Receptor
PDB id Resolution Class Description Source Keywords
4YNM 2.19 Å EC: 2.1.1.43 ASH1L WILD-TYPE SET DOMAIN IN COMPLEX WITH S-ADENOSYL METHIO HOMO SAPIENS HISTONE METHYLATION SET DOMAIN TRANSFERASE
Ref.: TWO LOOPS UNDERGOING CONCERTED DYNAMICS REGULATE TH ACTIVITY OF THE ASH1L HISTONE METHYLTRANSFERASE. BIOCHEMISTRY V. 54 5401 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN B:2303;
B:2301;
B:2302;
A:2303;
A:2302;
A:2301;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
SAM B:2304;
A:2304;
Valid;
Valid;
none;
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
4YNM 2.19 Å EC: 2.1.1.43 ASH1L WILD-TYPE SET DOMAIN IN COMPLEX WITH S-ADENOSYL METHIO HOMO SAPIENS HISTONE METHYLATION SET DOMAIN TRANSFERASE
Ref.: TWO LOOPS UNDERGOING CONCERTED DYNAMICS REGULATE TH ACTIVITY OF THE ASH1L HISTONE METHYLTRANSFERASE. BIOCHEMISTRY V. 54 5401 2015
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 36 families.
1 4YNM - SAM C15 H22 N6 O5 S C[S@@+](CC....
2 4YPE - SAM C15 H22 N6 O5 S C[S@@+](CC....
3 4YPA - SAM C15 H22 N6 O5 S C[S@@+](CC....
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 4YNM - SAM C15 H22 N6 O5 S C[S@@+](CC....
2 4YPE - SAM C15 H22 N6 O5 S C[S@@+](CC....
3 4YPA - SAM C15 H22 N6 O5 S C[S@@+](CC....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 22 families.
1 3OOI - SAM C15 H22 N6 O5 S C[S@@+](CC....
2 4YNM - SAM C15 H22 N6 O5 S C[S@@+](CC....
3 4YPE - SAM C15 H22 N6 O5 S C[S@@+](CC....
4 4YPA - SAM C15 H22 N6 O5 S C[S@@+](CC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SAM; Similar ligands found: 192
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 XYA 0.565789 0.773333
9 ADN 0.565789 0.773333
10 RAB 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 AMP MG 0.511364 0.710843
25 5AL 0.510417 0.743902
26 VMS 0.510204 0.673913
27 54H 0.510204 0.673913
28 0UM 0.51 0.857143
29 A 0.505747 0.707317
30 AMP 0.505747 0.707317
31 ABM 0.505618 0.753086
32 A5A 0.505155 0.688889
33 DAL AMP 0.50505 0.765432
34 NVA LMS 0.504951 0.725275
35 K15 0.5 0.883117
36 6RE 0.5 0.78481
37 5AD 0.5 0.75
38 SSA 0.5 0.684783
39 SON 0.5 0.746988
40 SRP 0.5 0.746988
41 LSS 0.49505 0.706522
42 CA0 0.494624 0.714286
43 A12 0.494505 0.705882
44 AP2 0.494505 0.705882
45 ME8 0.490385 0.841463
46 5CA 0.49 0.684783
47 TSB 0.49 0.681319
48 53H 0.49 0.666667
49 ACP 0.489362 0.694118
50 5AS 0.48913 0.648936
51 ADP 0.48913 0.690476
52 A2D 0.488889 0.690476
53 J7C 0.488889 0.772152
54 ZAS 0.488636 0.769231
55 8QN 0.485149 0.743902
56 GAP 0.484536 0.73494
57 AN2 0.483871 0.682353
58 A3S 0.483871 0.813333
59 A7D 0.483871 0.851351
60 GJV 0.483516 0.775
61 SRA 0.483146 0.694118
62 LAD 0.480769 0.752941
63 KAA 0.480769 0.698925
64 GSU 0.480769 0.722222
65 AMO 0.480392 0.746988
66 DSZ 0.480392 0.703297
67 52H 0.48 0.666667
68 ADP MG 0.478723 0.702381
69 M33 0.478723 0.722892
70 MAO 0.478261 0.82716
71 BA3 0.478261 0.690476
72 AOC 0.477778 0.776316
