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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 METHYLTRANSFERASES, SET8-Y334F / H4-LYS20ME2 / ADOHCY HOMO SAPIENS METHYLTRANSFERASE HISTONE SET LYSINE ALTERNATIVE SPLICINCYCLE CELL DIVISION CHROMATIN REGULATOR CHROMOSOMAL PROTCOILED COIL MITOSIS NUCLEUS REPRESSOR S-ADENOSYL-L-METHTRANSCRIPTION TRANSCRIPTION REGULATION ACETYLATION DNA-BMETHYLATION NUCLEOSOME CORE TRANSFERASE
Ref.: STRUCTURAL ORIGINS FOR THE PRODUCT SPECIFICITY OF S 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
1110.47 n/a O=C(N...
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 METHYLTRANSFERASES, SET8-Y334F / H4-LYS20 / ADOHCY HOMO SAPIENS METHYLTRANSFERASE HISTONE SET LYSINE ALTERNATIVE SPLICINCYCLE CELL DIVISION CHROMATIN REGULATOR CHROMOSOMAL PROTCOILED COIL MITOSIS NUCLEUS REPRESSOR S-ADENOSYL-L-METHTRANSCRIPTION TRANSCRIPTION REGULATION ACETYLATION DNA-BMETHYLATION NUCLEOSOME CORE TRANSFERASE
Ref.: STRUCTURAL ORIGINS FOR THE PRODUCT SPECIFICITY OF S 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 39 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 28 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: 71
No: Ligand ECFP6 Tc MDL keys Tc
1 ALA LYS ARG HIS ARG MLY VAL LEU ARG ASP 1 1
2 ALA LYS ARG HIS ARG MLZ VAL LEU ARG ASP 0.713178 0.95082
3 ARG HIS ARG MLY VAL LEU ARG ASP ASN 0.630435 0.924242
4 ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP 0.62406 0.868852
5 ALA ILE LEU HIS ARG LEU LEU GLN 0.621212 0.825397
6 HIS LYS ILE LEU HIS ARG LEU LEU GLN GLU 0.60274 0.80303
7 ARG HIS ARG MLY VAL LEU ARG ASP TYR 0.587838 0.859155
8 LYS ILE LEU HIS ARG LEU LEU GLN ASP SER 0.58 0.768116
9 LYS GLY GLY ALA ALY ARG HIS ARG LYS ILE 0.576389 0.857143
10 HIS LYS ILE LEU HIS ARG LEU LEU GLN ASP 0.569444 0.828125
11 LYS GLY GLY ALA ALY ARG HIS ARG LYS VAL 0.540741 0.870968
12 GLY HIS LYS ILE LEU HIS ARG LEU LEU GLN 0.534722 0.791045
13 ILE LEU ALA LYS PHE LEU HIS ARG LEU 0.530201 0.828125
14 ARG ARG LYS TRP ARG ARG TRP HIS LEU 0.527397 0.80597
15 ARG HIS LYS ALY LEU MET PHE LYS 0.523179 0.890625
16 ARG ARG LYS TRP CIR ARG TRP HIS LEU 0.513333 0.794118
17 ARG HIS ARG MLZ VAL LEU ARG ASP ASN TYR 0.509317 0.805556
18 PRO ALA ALA LYS ARG VAL LYS LEU ASP 0.5 0.704918
19 ILE LEU GLY LYS PHE LEU HIS ARG LEU 0.493421 0.779412
20 GLU VAL ALA PRO PRO GLU TYR HIS ARG LYS 0.491525 0.77027
21 LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG 0.491525 0.672131
22 ARG ARG ARG TRP HIS ARG TRP ARG LEU 0.482759 0.791045
23 LYS ARG ARG ARG HIS PRO SER 0.47973 0.768116
24 ALA LYS PHE ARG HIS ASP 0.478873 0.746269
25 LYS GLY GLY ALA ALY ARG HIS ARG 0.476821 0.830769
26 GLU LYS VAL HIS VAL GLN 0.474453 0.734375
27 HIS HIS ALA SER PRO ARG LYS 0.471338 0.746479
28 THR SER ARG HIS LYS ALY LEU MET ALA 0.467949 0.828571
29 LYS ARG ARG ARG HIS PRO SER GLY 0.467105 0.736111
30 SER HIS LYS ILE ASP ASN LEU ASP 0.466667 0.7
31 TYR HIS SEP VAL VAL ARG TYR ALA 0.464968 0.679487
32 LYS ILE LEU HIS ARG LEU LEU GLN ASP 0.462585 0.761905
