Receptor
PDB id Resolution Class Description Source Keywords
2w5z 2.2 Å EC: 2.1.1.43 TERNARY COMPLEX OF THE MIXED LINEAGE LEUKAEMIA (MLL1) SET DOMAIN WITH THE COFACTOR PRODUCT S-ADENOSYLHOMOCYSTEINE A ND HISTONE PEPTIDE. HOMO SAPIENS TRANSCRIPTION REGULATION CHROMOSOMAL REARRANGEMENT PROTEIN LYSINE METHYLTRANSFERASE PROTO-ONCOGENE PHOSPHOPROTEIN UBL CONJUGATION S-ADENOSYL-L-METHIONINE MIXED LINEAGE LEUKAEMIA POLYMORPHISM TRANSCRIPTION METAL-BINDING ZINC-FINGER DNA-BINDING BROMODOMAIN TRANSFERASE METHYLTRANSFERASE CHROMATIN REGULATOR ALTERNATIVE SPLICING HISTONE MODIFICATION MLL1 ZINC KMT2A NUCLEUS APOPTOSIS SET DOMAIN
Ref.: STRUCTURAL BASIS FOR THE REQUIREMENT OF ADDITIONAL FACTORS FOR MLL1 SET DOMAIN ACTIVITY AND RECOGNITION OF EPIGENETIC MARKS. MOL.CELL V. 33 181 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ALA ARG THR MLY GLN THR ALA ARG TYR C:2;
 Valid;
 none;
 submit data
967.116 n/a O=C([...
GOL A:4972;
A:4973;
 Invalid;
Invalid;
 none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
SAH A:4971;
 Valid;
 none;
 submit data
384.411 C14 H20 N6 O5 S c1nc(...
ZN A:4970;
 Part of Protein;
 none;
 submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2W5Z 2.2 Å EC: 2.1.1.43 TERNARY COMPLEX OF THE MIXED LINEAGE LEUKAEMIA (MLL1) SET DOMAIN WITH THE COFACTOR PRODUCT S-ADENOSYLHOMOCYSTEINE A ND HISTONE PEPTIDE. HOMO SAPIENS TRANSCRIPTION REGULATION CHROMOSOMAL REARRANGEMENT PROTEIN LYSINE METHYLTRANSFERASE PROTO-ONCOGENE PHOSPHOPROTEIN UBL CONJUGATION S-ADENOSYL-L-METHIONINE MIXED LINEAGE LEUKAEMIA POLYMORPHISM TRANSCRIPTION METAL-BINDING ZINC-FINGER DNA-BINDING BROMODOMAIN TRANSFERASE METHYLTRANSFERASE CHROMATIN REGULATOR ALTERNATIVE SPLICING HISTONE MODIFICATION MLL1 ZINC KMT2A NUCLEUS APOPTOSIS SET DOMAIN
Ref.: STRUCTURAL BASIS FOR THE REQUIREMENT OF ADDITIONAL FACTORS FOR MLL1 SET DOMAIN ACTIVITY AND RECOGNITION OF EPIGENETIC MARKS. MOL.CELL V. 33 181 2009
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 37 families.
1 2W5Z - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 2W5Y - SAH C14 H20 N6 O5 S c1nc(c2c(n....
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 6U9M ic50 = 66.5 nM Q2M C23 H32 N8 O5 S c1cc(sc1)C....
2 6U9N ic50 = 55.6 nM Q34 C25 H33 Cl N8 O5 c1cc(ccc1C....
3 6U9K ic50 = 138.4 nM Q2V C33 H42 N8 O5 c1ccc(cc1)....
4 6U9R ic50 = 99.5 nM Q2P C25 H33 Cl N8 O5 c1cc(cc(c1....
5 2W5Z - SAH C14 H20 N6 O5 S c1nc(c2c(n....
6 2W5Y - SAH C14 H20 N6 O5 S c1nc(c2c(n....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 21 families.
1 6U9M ic50 = 66.5 nM Q2M C23 H32 N8 O5 S c1cc(sc1)C....
