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Receptor
PDB id Resolution Class Description Source Keywords
1N6A 1.7 Å EC: 2.1.1.43 STRUCTURE OF SET7/9 HOMO SAPIENS PROTEIN-LIGAND COMPLEX TRANSFERASE
Ref.: MECHANISM OF HISTONE LYSINE METHYL TRANSFER REVEALED BY THE STRUCTURE OF SET7/9-ADOMET EMBO J. V. 22 292 2003
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SAM A:402;
Valid;
none;
submit data
398.437 C15 H22 N6 O5 S C[S@@...
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: SAM; Similar ligands found: 202
No: Ligand ECFP6 Tc MDL keys Tc
1 SAM 1 1
2 SMM 0.792683 0.96
3 S4M 0.6875 0.909091
4 S7M 0.670455 0.945946
5 M2T 0.636364 0.878378
6 GEK 0.612903 0.931507
7 SAI 0.571429 0.878378
8 ADN 0.565789 0.773333
9 RAB 0.565789 0.773333
10 XYA 0.565789 0.773333
11 5CD 0.564103 0.783784
12 EP4 0.5625 0.826667
13 SA8 0.56044 0.945205
14 SFG 0.555556 0.875
15 5X8 0.555556 0.888889
16 5N5 0.551282 0.773333
17 A4D 0.544304 0.797297
18 EEM 0.542553 0.945946
19 SAH 0.537634 0.916667
20 DTA 0.536585 0.789474
21 62X 0.535354 0.884615
22 MTA 0.53012 0.875
23 3DH 0.517647 0.849315
24 5AL 0.510417 0.743902
25 54H 0.510204 0.673913
26 VMS 0.510204 0.673913
27 0UM 0.51 0.857143
28 AMP 0.505747 0.707317
29 LMS 0.505747 0.666667
30 A 0.505747 0.707317
31 ABM 0.505618 0.753086
32 A5A 0.505155 0.688889
33 SON 0.5 0.746988
34 SSA 0.5 0.684783
35 6RE 0.5 0.78481
36 K15 0.5 0.883117
37 5AD 0.5 0.75
38 SRP 0.5 0.746988
39 LSS 0.49505 0.706522
40 CA0 0.494624 0.714286
41 A12 0.494505 0.705882
42 AP2 0.494505 0.705882
43 ME8 0.490385 0.841463
44 TSB 0.49 0.681319
45 53H 0.49 0.666667
46 DAL AMP 0.49 0.765432
47 5CA 0.49 0.684783
48 ACP 0.489362 0.694118
49 ADP 0.48913 0.690476
50 5AS 0.48913 0.648936
51 J7C 0.488889 0.772152
52 A2D 0.488889 0.690476
53 ZAS 0.488636 0.769231
54 9ZD 0.485149 0.729412
55 9ZA 0.485149 0.729412
56 8QN 0.485149 0.743902
57 GAP 0.484536 0.73494
58 AN2 0.483871 0.682353
59 A3S 0.483871 0.813333
60 A7D 0.483871 0.851351
61 GJV 0.483516 0.775
62 SRA 0.483146 0.694118
63 LAD 0.480769 0.752941
64 KAA 0.480769 0.698925
65 GSU 0.480769 0.722222
66 AMO 0.480392 0.746988
67 DSZ 0.480392 0.703297
68 52H 0.48 0.666667
69 M33 0.478723 0.722892
70 BA3 0.478261 0.690476
71 MAO 0.478261 0.82716
72 NEC 0.477778 0.75
73 AOC 0.477778 0.776316
74 DSH 0.477778 0.842105
75 SXZ 0.47619 0.894737
76 AHX 0.475728 0.701149
77 NVA LMS 0.475728 0.736264
78 Y3J 0.47561 0.706667
79 G5A 0.474227 0.684783
80 A3T 0.473684 0.8
81 B4P 0.473118 0.690476
82 AP5 0.473118 0.690476
83 A3N 0.472527 0.766234
84 KB1 0.471698 0.833333
85 PRX 0.46875 0.73494
86 APC 0.46875 0.705882
87 AT4 0.468085 0.686047
88 PAJ 0.466019 0.712644
89 4AD 0.466019 0.759036
90 RBY 0.463918 0.72619
91 ADP PO3 0.463918 0.728395
92 ADV 0.463918 0.72619
93 ADX 0.463158 0.666667
94 MHZ 0.463158 0.82716
95 AU1 0.463158 0.674419
96 YAP 0.462963 0.738095