33 SER THR GLY GLY VAL M3L LYS PRO HIS ARG 0.461111 0.813333
34 ALA PRO ALA LEU ARG VAL VAL LYS 0.457364 0.698413
35 ALA ARG THR MLY GLN THR ALA ARG MLY SER 0.454545 0.75
36 PRO PRO LYS LYS LYS ARG LYS VAL 0.45082 0.704918
37 HIS LYS LEU VAL GLN LEU LEU THR THR THR 0.448276 0.710145
38 ARG ARG ARG ARG ARG ARG ARG ARG 0.448276 0.655738
39 ARG ARG ARG ARG ARG ARG ARG ARG ARG ARG 0.448276 0.655738
40 GLY ALA ALA ARG ALA GLU VAL TYR LEU ARG 0.44586 0.695652
41 ARG ARG LEU LEU ARG GLY HIS ASN GLN TYR 0.44375 0.726027
42 GLY ASP GLU VAL LYS VAL PHE ARG 0.443709 0.671642
43 ARG ILE ILE PRO ARG HIS LEU GLN LEU 0.436364 0.826087
44 ILE LYS ARG SER LYS LYS ASN SER LEU ALA 0.432 0.61194
45 ALA ARG LYS ILE ASP ASN LEU ASP 0.431507 0.701493
46 ARG GLY PHE ALA LEU M3L SER THR HIS GLY 0.430233 0.824324
47 SER ARG LYS ILE ASP ASN LEU ASP 0.42953 0.671429
48 ARG HIS LYS FDL 0.426752 0.670886
49 ARG ARG ARG VAL ARG 00S 0.424242 0.703125
50 LYS HIS LYS 0.422764 0.698413
51 ALA ARG THR LYS GLN THR ALA ARG 0.421053 0.617647
52 ACE ARG HIS LYS ALY MCM 0.41875 0.6625
53 ARG ARG ARG TRP ARG ARG LEU THR VAL 0.418301 0.732394
54 ALA LEU PRO HIS ALA ILE LEU ARG LEU 0.415663 0.823529
55 ASP ALA GLU PHE ARG HIS ASP SER 0.415584 0.731343
56 PRO VAL LYS ARG ARG LEU ASP LEU GLU 0.415584 0.757576
57 ALA ARG THR LYS GLN THR ALA ARG LYS 0.415493 0.632353
58 LYS ARG TRP ILE ILE LEU GLY LEU ASN LYS 0.410405 0.746479
59 ALA ARG THR MLY GLN THR ALA ARG LYS TYR 0.410072 0.764706
60 ALA ARG THR MLY GLN THR ALA 0.410072 0.764706
61 LYS SER HIS GLN GLU 0.407143 0.637681
62 THR ARG SER GLY ALY VAL MET ARG ARG LEU 0.406897 0.765625
63 GLU LEU PRO PRO VAL LYS ILE HIS CYS 0.40678 0.742857
64 ILE LEU MET GLU HIS ILE HIS LYS LEU 0.406452 0.761194
65 PCA PHE ARG HIS ASP SER 0.406452 0.695652
66 LYS ALA ARG VAL LEU ALA GLU ALA MET 0.402685 0.692308
67 LYS ALA ARG VAL LEU ALA GLU ALA MET SER 0.402685 0.692308
68 ILE ARG LYS ILE LEU PHE LEU ASP GLY ILE 0.402439 0.691176
69 PTR LEU ARG VAL ALA 0.4 0.643836
70 GLY VAL TYR ASP GLY ARG GLU HIS THR VAL 0.4 0.702703
71 ASN ARG LEU ILE LEU THR GLY 0.4 0.661538
Ligand no: 2; Ligand: SAH; Similar ligands found: 211
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 DSH 0.692308 0.914286
6 SXZ 0.692308 0.916667
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 ADN 0.573333 0.84058
19 RAB 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 SMM 0.536842 0.88
28 SSA 0.536842 0.712644
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 A 0.529412 0.763158
36 LMS 0.529412 0.694118
37 AMP 0.529412 0.763158
38 5CA 0.525773 0.712644
39 ME8 0.524752 0.8125
40 M2T 0.52439 0.821918
41 6RE 0.523256 0.824324
42 GJV 0.522727 0.813333
43 AAT 0.515789 0.863014
44 LSS 0.515152 0.696629
45 KAA 0.514852 0.727273
46 J7C 0.511364 0.835616
47 A5A 0.510417 0.697674
48 SON 0.505495 0.805195
49 SRP 0.505155 0.805195
50 F0P 0.504505 0.915493
51 54H 0.5 0.681818
52 VMS 0.5 0.681818
53 ADX 0.5 0.694118
54 CA0 0.5 0.769231
55 AMO 0.5 0.805195
56 5AL 0.5 0.779221
57 KH3 0.5 0.866667
