947
99 DAL AMP 0.4 0.72619
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5AYF; Ligand: SAM; Similar sites found: 20
This union binding pocket(no: 1) in the query (biounit: 5ayf.bio1) has 39 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2BVE PH5 0.007458 0.41372 None
2 5LFV SIA GAL NAG 0.003033 0.47045 1.52091
3 4CU1 H4B 0.02241 0.42612 2.28137
4 1Z82 G3H 0.02654 0.41468 2.6616
5 1Z82 G3P 0.03229 0.41008 2.6616
6 4BGB ADP 0.02111 0.41184 3.42205
7 2H21 SAM 0.000009943 0.52429 3.80228
8 4PPF FLC 0.03158 0.41612 3.80228
9 3LRE ADP 0.03262 0.41289 4.18251
10 3N71 SFG 0.000003927 0.40619 7.98479
11 1U1J C2F 0.01074 0.4385 11.0266
12 4NOS H4B 0.04007 0.41112 11.7871
13 4NOS H2B 0.0482 0.40592 11.7871
14 4DS0 A2G GAL NAG FUC 0.02425 0.42861 12.8834
15 1JZN BGC GAL 0.01429 0.41857 15.5556
16 5T0K SAM 0.00002878 0.41022 17.4905
17 5JIY SAM 0.00001923 0.40822 17.4905
18 5M5G SAH 0.00001886 0.53362 20.9125
19 5M5G VAL MET LEU PRO GLY ARG GLY VAL PRO 0.0000004466 0.50259 20.9125
20 3KMT SAH 0.000008955 0.5678 21.8487
Pocket No.: 2; Query (leader) PDB : 5AYF; Ligand: C7H; Similar sites found: 18
This union binding pocket(no: 2) in the query (biounit: 5ayf.bio1) has 41 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2BVE PH5 0.00813 0.41372 None
2 5LFV SIA GAL NAG 0.003345 0.47045 1.52091
3 4CU1 H4B 0.02447 0.42612 2.28137
4 1Z82 G3H 0.0276 0.41598 2.6616
5 1Z82 G3P 0.03337 0.4115 2.6616
6 5AHS FAD 0.01375 0.40299 3.04183
7 2H21 SAM 0.00001052 0.52667 3.80228
8 4PPF FLC 0.03432 0.41612 3.80228
9 3LRE ADP 0.03553 0.41289 4.18251
10 1U1J C2F 0.01182 0.4385 11.0266
11 4NOS H4B 0.04368 0.41112 11.7871
12 4DS0 A2G GAL NAG FUC 0.02632 0.42861 12.8834
13 1JZN BGC GAL 0.01552 0.41857 15.5556
14 5T0K SAM 0.00002349 0.404 17.4905
15 5JIY SAM 0.00001656 0.40119 17.4905
16 5M5G SAH 0.00001241 0.54524 20.9125
17 5M5G VAL MET LEU PRO GLY ARG GLY VAL PRO 0.000000594 0.5076 20.9125
18 3KMT SAH 0.00000796 0.57373 21.8487
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