2 6U9N ic50 = 55.6 nM Q34 C25 H33 Cl N8 O5 c1cc(ccc1C....
3 6U9K ic50 = 138.4 nM Q2V C33 H42 N8 O5 c1ccc(cc1)....
4 6U9R ic50 = 99.5 nM Q2P C25 H33 Cl N8 O5 c1cc(cc(c1....
5 4Z4P - SAH C14 H20 N6 O5 S c1nc(c2c(n....
6 2W5Z - SAH C14 H20 N6 O5 S c1nc(c2c(n....
7 2W5Y - SAH C14 H20 N6 O5 S c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: ALA ARG THR MLY GLN THR ALA ARG TYR; Similar ligands found: 90
No: Ligand ECFP6 Tc MDL keys Tc
1 ALA ARG THR MLY GLN THR ALA ARG TYR 1 1
2 ALA ARG THR MLY GLN 0.60177 0.893939
3 ALA ARG THR MLY GLN THR ALA ARG LYS TYR 0.576271 0.893939
4 ALA ARG THR M3L GLN THR ALA ARG 0.570248 0.882353
5 ALA 2MR THR MLY GLN THR ALA ALA 0.563492 0.909091
6 ALA ARG THR MLY GLN THR ALA ARG LYS 0.558333 0.878788
7 ACE GLU ALA GLN THR ARG LEU 0.54918 0.772727
8 LEU GLU LYS ALA ARG GLY SER THR TYR 0.541096 0.867647
9 ACE ALA ARG THR GLU VAL TYR NH2 0.539062 0.833333
10 ALA ARG THR M3L GLN THR ALA ALA LYS ALA 0.530769 0.882353
11 GLU ALA GLN THR ARG LEU 0.52 0.757576
12 ALA ARG THR LYS GLN THR ALA ARG LYS 0.515873 0.757576
13 VAL LYS VAL VAL ALA LYS LYS TYR ARG ASN 0.515625 0.835821
14 ACE GLN THR ALA ARG PRK SER THR 0.511628 0.724638
15 ALA ARG THR GLU LEU TYR ARG SER LEU 0.510949 0.865672
16 ARG HIS ARG MLY VAL LEU ARG ASP TYR 0.510067 0.876712
17 SER ASP TYR GLN ARG LEU 0.508065 0.818182
18 ALA ARG THR MLY GLN THR ALA ARG MLY SER 0.504132 0.878788
19 SER SER ARG LYS GLU TYR TYR ALA 0.503937 0.779412
20 ALA ARG THR MLZ GLN THR ALA ARG LYS 0.5 0.833333
21 GLU LEU LYS TPO GLU ARG TYR 0.496504 0.819444
22 ALA DA2 THR M3L GLN THR ALA ARG ALA 0.496403 0.882353
23 ALA GLN THR ALA ARG ALY SER THR 0.496183 0.776119
24 SER GLU LEU GLU ILE LYS ARG TYR 0.492857 0.852941
25 PHE ALA GLY LEU ARG GLN ALA VAL THR GLN 0.492188 0.746269
26 ALA THR ALA ALA ALA THR GLU ALA TYR 0.487603 0.681818
27 ACE GLN THR ALA ARG KCR SER THR 0.485075 0.735294
28 ARG ARG ARG GLU THR GLN VAL 0.483333 0.772727
29 ARG ARG GLU VAL HIS THR TYR TYR 0.482993 0.77027
30 SER ARG TYR TRP ALA ILE ARG THR ARG 0.477419 0.736842
31 THR ARG ARG GLU THR GLN LEU 0.475806 0.787879
32 ACE GLN THR ALA ARG BTK SER THR 0.473282 0.75
33 ARG VAL ALA GLN LEU GLU GLN VAL TYR ILE 0.472222 0.791045
34 ALA GLN ASP ILE TYR ARG ALA SER TYR 0.469799 0.8
35 GLU GLU TYR LEU GLN ALA PHE THR TYR 0.464789 0.691176
36 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.461538 0.787879
37 ALA ARG THR ALY GLN THR ALA 0.460317 0.787879
38 ALA ARG THR M3L GLN THR ALA 2MR LYS 0.460317 0.867647
