Receptor
PDB id Resolution Class Description Source Keywords
5JLE 2.4 Å EC: 2.1.1.43 CRYSTAL STRUCTURE OF SETD2 BOUND TO SAH HOMO SAPIENS SET DOMAIN TRANSFERASE
Ref.: MOLECULAR BASIS FOR ONCOHISTONE H3 RECOGNITION BY S METHYLTRANSFERASE GENES DEV. V. 30 1611 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN A:1801;
A:1803;
A:1802;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
SAH A:1804;
Valid;
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
4FMU 2.1 Å EC: 2.1.1.43 CRYSTAL STRUCTURE OF METHYLTRANSFERASE DOMAIN OF HUMAN SET D CONTAINING PROTEIN 2 COMPOUND: PR-SNF HOMO SAPIENS STRUCTURAL GENOMICS CONSORTIUM SGC METHYLTRANSFERASESET DCONTAINING PROTEIN 2 PR-SNF TRANSFERASE
Ref.: SINEFUNGIN DERIVATIVES AS INHIBITORS AND STRUCTURE PROTEIN LYSINE METHYLTRANSFERASE SETD2. J.AM.CHEM.SOC. V. 134 18004 2012
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 36 families.
1 4FMU ic50 = 8.2 uM 0UM C18 H29 N7 O5 CCCN[C@@H]....
2 4H12 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
3 5JLE - SAH C14 H20 N6 O5 S c1nc(c2c(n....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 26 families.
1 4FMU ic50 = 8.2 uM 0UM C18 H29 N7 O5 CCCN[C@@H]....
2 4H12 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
3 5JLE - SAH C14 H20 N6 O5 S c1nc(c2c(n....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 22 families.
1 4FMU ic50 = 8.2 uM 0UM C18 H29 N7 O5 CCCN[C@@H]....
2 4H12 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
3 5JLE - SAH C14 H20 N6 O5 S c1nc(c2c(n....
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
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4FMU; Ligand: 0UM; Similar sites found: 44
This union binding pocket(no: 1) in the query (biounit: 4fmu.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3HAV ATP 0.01573 0.41876 1.79856
2 2V7O DRN 0.01329 0.41523 1.79856
3 4BCQ TJF 0.01865 0.40779 1.9084
4 3SZB I1E 0.01922 0.41752 2.15827
5 2IF8 ADP 0.01492 0.41713 2.20386
6 3X01 AMP 0.01794 0.41488 2.51799
7 3DAK ANP 0.007727 0.40703 2.51799
8 3VSV XYS 0.02887 0.40522 2.51799
9 1TZD ADP 0.02525 0.412 2.54545
10 5AWM ANP 0.01996 0.40231 2.79188
11 3OFM 4B0 0.007047 0.4203 2.8777
12 2PUL ACP 0.007734 0.4106 2.8777
13 2H21 SAM 0.00001542 0.49631 3.23741
14 3GGF GVD 0.01807 0.40065 3.23741
15 4IDT T28 0.013 0.40025 3.23741
16 5HVJ ANP 0.002673 0.46124 3.59712
17 4LH7 1X8 0.02687 0.4047 3.59712
18 3TBK ANP 0.02356 0.4068 3.95683
19 3AKK ADP 0.001915 0.40621 3.95683
20 2A19 ANP 0.01937 0.40295 4
21 3QXY SAM 0.00009204 0.43699 4.67626
22 3M2W L8I 0.006028 0.42355 4.67626
23 3WVR AMP 0.004936 0.4235 4.67626
24 2B9J ADP 0.01295 0.40033 4.67626
25 5AIP 4HP 0.01578 0.41336 4.79452
26 4KPM BEN 0.01752 0.41425 5
27 2AF6 BRU 0.01009 0.42887 5.42636
28 4MDB RLT 0.007152 0.44373 5.77778
29 2Q37 3AL 0.02148 0.40971 6.07735
30 2VZ6 FEF 0.006386 0.42234 6.47482
31 3N71 SFG 0.00001689 0.44497 7.19424
32 1FUT 2GP 0.03027 0.40299 7.54717
33 4GDX GLU 0.007254 0.43811 8.27338
34 1H8P PC 0.01623 0.41103 9.17431
35 3DGY 2GP 0.02372 0.40889 10.3093
36 1ZX5 LFR 0.002449 0.44233 10.4317
37 3GQI ACP 0.009556 0.4029 10.4317
38 3QMN A3P 0.01674 0.41549 11.6279
39 3KMT SAH 0.00000279 0.5751 15.9664
40 5M5G SAH 0.0000004977 0.58677 24.8201
41 5M5G VAL MET LEU PRO GLY ARG GLY VAL PRO 0.00000008266 0.48094 24.8201
42 5CZY SAM 0.000001635 0.47006 25.8993
43 5T0K SAM 0.000000001968 0.70137 32.3741
44 5JIY SAM 0.000000004324 0.6959 32.8467
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