73 DSH 0.477778 0.842105
74 NEC 0.477778 0.75
75 SXZ 0.47619 0.894737
76 AHX 0.475728 0.701149
77 Y3J 0.47561 0.706667
78 G5A 0.474227 0.684783
79 A3T 0.473684 0.8
80 ADP BEF 0.473684 0.686047
81 BEF ADP 0.473684 0.686047
82 B4P 0.473118 0.690476
83 AP5 0.473118 0.690476
84 A3N 0.472527 0.766234
85 KB1 0.471698 0.833333
86 LEU LMS 0.471154 0.706522
87 APC 0.46875 0.705882
88 PRX 0.46875 0.73494
89 PAJ 0.466019 0.712644
90 4AD 0.466019 0.759036
91 RBY 0.463918 0.72619
92 ADP PO3 0.463918 0.728395
93 ADV 0.463918 0.72619
94 ADX 0.463158 0.666667
95 MHZ 0.463158 0.82716
96 AU1 0.463158 0.674419
97 YAP 0.462963 0.738095
98 TXA 0.462264 0.72619
99 NB8 0.462264 0.72093
100 A3G 0.461538 0.802632
101 VRT 0.459184 0.842105
102 ATP MG 0.459184 0.702381
103 YSA 0.458716 0.684783
104 XAH 0.458716 0.715909
105 50T 0.458333 0.682353
106 ATP 0.458333 0.690476
107 7D7 0.45679 0.723684
108 ANP MG 0.455446 0.678161
109 KH3 0.455357 0.871795
110 ACQ 0.454545 0.694118
111 AQP 0.453608 0.690476
112 5FA 0.453608 0.690476
113 AR6 0.453608 0.710843
114 APR 0.453608 0.710843
115 NSS 0.451923 0.703297
116 FA5 0.449541 0.746988
117 AGS 0.44898 0.678161
118 SAP 0.44898 0.678161
119 A5D 0.44898 0.789474
120 AD9 0.44898 0.674419
121 PTJ 0.448598 0.72093
122 YLB 0.448276 0.758621
123 YLP 0.447368 0.738636
124 D3Y 0.446602 0.792208
125 ADP ALF 0.445545 0.678161
126 ALF ADP 0.445545 0.678161
127 TYR AMP 0.445455 0.746988
128 MYR AMP 0.444444 0.776471
129 3AM 0.444444 0.674699
130 OAD 0.443396 0.73494
131 2VA 0.443299 0.779221
132 OOB 0.442308 0.722892
133 S8M 0.442308 0.831169
134 ADP VO4 0.441176 0.702381
135 VO4 ADP 0.441176 0.702381
136 ANP 0.44 0.674419
137 TAT 0.44 0.686047
138 WAQ 0.439252 0.75
139 ARG AMP 0.438596 0.727273
140 YLC 0.435897 0.755814
141 AAT 0.435644 0.797468
142 3OD 0.435185 0.73494
143 1ZZ 0.435185 0.755814
144 NVA 2AD 0.434343 0.815789
145 DLL 0.433962 0.722892
146 00A 0.433962 0.689655
147 7MD 0.433628 0.715909
148 ATF 0.431373 0.666667
149 SO8 0.43 0.792208
150 3UK 0.429907 0.714286
151 A6D 0.429907 0.72619
152 5SV 0.428571 0.741176
153 AMP DBH 0.428571 0.714286
154 WSA 0.42735 0.692308
155 TYM 0.42735 0.746988
156 9SN 0.427273 0.681818
157 AHZ 0.426087 0.755814
158 A A 0.425926 0.710843
159 3NZ 0.425926 0.807692
160 P5A 0.425926 0.691489
161 PR8 0.425926 0.744186
162 A1R 0.424528 0.709302
163 2A5 0.424242 0.674419
164 7MC 0.423729 0.719101
165 7D5 0.422222 0.658824
166 FYA 0.422018 0.722892
167 JB6 0.422018 0.709302
168 AYB 0.421488 0.75
169 PLP AAD 0.419355 0.764045
170 A22 0.419048 0.682353
171 MAP 0.419048 0.659091
172 2AM 0.417582 0.666667
173 TAD 0.417391 0.712644
174 A3P 0.416667 0.686747
175 ADP BMA 0.416667 0.714286
176 25A 0.415094 0.690476
177 YLA 0.413223 0.719101
178 ADQ 0.411215 0.694118
179 48N 0.410256 0.72093
180 0XU 0.41 0.824324
181 NAD IBO 0.406504 0.717647
182 7D3 0.40625 0.643678
183 PAP 0.405941 0.678571
184 OVE 0.404255 0.662791
