Receptor
PDB id Resolution Class Description Source Keywords
3F9X 1.25 Å EC: 2.1.1.43 STRUCTURAL INSIGHTS INTO LYSINE MULTIPLE METHYLATION BY SET DOMAIN METHYLTRANSFERASES, SET8-Y334F / H4-LYS20ME2 / A DOHCY HOMO SAPIENS METHYLTRANSFERASE HISTONE SET LYSINE ALTERNATIVE SPLICING CELL CYCLE CELL DIVISION CHROMATIN REGULATOR CHROMOSOMAL PROTEIN COILED COIL MITOSIS NUCLEUS REPRESSOR S-ADENOSYL-L-METHIONINE TRANSCRIPTION TRANSCRIPTION REGULATION ACETYLATION DNA-BINDING METHYLATION NUCLEOSOME CORE
Ref.: STRUCTURAL ORIGINS FOR THE PRODUCT SPECIFICITY OF SET DOMAIN PROTEIN METHYLTRANSFERASES. PROC.NATL.ACAD.SCI.USA V. 105 20659 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ALA LYS ARG HIS ARG MLY VAL LEU ARG ASP E:16;
F:16;
G:16;
H:16;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
1181.44 n/a O=C([...
SAH A:801;
B:801;
C:801;
D:801;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
384.411 C14 H20 N6 O5 S c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3F9W 1.6 Å EC: 2.1.1.43 STRUCTURAL INSIGHTS INTO LYSINE MULTIPLE METHYLATION BY SET DOMAIN METHYLTRANSFERASES, SET8-Y334F / H4-LYS20 / ADOHCY HOMO SAPIENS METHYLTRANSFERASE HISTONE SET LYSINE ALTERNATIVE SPLICING CELL CYCLE CELL DIVISION CHROMATIN REGULATOR CHROMOSOMAL PROTEIN COILED COIL MITOSIS NUCLEUS REPRESSOR S-ADENOSYL-L-METHIONINE TRANSCRIPTION TRANSCRIPTION REGULATION ACETYLATION DNA-BINDING METHYLATION NUCLEOSOME CORE
Ref.: STRUCTURAL ORIGINS FOR THE PRODUCT SPECIFICITY OF SET DOMAIN PROTEIN METHYLTRANSFERASES. PROC.NATL.ACAD.SCI.USA V. 105 20659 2008
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 36 families.
1 3F9W Kd = 19 uM ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP n/a n/a
2 3F9Z - SAH C14 H20 N6 O5 S c1nc(c2c(n....
3 2BQZ Kd = 20 uM ARG HIS ARG MLZ VAL LEU ARG ASP ASN TYR n/a n/a
4 3F9X - SAH C14 H20 N6 O5 S c1nc(c2c(n....
5 1ZKK Kd = 33 uM ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP n/a n/a
6 3F9Y Kd = 32 uM ALA LYS ARG HIS ARG MLZ VAL LEU ARG ASP n/a n/a
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 26 families.
1 3F9W Kd = 19 uM ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP n/a n/a
2 3F9Z - SAH C14 H20 N6 O5 S c1nc(c2c(n....
3 2BQZ Kd = 20 uM ARG HIS ARG MLZ VAL LEU ARG ASP ASN TYR n/a n/a
4 3F9X - SAH C14 H20 N6 O5 S c1nc(c2c(n....
5 1ZKK Kd = 33 uM ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP n/a n/a
6 3F9Y Kd = 32 uM ALA LYS ARG HIS ARG MLZ VAL LEU ARG ASP n/a n/a
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 22 families.
1 3F9W Kd = 19 uM ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP n/a n/a
2 3F9Z - SAH C14 H20 N6 O5 S c1nc(c2c(n....
3 2BQZ Kd = 20 uM ARG HIS ARG MLZ VAL LEU ARG ASP ASN TYR n/a n/a
4 3F9X - SAH C14 H20 N6 O5 S c1nc(c2c(n....
