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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 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: 85
This union binding pocket(no: 1) in the query (biounit: 5ylt.bio1) has 41 residues
No: Leader PDB Ligand Sequence Similarity
1 4DDY DN6 0.760456
2 4DE3 DN8 0.760456
3 3O03 GCO 1.52091
4 5AHS FAD 1.52091
5 2BVE PH5 1.68067
6 5VEQ PMP 1.90114
7 4LIK CIT 2.28137
8 2FB3 MET 2.28137
9 1U08 PLP 2.28137
10 3THR C2F 2.28137
11 2BQP GLC 2.5641
12 3ZOK GLY 2.6616
13 5XSS XYP 2.6616
14 3R9V DXC 2.6616
15 4XH0 ADP 2.6616
16 1XHL TNE 2.6616
17 1F6D UDP 2.6616
18 3I9U DTU 2.6616
19 2GMM MAN MAN 2.77778
20 1Q8S MAN MMA 2.77778
21 2PHX MAN MAN 2.77778
22 2OFW ADX 2.88462
23 1BG2 ADP 3.04183
24 1PCA CIT 3.04183
25 4KYS VIB 3.04183
26 4INI AMP 3.07692
27 4XO8 KGM 3.16456
28 4KFU ACP 3.30189
29 6C0B MLI 3.42205
30 5M90 JIF 3.42205
31 1IZC PYR 3.42205
32 3W6X HZP 3.49345
33 2H21 SAM 3.80228
34 3QXY SAM 3.80228
35 3HCH RSM 4.10959
36 1GOJ ADP 4.18251
37 1D8C SOR 4.18251
38 3LRE ADP 4.18251
39 4YJK URA 4.36508
40 2Y65 ADP 4.56274
41 4LEB THR THR THR THR THR THR THR 4.56274
42 5LFV SIA GAL NAG 4.94297
43 1EQ2 ADQ 4.94297
44 4CP8 MLI 4.94297
45 3AQT RCO 5.30612
46 5N6N SUC 5.32319
47 2X5F PLP 5.32319
48 1VBO MAN MAN MAN 5.36913
49 2KIN ADP 5.46218
50 5IXB LGA 5.55556
51 3KIF GDL 5.66038
52 1T5C ADP 5.70342
53 3W68 PBU 5.70342
54 4PPF FLC 5.70342
55 1PVC ILE SER GLU VAL 5.88235
56 3VCY UD1 6.46388
57 3LL2 MAN MAN MAN MAN MAN MAN MAN MAN 6.50407
58 2HYQ MAN MAN 6.55738
59 2GUE NAG 6.55738
60 2HYR BGC GLC 6.55738
61 2GUC MAN 6.55738
62 2NU5 NAG 6.55738
63 2NUO BGC 6.55738
64 2GUD MAN 6.55738
65 1TL2 NDG 6.77966
66 4P83 U5P 7.14286
67 5WHT SIA GAL 7.24638
68 5WHT SIA 7.24638
69 5T63 ALA ALA ALA ALA 7.60456
70 3N71 SFG 7.98479
71 2VL1 GLY GLY 7.98479
72 3KIH GDL 8.24742
73 3A3B RBF 8.42105
74 2ZL4 ALA ALA ALA ALA 9.18367
75 2DUR MAN MAN 9.48617
76 5CZY SAM 10.6464
77 2VVG ADP 10.6464
78 1OFS SUC 12.5
79 4DS0 A2G GAL NAG FUC 12.8834
80 5JIY SAM 17.4905
81 5T0K SAM 17.4905
82 4MA6 28E 19.1083
83 5C2N NAG 20.8333
84 5WFC A97 20.9125
85 3KMT SAH 23.5294
Pocket No.: 2; Query (leader) PDB : 5YLT; Ligand: C7N; Similar sites found with APoc: 80
This union binding pocket(no: 2) in the query (biounit: 5ylt.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
1 4DDY DN6 0.760456
2 4DE3 DN8 0.760456
3 3O03 GCO 1.52091
4 2BVE PH5 1.68067
5 5VEQ PMP 1.90114
6 5GP0 GPP 2.01342
7 4LIK CIT 2.28137
8 2ZWI C5P 2.28137
9 1U08 PLP 2.28137
10 3THR C2F 2.28137
11 3ZOK GLY 2.6616
12 3I9U DTU 2.6616
13 4XH0 ADP 2.6616
14 1F6D UDP 2.6616
15 2GNB MAN 2.77778
16 2GMM MAN MAN 2.77778
17 2PHU MAN MAN 2.77778
18 2PHT MAN MAN MAN BMA MAN 2.77778
19 2GND MAN 2.77778
20 2PHU MAN MAN MAN BMA MAN 2.77778
21 1Q8V MAN MAN 2.77778
22 2PHW MAN MAN MAN BMA MAN MAN MAN 2.77778
23 2OFW ADX 2.88462
24 1BG2 ADP 3.04183
25 1PCA CIT 3.04183
26 4INI AMP 3.07692
27 4KFU ACP 3.30189
28 6C0B MLI 3.42205
29 5M90 JIF 3.42205
30 1IZC PYR 3.42205
31 2H21 SAM 3.80228
32 3QXY SAM 3.80228
33 1GOJ ADP 4.18251
34 1D8C SOR 4.18251
35 3LRE ADP 4.18251
36 2JHP SAH 4.18251
37 2Y65 ADP 4.56274
38 3CM2 X23 4.61538
39 5LFV SIA GAL NAG 4.94297
40 1EQ2 ADQ 4.94297
41 4CP8 MLI 4.94297
42 3AQT RCO 5.30612
43 5N6N SUC 5.32319
44 2X5F PLP 5.32319
45 2DVX 23A 5.32319
46 1VBO MAN MAN MAN 5.36913
47 2KIN ADP 5.46218
48 3KIF GDL 5.66038
49 3W68 PBU 5.70342
50 1T5C ADP 5.70342
51 4PPF FLC 5.70342
52 1PVC ILE SER GLU VAL 5.88235
53 3VCY UD1 6.46388
54 3LL2 MAN MAN MAN MAN MAN MAN MAN MAN 6.50407
55 1TL2 NDG 6.77966
56 4P83 U5P 7.14286
57 5WHT SIA GAL 7.24638
58 5WHT SIA 7.24638
59 5T63 ALA ALA ALA ALA 7.60456
60 3N71 SFG 7.98479
61 2VL1 GLY GLY 7.98479
62 4B1M FRU FRU 8.10811
63 3KIH GDL 8.24742
64 3A3B RBF 8.42105
65 5BV6 35G 8.55263
66 2ZL4 ALA ALA ALA ALA 9.18367
67 2F7A BEZ 9.48276
68 2DUR MAN MAN 9.48617
69 4UCC ZKW 10.3004
70 5CZY SAM 10.6464
71 2VVG ADP 10.6464
72 1OFS SUC 12.5
73 4DS0 A2G GAL NAG FUC 12.8834
74 3T01 PPF 13.6882
75 2YVE MBT 16.7568
76 5JIY SAM 17.4905
77 5T0K SAM 17.4905
78 4MA6 28E 19.1083
79 5C2N NAG 20.8333
80 3KMT SAH 23.5294
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