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Receptor
PDB id Resolution Class Description Source Keywords
3VUZ 2.5 Å EC: 2.1.1.43 CRYSTAL STRUCTURE OF HISTONE METHYLTRANSFERASE SET7/9 IN COM AAM-1 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
K15 A:401;
Valid;
none;
submit data
451.52 C20 H33 N7 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: K15; Similar ligands found: 172
No: Ligand ECFP6 Tc MDL keys Tc
1 K15 1 1
2 62X 0.808989 0.947368
3 KH3 0.791667 0.986486
4 SA8 0.677778 0.932432
5 KB1 0.666667 0.846154
6 F0P 0.594595 0.906667
7 SAH 0.583333 0.878378
8 SFG 0.568421 0.863014
9 5X8 0.568421 0.851351
10 S7M 0.56 0.907895
11 EP4 0.55814 0.815789
12 EEM 0.555556 0.883117
13 0UM 0.553398 0.945946
14 SAI 0.55102 0.866667
15 3DH 0.516484 0.837838
16 MAO 0.510417 0.817073
17 MHZ 0.510204 0.886076
18 RAB 0.505882 0.763158
19 ADN 0.505882 0.763158
20 XYA 0.505882 0.763158
21 5CD 0.505747 0.773333
22 SXZ 0.504587 0.883117
23 GJV 0.5 0.7875
24 SAM 0.5 0.883117
25 SMM 0.5 0.873418
26 5N5 0.494253 0.786667
27 1ZZ 0.490909 0.831325
28 A4D 0.488636 0.763158
29 MYR AMP 0.486486 0.831325
30 5SV 0.485981 0.817073
31 SSA 0.485714 0.642105
32 6RE 0.484211 0.775
33 M2T 0.483516 0.772152
34 DTA 0.483516 0.75641
35 KAA 0.481818 0.691489
36 LAD 0.481818 0.785714
37 DSH 0.479167 0.88
38 MTA 0.478261 0.813333
39 NVA LMS 0.477064 0.691489
40 A5A 0.47619 0.645161
41 YLB 0.475 0.833333
42 YLP 0.474576 0.833333
43 J7C 0.474227 0.78481
44 A7D 0.47 0.815789
45 S4M 0.469388 0.897436
46 GSU 0.468468 0.677419
47 WAQ 0.468468 0.783133
48 LSS 0.46789 0.663158
49 DSZ 0.46789 0.659574
50 VMS 0.46729 0.631579
51 54H 0.46729 0.631579
52 OMR 0.466667 0.821429
53 5AL 0.466667 0.73494
54 CA0 0.465347 0.705882
55 ME8 0.464286 0.788235
56 NEC 0.463918 0.786667
57 53H 0.462963 0.625
58 5CA 0.462963 0.642105
59 TSB 0.462963 0.638298
60 YLC 0.46281 0.788235
61 5AS 0.46 0.659574
62 AYB 0.459677 0.823529
63 ABM 0.459184 0.722892
64 GEK 0.458716 0.844156
65 A 0.458333 0.698795
66 LMS 0.458333 0.623656
67 ZAS 0.458333 0.759494
68 AMP 0.458333 0.698795
69 SRP 0.457944 0.738095
70 PRX 0.456311 0.768293
71 F2R 0.456 0.730337
72 SON 0.455446 0.738095
73 AMO 0.454545 0.738095
74 52H 0.453704 0.625
75 BA3 0.45 0.682353
76 AOC 0.44898 0.766234
77 XAH 0.448276 0.747126
78 VRT 0.447619 0.855263
79 G5A 0.447619 0.659574
80 HEJ 0.446602 0.682353
81 ATP 0.446602 0.682353
82 LEU LMS 0.446429 0.65625
83 B4P 0.445545 0.682353
84 AP5 0.445545 0.682353
85 8QN 0.445455 0.73494
86 A2D 0.444444 0.682353
87 5FA 0.442308 0.682353
88 AQP 0.442308 0.682353
89 NSS 0.441441 0.642105
90 AN2 0.441176 0.674419
91 A3S 0.441176 0.802632
92 TT8 0.440367 0.88
93 SRA 0.438776 0.666667
94 TXA 0.438596 0.717647
95 AHX 0.4375 0.693182
96 7MD 0.436975 0.767442
97 ARG AMP 0.436975 0.738636
98 ADX 0.436893 0.623656
99 M33 0.436893 0.694118
100 DAL AMP 0.436364 0.73494
101 A12 0.435644 0.697674
102 AP2 0.435644 0.697674
103 50T 0.432692 0.674419
104 A3T 0.432692 0.789474
105 9ZD 0.432432 0.701149
106 S8M 0.432432 0.797468
107 9ZA 0.432432 0.701149
108 5AD 0.431818 0.739726
109 ADP 0.431373 0.682353
110 A3N 0.43 0.779221
111 GAP 0.429907 0.72619
112 PAJ 0.428571 0.704545
113 Y3J 0.428571 0.697368
114 0XU 0.428571 0.813333
115 YLA 0.428571 0.770115
116 4AD 0.428571 0.729412
117 FA5 0.42735 0.738095
118 AT4 0.427184 0.659091
119 7D7 0.426966 0.714286
120 NB8 0.426087 0.712644
121 PTJ 0.426087 0.712644
122 AAT 0.425926 0.833333
123 SAP 0.424528 0.651685
124 AGS 0.424528 0.651685
125 NVA 2AD 0.424528 0.844156
126 YSA 0.423729 0.642105
127 8X1 0.423423 0.65625
128 AU1 0.423077 0.666667
129 SO8 0.420561 0.805195
130 A3G 0.42 0.815789
131 ACP 0.419048 0.686047
132 3AM 0.418367 0.666667
133 T99 0.416667 0.659091
134 TAT 0.416667 0.659091
135 ANP 0.416667 0.666667
136 8PZ 0.415254 0.642105
137 YAP 0.415254 0.729412
138 AR6 0.415094 0.702381
139 APR 0.415094 0.702381
140 APC 0.415094 0.697674
141 9K8 0.413793 0.639175
142 YLY 0.413534 0.845238
143 00A 0.412281 0.681818
144 ADP PO3 0.411215 0.698795
145 AD9 0.411215 0.666667
146 A5D 0.411215 0.75641
147 RBY 0.411215 0.717647
148 ADV 0.411215 0.717647
149 A22 0.410714 0.674419
150 4YB 0.409836 0.663158
151 IOT 0.409449 0.761364
152 ALF ADP 0.409091 0.651685
153 ADP ALF 0.409091 0.651685
154 3UK 0.408696 0.705882
155 OAD 0.408696 0.72619
156 2AM 0.408163 0.658824
157 OOB 0.40708 0.714286
158 9SN 0.40678 0.674157
159 2VA 0.40566 0.769231
160 6YZ 0.405405 0.686047
161 P5A 0.405172 0.702128
162 B5V 0.405172 0.697674
163 7MC 0.404762 0.790698
164 N0B 0.404412 0.770115
165 ACQ 0.40367 0.686047
166 A1R 0.403509 0.741176
167 B5Y 0.403361 0.709302
168 48N 0.403226 0.732558
169 BIS 0.401709 0.681818
170 3OD 0.401709 0.72619
171 80F 0.401515 0.673913
172 DLL 0.4 0.714286
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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