39 ARG ARG LEU LEU ARG GLY HIS ASN GLN TYR 0.453947 0.77027
40 PHQ GLN THR ALA ARG LYS NH2 FOA 0.453333 0.72
41 GLN THR ALA ARG M3L SER 0.447761 0.855072
42 LYS LYS ALA THR GLN ALA SEP GLN GLU TYR 0.447154 0.643836
43 SAC ARG GLY THR GLN THR GLU 0.44697 0.735294
44 ALA ARG THR M3L GLN THR ALA ARG LYS SER 0.445312 0.867647
45 ASN ALA LEU LEU ARG TYR LEU LEU ASP 0.445255 0.835821
46 ARG TYR GLY PHE VAL ALA ASN PHE 0.445205 0.771429
47 ALA ARG THR M3L GLN THR ALA DA2 LYS 0.443709 0.867647
48 ALA ARG THR MLZ GLN THR ALA ARG LYS TYR 0.438462 0.818182
49 GLY ALA ALA ARG ALA GLU VAL TYR LEU ARG 0.437086 0.848485
50 ALA GLN PHE SER ALA SER ALA SER ARG 0.43609 0.761194
51 GLN THR ALA ARG M3L SER THR GLY 0.435714 0.855072
52 PHE TYR ARG ALA LEU MET 0.433566 0.797101
53 PRO ALA THR ILE MET MET GLN ARG GLY ASN 0.431818 0.753623
54 CYS THR GLU LEU LYS LEU ASN ASP TYR 0.430556 0.764706
55 ASP ASN ARG LEU GLY LEU VAL TYR GLN PHE 0.429688 0.632353
56 ALA ASN SER ARG TRP GLN VAL THR ARG VAL 0.42953 0.733333
57 ASP VAL GLN THR GLY ARG ARG PRO TYR GLU 0.428571 0.824324
58 PHE LEU ARG GLY ARG ALA TYR VAL LEU 0.427632 0.782609
59 PHE LEU ARG GLY ARG ALA TYR GLY LEU 0.427586 0.782609
60 ARG LYS LYS ARG TYR THR VAL VAL GLY ASN 0.426667 0.838235
61 VAL PRO LEU ARG PRO MET THR TYR 0.424051 0.853333
62 THR LYS ASN TYR LYS GLN THR SER VAL 0.423611 0.764706
63 GLY GLY ARG LYS LYS TYR LYS LEU 0.423358 0.820895
64 GLY GLY LYS LYS LYS TYR ARG LEU 0.423358 0.820895
65 GLY GLY LYS LYS ARG TYR LYS LEU 0.423358 0.820895
66 GLU THR VAL ARG PHE GLN SER ASP 0.421769 0.776119
67 ALA ARG THR ALA ALA THR ALA ARG LYS SER 0.418033 0.712121
68 LEU ARG ASN GLN SER VAL PHE ASN PHE 0.417808 0.771429
69 SER GLU ILE GLU PHE ALA ARG LEU 0.417808 0.764706
70 ALA ASN SER ARG TYR PRO THR SER ILE ILE 0.417722 0.779221
71 ASP GLU LEU GLU ILE LYS ALA TYR 0.416667 0.746269
72 ASN TYR THR PRO GLY PRO GLY THR ARG PHE 0.416667 0.779221
73 ARG GLY TYR LEU TYR GLN GLY LEU 0.415493 0.768116
74 ARG ARG ILE TYR ASP LEU ILE GLU LEU 0.413333 0.835821
75 ALA ALA LEU THR ARG ALA 0.412698 0.727273
76 ARG GLY TYR VAL TYR GLN GLY LEU 0.410959 0.768116
77 GLU ASN GLN LYS GLU TYR PHE PHE 0.410448 0.681159
78 ALA ARG THR LYS GLN THR ALA ARG 0.409449 0.742424
79 GLY ALA GLN THR PHE TYR VAL ASP GLY ALA 0.408451 0.710145
80 CYS THR GLU LEU LYS LEU SER ASP TYR 0.408163 0.764706
81 ALA ARG THR M3L GLN THR ALA ARG LYS 0.407692 0.852941
82 SER ARG ILE ARG ILE ARG GLY TYR VAL ARG 0.406897 0.84058