97 TXA 0.462264 0.72619
98 NB8 0.462264 0.72093
99 A3G 0.461538 0.802632
100 VRT 0.459184 0.842105
101 XAH 0.458716 0.715909
102 YSA 0.458716 0.684783
103 HEJ 0.458333 0.690476
104 50T 0.458333 0.682353
105 ATP 0.458333 0.690476
106 LEU LMS 0.457143 0.717391
107 7D7 0.45679 0.723684
108 KH3 0.455357 0.871795
109 ACQ 0.454545 0.694118
110 AR6 0.453608 0.710843
111 APR 0.453608 0.710843
112 AQP 0.453608 0.690476
113 5FA 0.453608 0.690476
114 NSS 0.451923 0.703297
115 FA5 0.449541 0.746988
116 A5D 0.44898 0.789474
117 AD9 0.44898 0.674419
118 AGS 0.44898 0.678161
119 SAP 0.44898 0.678161
120 PTJ 0.448598 0.72093
121 YLB 0.448276 0.758621
122 YLP 0.447368 0.738636
123 8X1 0.446602 0.680851
124 D3Y 0.446602 0.792208
125 ADP ALF 0.445545 0.678161
126 ALF ADP 0.445545 0.678161
127 3AM 0.444444 0.674699
128 MYR AMP 0.444444 0.776471
129 OAD 0.443396 0.73494
130 2VA 0.443299 0.779221
131 S8M 0.442308 0.831169
132 OOB 0.442308 0.722892
133 TYR AMP 0.441441 0.759036
134 6YZ 0.441176 0.694118
135 ADP VO4 0.441176 0.702381
136 VO4 ADP 0.441176 0.702381
137 T99 0.44 0.686047
138 TAT 0.44 0.686047
139 ANP 0.44 0.674419
140 WAQ 0.439252 0.75
141 B5Y 0.436364 0.717647
142 8PZ 0.436364 0.684783
143 F0P 0.435897 0.844156
144 YLC 0.435897 0.755814
145 AAT 0.435644 0.797468
146 1ZZ 0.435185 0.755814
147 9K8 0.435185 0.663158
148 3OD 0.435185 0.73494
149 NVA 2AD 0.434343 0.855263
150 00A 0.433962 0.689655
151 DLL 0.433962 0.722892
152 ARG AMP 0.433628 0.727273
153 7MD 0.433628 0.715909
154 ATF 0.431373 0.666667
155 SO8 0.43 0.792208
156 3UK 0.429907 0.714286
157 A6D 0.429907 0.72619
158 9X8 0.429907 0.717647
159 F2R 0.429752 0.7
160 5SV 0.428571 0.741176
161 AMP DBH 0.428571 0.714286
162 TYM 0.42735 0.746988
163 WSA 0.42735 0.692308
164 9SN 0.427273 0.681818
165 AHZ 0.426087 0.755814
166 P5A 0.425926 0.691489
167 B5V 0.425926 0.705882
168 PR8 0.425926 0.744186
169 A A 0.425926 0.710843
170 3NZ 0.425926 0.807692
171 A1R 0.424528 0.709302
172 2A5 0.424242 0.674419
173 7MC 0.423729 0.719101
174 B5M 0.423423 0.717647
175 7D5 0.422222 0.658824
176 JB6 0.422018 0.709302
177 FYA 0.422018 0.722892
178 AYB 0.421488 0.75
179 A22 0.419048 0.682353
180 MAP 0.419048 0.659091
181 2AM 0.417582 0.666667
182 TAD 0.417391 0.712644
183 A3P 0.416667 0.686747
184 ADP BMA 0.416667 0.714286
185 25A 0.415094 0.690476
186 YLA 0.413223 0.719101
187 8Q2 0.411765 0.663158
188 A3R 0.411215 0.709302
189 ADQ 0.411215 0.694118
190 48N 0.410256 0.72093
191 0XU 0.41 0.824324
192 GA7 0.408696 0.72619
193 7D3 0.40625 0.643678
194 PAP 0.405941 0.678571
195 DQV 0.405172 0.702381
196 OVE 0.404255 0.662791
197 4UV 0.403509 0.697674
198 AF3 ADP 3PG 0.403361 0.712644
199 3AD 0.402299 0.783784
200 CMP 0.402062 0.691358
201 2BA 0.402062 0.682927
202 7C5 0.4 0.731707
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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