-->
Receptor
PDB id Resolution Class Description Source Keywords
5TUZ 1.95 Å EC: 2.1.1.43 STRUCTURE OF HUMAN GLP SET-DOMAIN (EHMT1) IN COMPLEX WITH IN MS0124 HOMO SAPIENS METHYL TRANSFERASE TRANSFERASE-TRANSFERASE INHIBITOR COMPLE
Ref.: DISCOVERY OF POTENT AND SELECTIVE INHIBITORS FOR G9 PROTEIN (GLP) LYSINE METHYLTRANSFERASE. J. MED. CHEM. V. 60 1876 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN B:3005;
B:3002;
A:3005;
A:3002;
B:3003;
A:3004;
A:3003;
B:3004;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
EDO B:3007;
A:3007;
Invalid;
Invalid;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
7L6 B:3006;
A:3006;
Valid;
Valid;
none;
none;
ic50 = 13 nM
387.476 C20 H29 N5 O3 CN1CC...
SAM B:3001;
A:3001;
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
5TUZ 1.95 Å EC: 2.1.1.43 STRUCTURE OF HUMAN GLP SET-DOMAIN (EHMT1) IN COMPLEX WITH IN MS0124 HOMO SAPIENS METHYL TRANSFERASE TRANSFERASE-TRANSFERASE INHIBITOR COMPLE
Ref.: DISCOVERY OF POTENT AND SELECTIVE INHIBITORS FOR G9 PROTEIN (GLP) LYSINE METHYLTRANSFERASE. J. MED. CHEM. V. 60 1876 2017
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 39 families.
1 5VSF Kd = 94 nM 9HG C22 H33 N5 O2 CN1CCC(CC1....
2 3FPD ic50 = 0.7 uM Q4A C28 H38 N6 O2 C[N@@]1CCC....
3 2IGQ - SAH C14 H20 N6 O5 S c1nc(c2c(n....
4 5TUZ ic50 = 13 nM 7L6 C20 H29 N5 O3 CN1CCC(CC1....
5 5VSD Kd = 57 nM 9HJ C20 H31 N5 O2 CCCN(C)c1n....
6 3MO2 Kd = 244 nM E67 C31 H47 N7 O2 CN(C)CCCNc....
7 3MO5 Kd = 136 nM E72 C29 H52 N8 O2 CN(C)CCCNc....
70% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 28 families.
1 4NVQ ic50 = 3.3 nM 2OD C19 H27 N3 O2 COc1cc2c(c....
2 5VSE Kd = 1070 nM 9HG C22 H33 N5 O2 CN1CCC(CC1....
3 2O8J - SAH C14 H20 N6 O5 S c1nc(c2c(n....
4 5VSC Kd = 510 nM 9HJ C20 H31 N5 O2 CCCN(C)c1n....
5 3K5K Kd = 23 nM DXQ C26 H43 N7 O2 C[N@]1CCCN....
6 5VSF Kd = 94 nM 9HG C22 H33 N5 O2 CN1CCC(CC1....
7 3FPD ic50 = 0.7 uM Q4A C28 H38 N6 O2 C[N@@]1CCC....
8 2IGQ - SAH C14 H20 N6 O5 S c1nc(c2c(n....
9 5TUZ ic50 = 13 nM 7L6 C20 H29 N5 O3 CN1CCC(CC1....
10 5VSD Kd = 57 nM 9HJ C20 H31 N5 O2 CCCN(C)c1n....
11 3MO2 Kd = 244 nM E67 C31 H47 N7 O2 CN(C)CCCNc....
12 3MO5 Kd = 136 nM E72 C29 H52 N8 O2 CN(C)CCCNc....
50% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 22 families.
1 4NVQ ic50 = 3.3 nM 2OD C19 H27 N3 O2 COc1cc2c(c....
2 5VSE Kd = 1070 nM 9HG C22 H33 N5 O2 CN1CCC(CC1....
3 2O8J - SAH C14 H20 N6 O5 S c1nc(c2c(n....
4 5VSC Kd = 510 nM 9HJ C20 H31 N5 O2 CCCN(C)c1n....
5 3K5K Kd = 23 nM DXQ C26 H43 N7 O2 C[N@]1CCCN....
6 5VSF Kd = 94 nM 9HG C22 H33 N5 O2 CN1CCC(CC1....
7 3FPD ic50 = 0.7 uM Q4A C28 H38 N6 O2 C[N@@]1CCC....
8 2IGQ - SAH C14 H20 N6 O5 S c1nc(c2c(n....
9 5TUZ ic50 = 13 nM 7L6 C20 H29 N5 O3 CN1CCC(CC1....