83 ALA ARG MLY SER THR GLY GLY ALY 0.406897 0.882353
84 SER SER THR ARG GLY ILE SER GLN LEU TRP 0.406061 0.723684
85 VAL ALA ARG SER 0.405172 0.671642
86 ARG HIS ARG MLZ VAL LEU ARG ASP ASN TYR 0.403614 0.849315
87 ACE CSO ARG ALA THR LYS MET LEU 0.402778 0.780822
88 TYR PRO LYS ARG ILE ALA 0.401316 0.746667
89 GLU LEU LYS ARG LYS MET ILE TYR MET 0.4 0.852941
90 SER SER ILE GLU PHE ALA ARG LEU 0.4 0.779412
Ligand no: 2; Ligand: SAH; Similar ligands found: 256
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 U4Y 0.64 0.956522
11 SFG 0.635294 0.954545
12 SA8 0.62069 0.915493
13 EEM 0.617977 0.890411
14 MTA 0.615385 0.869565
15 SAI 0.613636 0.955882
16 S7M 0.586957 0.916667
17 36A 0.586538 0.90411
18 K15 0.583333 0.878378
19 ADN 0.573333 0.84058
20 RAB 0.573333 0.84058
21 XYA 0.573333 0.84058
22 62X 0.572917 0.855263
23 5CD 0.571429 0.852941
24 0UM 0.5625 0.876712
25 5N5 0.558442 0.84058
26 A4D 0.551282 0.867647
27 KYE 0.54902 0.866667
28 SAM 0.537634 0.916667
29 SSA 0.536842 0.712644
30 SMM 0.536842 0.88
31 KB1 0.534653 0.902778
32 A5D 0.532609 0.857143
33 SIB 0.53125 0.928571
34 EP4 0.530864 0.819444
35 DSZ 0.530612 0.732558
36 GSU 0.53 0.752941
37 LMS 0.529412 0.694118
38 AMP 0.529412 0.763158
39 A 0.529412 0.763158
40 5CA 0.525773 0.712644
41 ME8 0.524752 0.8125
42 M2T 0.52439 0.821918
43 6RE 0.523256 0.824324
44 GJV 0.522727 0.813333
45 OZP 0.518519 0.915493
46 AAT 0.515789 0.863014
47 LSS 0.515152 0.696629
48 KAA 0.514852 0.727273
49 KXW 0.514019 0.915493
50 NWW 0.5125 0.80597
51 J7C 0.511364 0.835616
52 KG4 0.51087 0.769231
53 A5A 0.510417 0.697674
54 AMP MG 0.505747 0.773333
55 SON 0.505495 0.805195
56 SRP 0.505155 0.805195
57 F0P 0.504505 0.915493
58 KH3 0.5 0.866667
59 HY8 0.5 0.890411
60 CA0 0.5 0.769231
61 AMO 0.5 0.805195
62 54H 0.5 0.681818
63 ADX 0.5 0.694118
64 5AL 0.5 0.779221
65 VMS 0.5 0.681818
66 N37 0.495495 0.9
67 HZ2 0.495413 0.890411
68 NVA LMS 0.49505 0.707865
69 AHX 0.49505 0.753086
70 TSB 0.494949 0.689655
71 53H 0.494949 0.674157
72 G5A 0.494737 0.712644
73 45A 0.494382 0.74359
74 ABM 0.494382 0.74359
75 A2D 0.494382 0.74359
76 ZAS 0.494253 0.808219
77 A6D 0.490196 0.759494
78 GEK 0.49 0.956522
79 8QN 0.49 0.779221
80 GAP 0.489583 0.769231
81 A3S 0.48913 0.884058
82 AN2 0.48913 0.734177
83 S4M 0.488889 0.831169
84 SRA 0.488636 0.746835
85 EU9 0.486486 0.825
86 LAD 0.485437 0.810127
87 52H 0.484848 0.674157
88 V2G 0.484536 0.753086
89 BA3 0.483516 0.74359
90 AP2 0.483516 0.759494