58 NVA LMS 0.49505 0.707865
59 AHX 0.49505 0.753086
60 TSB 0.494949 0.689655
61 53H 0.494949 0.674157
62 G5A 0.494737 0.712644
63 ABM 0.494382 0.74359
64 A2D 0.494382 0.74359
65 ZAS 0.494253 0.808219
66 A6D 0.490196 0.759494
67 8QN 0.49 0.779221
68 GEK 0.49 0.956522
69 GAP 0.489583 0.769231
70 AN2 0.48913 0.734177
71 A3S 0.48913 0.884058
72 S4M 0.488889 0.831169
73 SRA 0.488636 0.746835
74 LAD 0.485437 0.810127
75 52H 0.484848 0.674157
76 A12 0.483516 0.759494
77 BA3 0.483516 0.74359
78 AP2 0.483516 0.759494
79 NEC 0.483146 0.788732
80 AOC 0.483146 0.842857
81 Y3J 0.481481 0.768116
82 VRT 0.479167 0.861111
83 50T 0.478723 0.734177
84 B4P 0.478261 0.74359
85 ADP 0.478261 0.74359
86 5AS 0.478261 0.655556
87 AP5 0.478261 0.74359
88 A3N 0.477778 0.830986
89 YSA 0.476636 0.712644
90 XAH 0.476636 0.768293
91 0XU 0.473684 0.897059
92 AT4 0.473118 0.7375
93 WAQ 0.471154 0.807692
94 NSS 0.470588 0.712644
95 5AD 0.468354 0.791045
96 AU1 0.468085 0.725
97 M33 0.468085 0.734177
98 MAO 0.467391 0.797468
99 TXA 0.466667 0.759494
100 NB8 0.466667 0.775
101 A3G 0.466667 0.871429
102 3AM 0.465909 0.727273
103 DAL AMP 0.465347 0.779221
104 8X1 0.465347 0.707865
105 A3T 0.463158 0.842857
106 ATP 0.463158 0.74359
107 HEJ 0.463158 0.74359
108 ACP 0.463158 0.746835
109 7D7 0.4625 0.785714
110 LEU LMS 0.461538 0.688889
111 9ZA 0.460784 0.740741
112 9ZD 0.460784 0.740741
113 5FA 0.458333 0.74359
114 AQP 0.458333 0.74359
115 AR6 0.458333 0.766234
116 APC 0.458333 0.759494
117 APR 0.458333 0.766234
118 PRX 0.458333 0.746835
119 F2R 0.457627 0.75
120 IOT 0.456897 0.761905
121 4AD 0.456311 0.794872
122 PAJ 0.456311 0.722892
123 WSA 0.45614 0.72093
124 YAP 0.453704 0.794872
125 8PZ 0.453704 0.712644
126 FA5 0.453704 0.805195
127 ADP PO3 0.453608 0.763158
128 ADV 0.453608 0.782051
129 NVA 2AD 0.453608 0.849315
130 SAP 0.453608 0.728395
131 AGS 0.453608 0.728395
132 RBY 0.453608 0.782051
133 AD9 0.453608 0.725
134 PTJ 0.45283 0.731707
135 MHZ 0.452632 0.797468
136 00A 0.451923 0.740741
137 A3P 0.451613 0.74026
138 YLP 0.451327 0.771084
139 7MD 0.45045 0.768293
140 ALF ADP 0.45 0.707317
141 ADP ALF 0.45 0.707317
142 2VA 0.447917 0.819444
143 OOB 0.446602 0.779221
144 ANP 0.444444 0.725
145 T99 0.444444 0.7375
146 ACQ 0.444444 0.746835
147 TAT 0.444444 0.7375
148 P5A 0.443396 0.719101
149 7D5 0.443182 0.708861
150 A1R 0.442308 0.7625
151 YLC 0.439655 0.790123
152 2AM 0.438202 0.717949
153 DLL 0.438095 0.779221
154 ARG AMP 0.4375 0.759036
155 A22 0.436893 0.734177
156 D3Y 0.436893 0.859155
157 ATF 0.435644 0.716049
158 MYR AMP 0.435185 0.746988
159 80F 0.434426 0.75
160 SO8 0.434343 0.808219
161 OAD 0.433962 0.769231
162 3UK 0.433962 0.769231
163 TAD 0.433628 0.765432
164 25A 0.432692 0.74359
165 6YZ 0.431373 0.746835
166 VO4 ADP 0.431373 0.734177
167 ADP VO4 0.431373 0.734177
168 9SN 0.431193 0.731707
169 TYM 0.431034 0.805195
170 B5V 0.429907 0.759494
171 PR8 0.429907 0.8
172 ADQ 0.428571 0.746835
173 YLB 0.42735 0.771084
174 9K8 0.425926 0.67033
175 1ZZ 0.425926 0.746988
176 FYA 0.425926 0.779221
