Receptor
PDB id Resolution Class Description Source Keywords
3OS5 1.69 Å EC: 2.1.1.43 SET7/9-DNMT1 K142ME1 COMPLEX HOMO SAPIENS EPIGENETIC MODIFICATION SET DOMAIN PROTEIN LYSINE METHYLTRANSFERASE DNMT1 LYSINE MONO-METHYLATION K142 TR
Ref.: A METHYLATION AND PHOSPHORYLATION SWITCH BETWEEN AN LYSINE AND SERINE DETERMINES HUMAN DNMT1 STABILITY. NAT.STRUCT.MOL.BIOL. V. 18 42 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BME A:500;
Invalid;
none;
submit data
78.133 C2 H6 O S C(CS)...
EDO A:391;
A:392;
A:393;
A:394;
A:395;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
SAH A:1501;
Valid;
none;
submit data
384.411 C14 H20 N6 O5 S c1nc(...
THR PRO ARG ARG SER MLZ SER ALA B:137;
Valid;
none;
submit data
904.085 n/a O=C(N...
UNL A:400;
Invalid;
none;
submit data
n/a NULL NULL
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: SAH; Similar ligands found: 197
No: Ligand ECFP6 Tc MDL keys Tc
1 SAH 1 1
2 5X8 0.759494 0.969697
3 A7D 0.734177 0.926471
4 TT8 0.709302 0.970588
5 SXZ 0.692308 0.916667
6 DSH 0.692308 0.914286
7 DTA 0.666667 0.857143
8 3DH 0.662338 0.869565
9 S8M 0.655556 0.901408
10 SFG 0.635294 0.954545
11 SA8 0.62069 0.915493
12 EEM 0.617977 0.890411
13 MTA 0.615385 0.869565
14 SAI 0.613636 0.955882
15 S7M 0.586957 0.916667
16 36A 0.586538 0.90411
17 K15 0.583333 0.878378
18 RAB 0.573333 0.84058
19 ADN 0.573333 0.84058
20 XYA 0.573333 0.84058
21 62X 0.572917 0.855263
22 5CD 0.571429 0.852941
23 0UM 0.5625 0.876712
24 5N5 0.558442 0.84058
25 A4D 0.551282 0.867647
26 SAM 0.537634 0.916667
27 SSA 0.536842 0.712644
28 SMM 0.536842 0.88
29 KB1 0.534653 0.902778
30 A5D 0.532609 0.857143
31 SIB 0.53125 0.928571
32 EP4 0.530864 0.819444
33 DSZ 0.530612 0.732558
34 GSU 0.53 0.752941
35 AMP 0.529412 0.763158
36 A 0.529412 0.763158
37 5CA 0.525773 0.712644
38 ME8 0.524752 0.8125
39 M2T 0.52439 0.821918
40 6RE 0.523256 0.824324
41 GJV 0.522727 0.813333
42 AAT 0.515789 0.863014
43 LSS 0.515152 0.696629
44 KAA 0.514852 0.727273
45 J7C 0.511364 0.835616
46 A5A 0.510417 0.697674
47 SON 0.505495 0.805195
48 SRP 0.505155 0.805195
49 5AL 0.5 0.779221
50 VMS 0.5 0.681818
51 KH3 0.5 0.866667
52 ADX 0.5 0.694118
53 CA0 0.5 0.769231
54 AMP MG 0.5 0.74359
55 AMO 0.5 0.805195
56 54H 0.5 0.681818
57 AHX 0.49505 0.753086
58 TSB 0.494949 0.689655
59 53H 0.494949 0.674157
60 G5A 0.494737 0.712644
61 A2D 0.494382 0.74359
62 ABM 0.494382 0.74359
63 ZAS 0.494253 0.808219
64 A6D 0.490196 0.759494
65 8QN 0.49 0.779221