5 1ZKK Kd = 33 uM ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP n/a n/a
6 3F9Y Kd = 32 uM ALA LYS ARG HIS ARG MLZ VAL LEU ARG ASP n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ALA LYS ARG HIS ARG MLY VAL LEU ARG ASP; Similar ligands found: 76
No: Ligand ECFP6 Tc MDL keys Tc
1 ALA LYS ARG HIS ARG MLY VAL LEU ARG ASP 1 1
2 ARG HIS ARG MLY VAL LEU ARG ASP ASN 0.867257 0.984848
3 ARG HIS ARG MLY VAL LEU ARG ASP TYR 0.761905 0.915493
4 ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP 0.735043 0.892308
5 ALA LYS PHE ARG HIS ASP 0.644068 0.80597
6 ASP ALA GLU PHE ARG HIS ASP 0.61157 0.791045
7 LYS ILE LEU HIS ARG LEU LEU GLN ASP 0.582677 0.833333
8 ARG HIS ARG MLZ VAL LEU ARG ASP ASN TYR 0.572414 0.861111
9 GLY HIS LYS ILE LEU HIS ARG LEU LEU GLN 0.548872 0.823529
10 ALA LYS ARG HIS ARG MLZ VAL LEU ARG ASP 0.541353 0.892308
11 LYS GLY GLY ALA ALY ARG HIS ARG LYS VAL 0.534884 0.892308
12 ALA PRO ALA LEU ARG VAL VAL LYS 0.530973 0.707692
13 HIS LYS ILE LEU HIS ARG LEU LEU GLN ASP 0.520833 0.850746
14 HIS LYS ILE LEU HIS ARG LEU LEU GLN GLU 0.506849 0.835821
15 LYS ILE LEU HIS ARG LEU LEU GLN ASP SER 0.506757 0.826087
16 ARG ARG LYS TRP ARG ARG TRP HIS LEU 0.5 0.811594
17 PHE ASN GLU LEU SER HIS LEU 0.495868 0.695652
18 ARG ARG ARG TRP HIS ARG TRP ARG LEU 0.492537 0.797101
19 ALA LEU PRO HIS ALA ILE LEU ARG LEU 0.489933 0.828571
20 ILE LEU GLY LYS PHE LEU HIS ARG LEU 0.482759 0.811594
21 VAL VAL SER HIS PHE ASN ASP 0.473684 0.676056
22 THR SER ARG HIS LYS ALY LEU MET ALA 0.472603 0.859155
23 GLU LYS VAL HIS VAL GLN 0.472441 0.753846
24 ALA ARG THR MLY GLN 0.471074 0.797101
25 GLY ALA ARG ALA HIS SER SER 0.465116 0.811594
26 GLY VAL TYR ASP GLY ARG GLU HIS THR VAL 0.464052 0.756757
27 SER ARG ASP HIS SER ARG THR PRO MET 0.455696 0.84
28 ALA ARG LYS LEU ASP 0.452174 0.738462
29 GLU GLU ASN LEU LEU ASP PHE VAL ARG PHE 0.451389 0.73913
30 TYR HIS SEP VAL VAL ARG TYR ALA 0.450331 0.6875
31 ILE LEU ALA LYS PHE LEU HIS ARG LEU 0.449664 0.779412
32 VAL LEU HIS ASP ASP LEU LEU GLU ALA 0.448819 0.723077
33 ARG ARG LEU LEU ARG GLY HIS ASN GLN TYR 0.447368 0.780822
34 ALA ARG THR GLU LEU TYR ARG SER LEU 0.446809 0.69863
35 LYS GLY GLY ALA ALY ARG HIS ARG 0.443662 0.863636
36 ARG ILE ILE PRO ARG HIS LEU GLN LEU 0.443038 0.857143
37 HIS LYS LEU VAL GLN LEU LEU THR THR THR 0.441176 0.753623
38 ALA LEU ASP LYS TRP ASP 0.438462 0.705882
39 ALA ARG THR MLY GLN THR ALA 0.4375 0.797101
40 ALA ARG THR MLY GLN THR ALA ARG LYS TYR 0.4375 0.797101
41 ILE LEU MET GLU HIS ILE HIS LYS LEU 0.4375 0.764706
42 SER HIS VAL ALA VAL GLU ASN ALA LEU 0.435714 0.724638
43 PCA PHE ARG HIS ASP SER 0.433566 0.753623
44 LEU TYR LEU VAL CYS GLY GLU ARG VAL 0.432432 0.657534
45 ALA HIS HIS 0.429907 0.606061
46 ALA ARG THR MLY GLN THR ALA ARG MLY SER 0.428571 0.782609
47 ALA ARG LYS ILE ASP ASN LEU ASP 0.426471 0.761194
48 PTR LEU ARG VAL ALA 0.425373 0.653333
49 SER HIS LYS ILE ASP ASN LEU ASP 0.424658 0.757143
50 LEU GLY GLY ALA LYS GLN ARG GLY ASP VAL 0.423077 0.712121
51 ARG ARG ARG TRP ARG ARG LEU THR VAL 0.422535 0.763889
52 ARG ARG LYS TRP CIR ARG TRP HIS LEU 0.42236 0.8
53 ALA ARG THR MLY GLN THR ALA ARG TYR 0.416667 0.819444