91 A12 0.483516 0.759494
92 AOC 0.483146 0.842857
93 NEC 0.483146 0.788732
94 Y3J 0.481481 0.768116
95 VRT 0.479167 0.861111
96 50T 0.478723 0.734177
97 AP5 0.478261 0.74359
98 ADP 0.478261 0.74359
99 5AS 0.478261 0.655556
100 B4P 0.478261 0.74359
101 Q34 0.477876 0.866667
102 Q2M 0.477876 0.916667
103 A3N 0.477778 0.830986
104 YSA 0.476636 0.712644
105 XAH 0.476636 0.768293
106 8LH 0.474747 0.759494
107 V47 0.474747 0.882353
108 0XU 0.473684 0.897059
109 AT4 0.473118 0.7375
110 ADP MG 0.473118 0.763158
111 ADP BEF 0.473118 0.763158
112 J4G 0.471154 0.818182
113 WAQ 0.471154 0.807692
114 NSS 0.470588 0.712644
115 8LE 0.469388 0.75
116 5AD 0.468354 0.791045
117 AU1 0.468085 0.725
118 M33 0.468085 0.734177
119 MAO 0.467391 0.797468
120 NB8 0.466667 0.775
121 A3G 0.466667 0.871429
122 N5O 0.466667 0.857143
123 TXA 0.466667 0.759494
124 3AM 0.465909 0.727273
125 Q2V 0.465517 0.902778
126 QA7 0.465347 0.75
127 8X1 0.465347 0.707865
128 DAL AMP 0.465347 0.779221
129 8LQ 0.465347 0.782051
130 A3T 0.463158 0.842857
131 ATP 0.463158 0.74359
132 ACP 0.463158 0.746835
133 HEJ 0.463158 0.74359
134 7D7 0.4625 0.785714
135 QXP 0.460784 0.697674
136 9ZA 0.460784 0.740741
137 9ZD 0.460784 0.740741
138 APR 0.458333 0.766234
139 5FA 0.458333 0.74359
140 PRX 0.458333 0.746835
141 APC 0.458333 0.759494
142 AQP 0.458333 0.74359
143 AR6 0.458333 0.766234
144 F2R 0.457627 0.75
145 R2V 0.457143 0.697674
146 IOT 0.456897 0.761905
147 N5A 0.456522 0.855072
148 PAJ 0.456311 0.722892
149 4AD 0.456311 0.794872
150 WSA 0.45614 0.72093
151 HQG 0.455446 0.75641
152 NWQ 0.454545 0.782609
153 Q2P 0.453782 0.866667
154 8PZ 0.453704 0.712644
155 FA5 0.453704 0.805195
156 AGS 0.453608 0.728395
157 APC MG 0.453608 0.766234
158 RBY 0.453608 0.782051
159 ATP MG 0.453608 0.763158
160 AD9 0.453608 0.725
161 ADV 0.453608 0.782051
162 NVA 2AD 0.453608 0.849315
163 ADP PO3 0.453608 0.763158
164 PTJ 0.45283 0.731707
165 MHZ 0.452632 0.797468
166 00A 0.451923 0.740741
167 A3P 0.451613 0.74026
168 YLP 0.451327 0.771084
169 7MD 0.45045 0.768293
170 ALF ADP 0.45 0.707317
171 BEF ADP 0.44898 0.74359
172 2VA 0.447917 0.819444
173 H1Q 0.447917 0.753247
174 LEU LMS 0.447619 0.724138
175 QXG 0.447619 0.689655
176 OOB 0.446602 0.779221
177 ACQ 0.444444 0.746835
178 T99 0.444444 0.7375
179 TAT 0.444444 0.7375
180 ANP 0.444444 0.725
181 P5A 0.443396 0.719101
182 7D5 0.443182 0.708861
183 A1R 0.442308 0.7625
184 YLC 0.439655 0.790123
185 2AM 0.438202 0.717949