66 GEK 0.49 0.956522
67 GAP 0.489583 0.769231
68 A3S 0.48913 0.884058
69 AN2 0.48913 0.734177
70 S4M 0.488889 0.831169
71 SRA 0.488636 0.746835
72 LAD 0.485437 0.810127
73 52H 0.484848 0.674157
74 A12 0.483516 0.759494
75 BA3 0.483516 0.74359
76 AP2 0.483516 0.759494
77 AOC 0.483146 0.842857
78 NEC 0.483146 0.788732
79 Y3J 0.481481 0.768116
80 NVA LMS 0.480392 0.696629
81 VRT 0.479167 0.861111
82 50T 0.478723 0.734177
83 5AS 0.478261 0.655556
84 B4P 0.478261 0.74359
85 ADP 0.478261 0.74359
86 AP5 0.478261 0.74359
87 A3N 0.477778 0.830986
88 YSA 0.476636 0.712644
89 XAH 0.476636 0.768293
90 0XU 0.473684 0.897059
91 WAQ 0.471154 0.807692
92 NSS 0.470588 0.712644
93 5AD 0.468354 0.791045
94 ADP MG 0.468085 0.734177
95 AU1 0.468085 0.725
96 M33 0.468085 0.734177
97 MAO 0.467391 0.797468
98 TXA 0.466667 0.759494
99 A3G 0.466667 0.871429
100 NB8 0.466667 0.775
101 3AM 0.465909 0.727273
102 DAL AMP 0.465347 0.779221
103 ATP 0.463158 0.74359
104 ADP BEF 0.463158 0.716049
105 A3T 0.463158 0.842857
106 BEF ADP 0.463158 0.716049
107 ACP 0.463158 0.746835
108 7D7 0.4625 0.785714
109 LEU LMS 0.461538 0.677778
110 APC 0.458333 0.759494
111 AQP 0.458333 0.74359
112 APR 0.458333 0.766234
113 PRX 0.458333 0.746835
114 AR6 0.458333 0.766234
115 5FA 0.458333 0.74359
116 IOT 0.456897 0.761905
117 4AD 0.456311 0.794872
118 PAJ 0.456311 0.722892
119 WSA 0.45614 0.72093
120 FA5 0.453704 0.805195
121 YAP 0.453704 0.794872
122 RBY 0.453608 0.782051
123 ADV 0.453608 0.782051
124 ADP PO3 0.453608 0.763158
125 AD9 0.453608 0.725
126 SAP 0.453608 0.728395
127 AGS 0.453608 0.728395
128 PTJ 0.45283 0.731707
129 MHZ 0.452632 0.797468
130 00A 0.451923 0.740741
131 A3P 0.451613 0.74026
132 YLP 0.451327 0.771084
133 7MD 0.45045 0.768293
134 ALF ADP 0.45 0.707317
135 ADP ALF 0.45 0.707317
136 ATP MG 0.44898 0.734177
137 2VA 0.447917 0.819444
138 OOB 0.446602 0.779221
139 ANP 0.444444 0.725
140 ACQ 0.444444 0.746835
141 TAT 0.444444 0.7375
142 P5A 0.443396 0.719101
143 7D5 0.443182 0.708861
144 ARG AMP 0.442478 0.759036
145 A1R 0.442308 0.7625
146 YLC 0.439655 0.790123
147 2AM 0.438202 0.717949
148 DLL 0.438095 0.779221
149 A22 0.436893 0.734177
150 D3Y 0.436893 0.859155
151 TYR AMP 0.436364 0.782051
152 ATF 0.435644 0.716049
153 MYR AMP 0.435185 0.746988
154 SO8 0.434343 0.808219
155 3UK 0.433962 0.769231
156 OAD 0.433962 0.769231
157 TAD 0.433628 0.765432
158 25A 0.432692 0.74359
159 ANP MG 0.431373 0.707317
160 VO4 ADP 0.431373 0.734177