185 4UV 0.403509 0.697674
186 ALF ADP 3PG 0.403361 0.712644
187 AF3 ADP 3PG 0.403361 0.712644
188 LA8 ALF 3PG 0.403361 0.712644
189 3AD 0.402299 0.783784
190 CMP 0.402062 0.691358
191 2BA 0.402062 0.682927
192 7C5 0.4 0.731707
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4YNM; Ligand: SAM; Similar sites found: 51
This union binding pocket(no: 1) in the query (biounit: 4ynm.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3QMN A3P 0.01347 0.41345 None
2 1FTH A3P 0.01699 0.40729 None
3 5DA3 58V 0.01014 0.40967 0.884956
4 2RC8 DSN 0.01139 0.41438 1.76991
5 5F90 LMR 0.006097 0.43554 1.92308
6 5F90 GLA GAL 0.006067 0.43546 1.92308
7 5F90 GLA GAL BGC 5VQ 0.01873 0.40739 1.92308
8 3DGY 2GP 0.01477 0.41229 2.06186
9 3F5A SIA GAL NAG 0.002083 0.48541 2.21239
10 3ALN ANP 0.005597 0.40961 2.21239
11 2D3Y DU 0.02676 0.4082 2.28311
12 5JZJ AN2 0.005023 0.41171 2.6936
13 3WVR AMP 0.004096 0.41973 3.09735
14 2IF8 ADP 0.01213 0.41474 3.09735
15 3X01 AMP 0.01716 0.40949 3.09735
16 1RGE 2GP 0.02319 0.40163 3.125
17 2QEH SRO 0.01526 0.40525 3.44828
18 3DAK ANP 0.006018 0.40451 3.53982
19 4GDX GLU 0.004973 0.43916 3.9823
20 4LH7 1X8 0.006459 0.43229 3.9823
21 3TKI S25 0.04031 0.40088 3.9823
22 2H21 SAM 0.00002073 0.46288 4.42478
23 5G1X ADP 0.008418 0.40168 4.7619
24 3VSV XYS 0.007471 0.42747 4.86726
25 2AF6 BRU 0.01892 0.40644 4.86726
26 2QX0 PH2 0.02546 0.40583 5.03145
27 4CS9 AMP 0.01145 0.40254 5.29101
28 3QXY SAM 0.00003332 0.51509 5.30973
29 5HVJ ANP 0.003342 0.44596 5.30973
30 3M2W L8I 0.01009 0.40567 6.19469
31 5XG5 A2G 0.01945 0.40641 6.2069
32 4IDT T28 0.003714 0.41757 7.07965
33 1DLL LAT 0.01844 0.40738 7.52212
34 2Z48 NGA 0.02804 0.40254 7.52212
35 3HAV ATP 0.02613 0.40081 9.29204
36 2VZ6 FEF 0.004862 0.42054 10.177
37 2RIO ADP 0.005515 0.4099 10.177
38 3S6X SIA GAL BGC 0.02742 0.40397 10.177
39 2A19 ANP 0.01318 0.40418 10.2857
40 1DCP HBI 0.01467 0.41201 10.5769
41 3N71 SFG 0.000001564 0.59233 12.8319
42 2QLU ADE 0.0227 0.40647 12.8319
43 3BIB PSF 0.01378 0.41615 14.6552
44 5LXM ADP 0.00809 0.40246 18.4211
45 1JPA ANP 0.01148 0.41245 18.5841
46 5M5G SAH 0.00000004005 0.6146 29.646
47 5M5G VAL MET LEU PRO GLY ARG GLY VAL PRO 0.0000003302 0.43666 29.646
48 5CZY SAM 0.000001845 0.50886 35.3982
49 3KMT SAH 0.000000322 0.607 36.9748
50 5JIY SAM 0.000000001152 0.70767 42.0354
51 5T0K SAM 0.000000000724 0.70611 42.0354
Pocket No.: 2; Query (leader) PDB : 4YNM; Ligand: SAM; Similar sites found: 8
This union binding pocket(no: 2) in the query (biounit: 4ynm.bio2) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4JGP PYR 0.02126 0.40235 3.22581
2 1XVB BHL BHL 0.02623 0.40012 3.9823
3 2JBM SRT 0.04568 0.4 3.9823
4 1YFS ALA 0.01139 0.41595 6.63717
5 1NX0 ALA LYS ALA ILE ALA 0.0143 0.4097 6.93642
6 3GQI ACP 0.007427 0.40052 7.9646
7 2PVF ACP 0.007318 0.4044 8.40708
8 1TZD ADP 0.02599 0.4005 9.29204
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