186 DLL 0.438095 0.779221
187 ARG AMP 0.4375 0.759036
188 KY2 0.436893 0.84
189 D3Y 0.436893 0.859155
190 A22 0.436893 0.734177
191 ANP MG 0.435644 0.734177
192 VO4 ADP 0.435644 0.725
193 ATF 0.435644 0.716049
194 MYR AMP 0.435185 0.746988
195 80F 0.434426 0.75
196 SO8 0.434343 0.808219
197 OAD 0.433962 0.769231
198 3UK 0.433962 0.769231
199 TAD 0.433628 0.765432
200 25A 0.432692 0.74359
201 6YZ 0.431373 0.746835
202 9SN 0.431193 0.731707
203 TYM 0.431034 0.805195
204 PR8 0.429907 0.8
205 B5V 0.429907 0.759494
206 KYB 0.428571 0.84
207 ADQ 0.428571 0.746835
208 YLB 0.42735 0.771084
209 1ZZ 0.425926 0.746988
210 9K8 0.425926 0.67033
211 3OD 0.425926 0.769231
212 FYA 0.425926 0.779221
213 PPS 0.425743 0.674419
214 JNT 0.424528 0.746835
215 B1U 0.423423 0.638298
216 MAP 0.423077 0.707317
217 4YB 0.421053 0.735632
218 A2P 0.421053 0.727273
219 9X8 0.420561 0.75
220 ADP BMA 0.420561 0.746835
221 OZV 0.419048 0.74359
222 5SV 0.419048 0.731707
223 YLA 0.416667 0.771084
224 3NZ 0.416667 0.824324
225 NX8 0.415842 0.875
226 KL2 0.41573 0.692308
227 8Q2 0.415254 0.688889
228 A3R 0.415094 0.7625
229 B5M 0.414414 0.75
230 B5Y 0.414414 0.75
231 LPA AMP 0.413793 0.768293
232 48N 0.413793 0.753086
233 AYB 0.413223 0.761905
234 ACK 0.413043 0.710526
235 QQY 0.413043 0.696203
236 JB6 0.412844 0.7625
237 BIS 0.412844 0.719512
238 K2H 0.411215 0.797297
239 PAP 0.41 0.730769
240 KY5 0.409091 0.887324
241 DQV 0.408696 0.75641
242 OVE 0.408602 0.7125
243 4UV 0.40708 0.75
244 AMP DBH 0.40708 0.746835
245 3AD 0.406977 0.852941
246 OMR 0.40678 0.738095
247 AF3 ADP 3PG 0.40678 0.743902
248 K38 0.405405 0.797297
249 LAQ 0.405172 0.768293
250 K2K 0.40367 0.875
251 7C5 0.403509 0.789474
252 7MC 0.403361 0.75
253 K3K 0.401786 0.797297
254 KOY 0.401709 0.847222
255 NWZ 0.4 0.861111
256 4UU 0.4 0.75
Similar Ligands (3D)
Ligand no: 1; Ligand: ALA ARG THR MLY GLN THR ALA ARG TYR; Similar ligands found: 0
No: Ligand Similarity coefficient
Ligand no: 2; Ligand: SAH; Similar ligands found: 15
No: Ligand Similarity coefficient
1 HCE 0.9148
2 GMD 0.9105
3 IDP 0.8930
4 GDP 0.8927
5 2EL 0.8907
6 GDP MG 0.8895
7 CUU 0.8893
8 BIG 0.8840
9 M7G 0.8830
10 DAT 0.8738
11 UC5 0.8671
12 4CT 0.8669
13 DTP 0.8653
14 GNH 0.8616
15 OS3 0.8593
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2W5Z; Ligand: SAH; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 2w5z.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
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