177 3OD 0.425926 0.769231
178 PPS 0.425743 0.674419
179 MAP 0.423077 0.707317
180 A2P 0.421053 0.727273
181 4YB 0.421053 0.735632
182 9X8 0.420561 0.75
183 ADP BMA 0.420561 0.746835
184 TYR AMP 0.419643 0.794872
185 5SV 0.419048 0.731707
186 3NZ 0.416667 0.824324
187 YLA 0.416667 0.771084
188 8Q2 0.415254 0.688889
189 A3R 0.415094 0.7625
190 B5Y 0.414414 0.75
191 B5M 0.414414 0.75
192 48N 0.413793 0.753086
193 LPA AMP 0.413793 0.768293
194 AYB 0.413223 0.761905
195 ACK 0.413043 0.710526
196 QQY 0.413043 0.696203
197 BIS 0.412844 0.719512
198 JB6 0.412844 0.7625
199 PAP 0.41 0.730769
200 DQV 0.408696 0.75641
201 OVE 0.408602 0.7125
202 AMP DBH 0.40708 0.746835
203 4UV 0.40708 0.75
204 3AD 0.406977 0.852941
205 AF3 ADP 3PG 0.40678 0.743902
206 OMR 0.40678 0.738095
207 LAQ 0.405172 0.768293
208 A A 0.40367 0.74359
209 7C5 0.403509 0.789474
210 7MC 0.403361 0.75
211 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 with APoc: 45
This union binding pocket(no: 1) in the query (biounit: 3f9w.bio2) has 30 residues
No: Leader PDB Ligand Sequence Similarity
1 2CHT TSA None
2 4JNJ BTN None
3 4UXH T5A 1.20482
4 1Z4O GL1 2.40964
5 2QQ0 ANP 3.01205
6 2QQ0 TMP 3.01205
7 2QQ0 ADP 3.01205
8 2QQ0 THM 3.01205
9 4J4H NAI 3.01205
10 4J4H 1J1 3.01205
11 5H4S RAM 3.01205
12 4RKS MEV 3.01205
13 1PS9 FMN 3.61446
14 4D79 ATP 3.61446
15 4LOC BTN 4.21687
16 3WG6 NDP 4.81928
17 1SOX MTE 4.81928
18 2AHR NAP 4.81928
19 4K26 SFF 5.07246
20 4J36 FAD 5.42169
21 1W4R TTP 5.42169
22 1F76 ORO 7.83133
23 1GAR U89 7.83133
24 3QXY SAM 8.43373
25 5X8G S0N 8.43373
26 3KOX Z98 8.43373
27 5FRD COA 8.43373
28 4CFT H4B 9.03614
29 1XSE NDP 9.63855
30 3N71 SFG 11.4458
31 2B8T THM 11.4458
32 5IXB LGA 12.037
33 5NCB JZ3 13.253
34 1RC0 KT5 13.8554
35 1GZ6 NAI 14.4578
36 6FQZ 6PG 15.0602
37 2H21 SAM 16.2651
38 4I6G FAD 17.4699
39 5BVA FAD 18.0723
40 2BII MTV 18.6747
41 4NOS H4B 19.2771
42 3KMT SAH 20.1681
43 5CZY SAM 30.1205
44 5T0K SAM 39.1566
45 5JIY SAM 39.1566
Pocket No.: 2; Query (leader) PDB : 3F9W; Ligand: SAH; Similar sites found with APoc: 12
This union binding pocket(no: 2) in the query (biounit: 3f9w.bio4) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 5JBX COA None
2 1TL2 NDG 2.40964
3 5BUK FAD 4.21687
4 4J36 1HR 5.42169
5 1FQK GDP 5.44218
6 1FQJ GDP 5.44218
7 3T31 DCQ 6.0241
8 3T31 FAD 6.0241
9 2A9D MTE 6.0241
10 2ODE ALF GDP 6.38298
11 5K2M ADP 15.6627
12 4NOS H2B 19.2771
Pocket No.: 3; Query (leader) PDB : 3F9W; Ligand: SAH; Similar sites found with APoc: 4
This union binding pocket(no: 3) in the query (biounit: 3f9w.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 5EB4 FAD 3.61446
2 1GSA ADP 4.21687
3 1BH2 GSP 10.8434
4 1SVK ALF GDP 14.4578
Pocket No.: 4; Query (leader) PDB : 3F9W; Ligand: SAH; Similar sites found with APoc: 4
This union binding pocket(no: 4) in the query (biounit: 3f9w.bio3) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 3AXB FAD 2.40964
2 5T9F TYR 3.61446
3 1U6R IOM 4.81928
4 3OTX AP5 7.83133
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