161 ADP VO4 0.431373 0.734177
162 9SN 0.431193 0.731707
163 TYM 0.431034 0.805195
164 PR8 0.429907 0.8
165 ADQ 0.428571 0.746835
166 YLB 0.42735 0.771084
167 3OD 0.425926 0.769231
168 FYA 0.425926 0.779221
169 1ZZ 0.425926 0.746988
170 PPS 0.425743 0.674419
171 NVA 2AD 0.424242 0.808219
172 MAP 0.423077 0.707317
173 A2P 0.421053 0.727273
174 4YB 0.421053 0.735632
175 ADP BMA 0.420561 0.746835
176 5SV 0.419048 0.731707
177 3NZ 0.416667 0.824324
178 YLA 0.416667 0.771084
179 48N 0.413793 0.753086
180 LPA AMP 0.413793 0.768293
181 AYB 0.413223 0.761905
182 QQY 0.413043 0.696203
183 ACK 0.413043 0.710526
184 JB6 0.412844 0.7625
185 BIS 0.412844 0.719512
186 PAP 0.41 0.730769
187 OVE 0.408602 0.7125
188 4UV 0.40708 0.75
189 AMP DBH 0.40708 0.746835
190 3AD 0.406977 0.852941
191 AF3 ADP 3PG 0.40678 0.743902
192 OMR 0.40678 0.738095
193 LAQ 0.405172 0.768293
194 A A 0.40367 0.74359
195 7C5 0.403509 0.789474
196 7MC 0.403361 0.75
197 4UU 0.4 0.75
Ligand no: 2; Ligand: THR PRO ARG ARG SER MLZ SER ALA; Similar ligands found: 71
No: Ligand ECFP6 Tc MDL keys Tc
1 THR PRO ARG ARG SER MLZ SER ALA 1 1
2 ILE LYS ARG SER MLZ LYS ASN SER LEU ALA 0.623762 0.791045
3 ALA ARG MLZ SER ALA PRO ALA THR 0.616667 0.955882
4 DMG PRO ARG ARG ARG SER ARG LYS PRO 0.533898 0.927536
5 SER PRO LYS ARG ILE ALA 0.532258 0.869565
6 5JP PRO LYS ARG ILE ALA 0.527559 0.898551
7 LYS ALA ALA ARG ALY SER ALA PRO ALA 0.514019 0.746269
8 CYS THR PRO SER ARG 0.491803 0.869565
9 DPN PRO DAR DTH NH2 0.491803 0.826087
10 ARG PRO LYS ARG ILE ALA 0.488189 0.826087
11 ARG ARG ARG GLU ARG SER PRO THR ARG 0.481203 0.884058
12 LYS ARG ARG ARG HIS PRO SER GLY 0.477941 0.819444
13 ALA ARG SER HIS SEP TYR PRO ALA 0.473684 0.765432
14 TYR PRO LYS ARG ILE ALA 0.471014 0.783784
15 DPN PRO DAR CYS NH2 0.467213 0.728571
16 LYS ARG ARG ARG HIS PRO SER 0.466667 0.802817
17 PRO PRO LYS LYS LYS ARG LYS VAL 0.464 0.782609
18 LYS PRO VAL LEU ARG THR ALA 0.462687 0.884058
19 ARG ILE PRO SER TYR ARG TYR ARG TYR 0.461538 0.84
20 SER PRO ARG LEU PRO LEU LEU GLU SER 0.457364 0.797101
21 ALA ALA ARG KCR SER ALA PRO ALA 0.457143 0.884058
22 ALA ASN SER ARG ALY PRO THR SER ILE ILE 0.456376 0.915493
23 DPN PRO DAR ILE NH2 0.456 0.771429
24 ASN ARG PRO ILE LEU SER LEU 0.451852 0.847222
25 ALA ASN SER ARG ALA PRO THR SER ILE ILE 0.450704 0.887324
26 ALA ASN SER ARG PHE PRO THR SER ILE ILE 0.450331 0.849315
27 LYS ALA PRO ARG ALY GLN LEU ALA THR LYS 0.44898 0.9