54 ALA SER ASN GLU HIS MET GLU THR MET 0.415493 0.746479
55 ASP ALA GLU PHE ARG HIS ASP SER 0.413793 0.791045
56 ILE LEU ALA LYS PHE LEU HIS THR LEU 0.413333 0.680556
57 HIS VAL ALA VAL GLU ASN ALA LEU 0.413043 0.712121
58 LYS ALA ARG VAL LEU ALA GLU ALA MET SER 0.413043 0.727273
59 LYS ALA ARG VAL LEU ALA GLU ALA MET 0.413043 0.727273
60 ILE LEU ALA LYS PHE LEU HIS GLU LEU 0.412162 0.720588
61 ILE ARG LYS ILE LEU PHE LEU ASP GLY ILE 0.411765 0.75
62 ALA ARG THR MLY GLN THR ALA ARG LYS 0.411765 0.797101
63 ACE SER HIS VAL ALA VAL GLU ASN ALA LEU 0.410959 0.73913
64 ACE ARG HIS ALY ALY MCM 0.410959 0.7
65 MET ABA LEU ARG MET THR ALA VAL MET 0.410072 0.690141
66 LYS ARG ARG LYS SEP VAL 0.409836 0.657534
67 SER HIS PRO ARG PRO ILE ARG VAL 0.409091 0.810811
68 ARG HIS LYS ALY LEU MET PHE LYS 0.409091 0.838235
69 ASP ARG VAL TYR ILE HIS PRO PHE 0.406977 0.779221
70 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.406015 0.695652
71 ALA ARG MLY SER THR GLY GLY ALY 0.405594 0.788732
72 ILE LEU LYS GLU PRO VAL HIS GLY VAL 0.403727 0.757143
73 MET CYS LEU ARG MET THR ALA VAL MET 0.401408 0.714286
74 GLY SER HIS LEU GLU VAL GLN GLY TYR TRP 0.4 0.662338
75 MET CYS LEU ARG NLE THR ALA VAL MET 0.4 0.704225
76 LYS PRO ILE VAL VAL LEU HIS GLY TYR 0.4 0.697368
Ligand no: 2; 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
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3F9W; Ligand: SAH; Similar sites found: 14
This union binding pocket(no: 1) in the query (biounit: 3f9w.bio2) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2CHT TSA 0.01815 0.41424 None
2 1PVS 7HP 0.03004 0.41929 3.61446
3 3QXY SAM 0.0001095 0.42712 8.43373
4 4CU1 H4B 0.006961 0.44141 9.03614
5 4GK9 MAN BMA MAN MAN MAN 0.04257 0.4003 9.63855
6 3N71 SFG 0.0000005544 0.48241 11.4458
7 1BHX ASP PHE GLU GLU ILE 0.01788 0.40621 13.3333
8 2H21 SAM 0.00002537 0.49385 16.2651
9 3KMT SAH 0.000008796 0.55415 20.1681
10 5CZY SAM 0.0001506 0.40789 30.1205
11 5M5G VAL MET LEU PRO GLY ARG GLY VAL PRO 0.00001938 0.52155 36.747
12 5M5G SAH 0.000002357 0.50677 36.747
13 5T0K SAM 0.000003045 0.49242 39.1566
14 5JIY SAM 0.000005868 0.47364 39.1566
Pocket No.: 2; Query (leader) PDB : 3F9W; Ligand: SAH; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3f9w.bio4) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3F9W; Ligand: SAH; Similar sites found: 11
This union binding pocket(no: 3) in the query (biounit: 3f9w.bio1) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1Z4O GL1 0.008275 0.42562 2.40964
2 5EB4 FAD 0.04721 0.40696 3.61446
3 1PS9 FMN 0.02497 0.40136 3.61446
4 4D79 ATP 0.02075 0.40045 3.61446
5 1GSA ADP 0.02552 0.40087 4.21687
6 1SOX MTE 0.01666 0.40697 4.81928
7 2ODE ALF GDP 0.0342 0.40123 6.38298
8 3KOX Z98 0.01088 0.41622 8.43373
9 1XSE NDP 0.04581 0.40683 9.63855
10 1BH2 GSP 0.03379 0.40151 10.8434
11 1SVK ALF GDP 0.0343 0.40238 14.4578
Pocket No.: 4; Query (leader) PDB : 3F9W; Ligand: SAH; Similar sites found: 1
This union binding pocket(no: 4) in the query (biounit: 3f9w.bio3) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3QDW NDG 0.02153 0.40873 3.4965
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