28 SER SER TYR ARG ARG PRO VAL GLY ILE 0.446667 0.84
29 ALA ASN SER ARG VAL PRO THR SER ILE ILE 0.445255 0.885714
30 ALA ASN SER ARG TYR PRO THR SER ILE ILE 0.443709 0.815789
31 ARG ARG LEU PRO ILE PHE SER ARG LEU 0.439189 0.861111
32 SER LEU SER ARG THR PRO ALA ASP GLY ARG 0.438356 0.898551
33 LYS GLY PRO PRO LEU PRO ARG PRO ARG VAL 0.434109 0.811594
34 LYS ALA ALA ARG M3L SER ALA 0.432 0.814286
35 SER LYS SER MLZ ASP ARG LYS TYR THR LEU 0.431034 0.666667
36 THR LYS PRO ARG 0.429825 0.764706
37 PRO PRO LYS ARG ILE ALA 0.42963 0.8
38 ARG PRO PRO GLY PHE SER PRO PHE ALA 0.42953 0.808219
39 SER ARG ASP HIS SER ARG THR PRO MET 0.429487 0.891892
40 ALA MET ALA PRO ARG THR LEU LEU LEU 0.428571 0.928571
41 HIS HIS ALA SER PRO ARG LYS 0.425676 0.805556
42 GLY LEU LEU GLY SER PRO VAL ARG ALA 0.42446 0.842857
43 ALA PRO ASP THR ARG PRO 0.424242 0.885714
44 ALA ARG THR MLZ GLN THR ALA ARG LYS TYR 0.424 0.779412
45 3BY PRO LYS ARG ILE ALA 0.423358 0.871429
46 ASN PRO ARG ALA MET GLN ALA LEU LEU 0.422535 0.833333
47 VAL MET ALA PRO ARG ALA LEU LEU LEU 0.42029 0.857143
48 ACE GLN GLU ARG GLU VAL PRO CYS 0.42029 0.788732
49 GLU ARG THR ILE PRO ILE THR ARG GLU 0.42029 0.885714
50 ALA ARG MLZ SER THR GLY GLY ALY 0.419118 0.811594
51 ARG PRO GLY ASN PHE LEU GLN SER ARG LEU 0.41875 0.875
52 ARG GLU ARG SER PRO THR ARG 0.418033 0.84058
53 SER ALA PRO ASP THR ARG PRO ALA 0.417266 0.9
54 ALA ASN SER ARG TRP PRO ALY SER ILE ILE 0.417219 0.746667
55 ARG PRO LYS PRO LEU VAL ASP PRO 0.415385 0.811594
56 GLU LYS PRO SER SER SER 0.413223 0.753623
57 GLY ARG PRO ARG THR THR SER PHE ALA GLU 0.412903 0.873239
58 ALA ASN SER ARG TRP PRO THR SER ALY ILE 0.4125 0.866667
59 GLN ARG SER THR SEP THR PRO ASN VAL HIS 0.409396 0.802632
60 SER HIS PRO ARG PRO ILE ARG VAL 0.409396 0.837838
61 DPN PRO ARG 0.408333 0.728571
62 ALA ASN SER ARG TRP PRO THR THR ARG LEU 0.408163 0.826667
63 LEU ASP PRO ARG 0.408 0.785714
64 ASN PHE ASP ASN PRO VAL TYR ARG LYS THR 0.406061 0.782051
65 ACE ARG THR PRO SEP LEU PRO THR PIP 0.40411 0.831169
66 SER SER CYS PRO LEU SER LYS 0.403101 0.797101
67 VAL PRO LEU ARG PRO MET THR TYR 0.402597 0.866667
68 ILE LYS ARG SER LYS LYS ASN SER LEU ALA 0.401786 0.701493
69 PBE PRO LYS THR SER GLY LYS ALA ALA 0.401408 0.833333
70 PRO SER ILE ASP ARG SER THR LYS PRO 0.401316 0.887324
71 ALA ARG THR 4WQ GLN THR ALA ARG LYS SER 0.4 0.728571
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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