10 5VSD Kd = 57 nM 9HJ C20 H31 N5 O2 CCCN(C)c1n....
11 3MO2 Kd = 244 nM E67 C31 H47 N7 O2 CN(C)CCCNc....
12 3MO5 Kd = 136 nM E72 C29 H52 N8 O2 CN(C)CCCNc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 7L6; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 7L6 1 1
2 DXQ 0.552083 0.884058
3 Q4A 0.546392 0.867647
4 9HG 0.541176 0.878788
5 9HJ 0.535714 0.878788
Ligand no: 2; Ligand: SAM; Similar ligands found: 202
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 ADN 0.565789 0.773333
9 RAB 0.565789 0.773333
10 XYA 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 5AL 0.510417 0.743902
25 54H 0.510204 0.673913
26 VMS 0.510204 0.673913
27 0UM 0.51 0.857143
28 AMP 0.505747 0.707317
29 LMS 0.505747 0.666667
30 A 0.505747 0.707317
31 ABM 0.505618 0.753086
32 A5A 0.505155 0.688889
33 SON 0.5 0.746988
34 SSA 0.5 0.684783
35 6RE 0.5 0.78481
36 K15 0.5 0.883117
37 5AD 0.5 0.75
38 SRP 0.5 0.746988
39 LSS 0.49505 0.706522
40 CA0 0.494624 0.714286
41 A12 0.494505 0.705882
42 AP2 0.494505 0.705882
43 ME8 0.490385 0.841463
44 TSB 0.49 0.681319
45 53H 0.49 0.666667
46 DAL AMP 0.49 0.765432
47 5CA 0.49 0.684783
48 ACP 0.489362 0.694118
49 ADP 0.48913 0.690476
50 5AS 0.48913 0.648936
51 J7C 0.488889 0.772152
52 A2D 0.488889 0.690476
53 ZAS 0.488636 0.769231
54 9ZD 0.485149 0.729412
55 9ZA 0.485149 0.729412
56 8QN 0.485149 0.743902
57 GAP 0.484536 0.73494
58 AN2 0.483871 0.682353
59 A3S 0.483871 0.813333
60 A7D 0.483871 0.851351
61 GJV 0.483516 0.775
62 SRA 0.483146 0.694118
63 LAD 0.480769 0.752941
64 KAA 0.480769 0.698925
65 GSU 0.480769 0.722222
66 AMO 0.480392 0.746988
67 DSZ 0.480392 0.703297
68 52H 0.48 0.666667
69 M33 0.478723 0.722892
70 BA3 0.478261 0.690476
71 MAO 0.478261 0.82716
72 NEC 0.477778 0.75
73 AOC 0.477778 0.776316
74 DSH 0.477778 0.842105
75 SXZ 0.47619 0.894737
76 AHX 0.475728 0.701149
77 NVA LMS 0.475728 0.736264
78 Y3J 0.47561 0.706667
79 G5A 0.474227 0.684783
80 A3T 0.473684 0.8
81 B4P 0.473118 0.690476
82 AP5 0.473118 0.690476
83 A3N 0.472527 0.766234
84 KB1 0.471698 0.833333
85 PRX 0.46875 0.73494
86 APC 0.46875 0.705882
87 AT4 0.468085 0.686047
88 PAJ 0.466019 0.712644
89 4AD 0.466019 0.759036
90 RBY 0.463918 0.72619
91 ADP PO3 0.463918 0.728395
92 ADV 0.463918 0.72619
93 ADX 0.463158 0.666667
94 MHZ 0.463158 0.82716
95 AU1 0.463158 0.674419
96 YAP 0.462963 0.738095
97 TXA 0.462264 0.72619
98 NB8 0.462264 0.72093
99 A3G 0.461538 0.802632
100 VRT 0.459184 0.842105
101 XAH 0.458716 0.715909
102 YSA 0.458716 0.684783
103 HEJ 0.458333 0.690476
104 50T 0.458333 0.682353
105 ATP 0.458333 0.690476
106 LEU LMS 0.457143 0.717391
107 7D7 0.45679 0.723684
108 KH3 0.455357 0.871795
109 ACQ 0.454545 0.694118
110 AR6 0.453608 0.710843
111 APR 0.453608 0.710843
112 AQP 0.453608 0.690476
113 5FA 0.453608 0.690476
114 NSS 0.451923 0.703297
115 FA5 0.449541 0.746988
116 A5D 0.44898 0.789474
117 AD9 0.44898 0.674419
118 AGS 0.44898 0.678161
119 SAP 0.44898 0.678161
120 PTJ 0.448598 0.72093
121 YLB 0.448276 0.758621
122 YLP 0.447368 0.738636
123 8X1 0.446602 0.680851
124 D3Y 0.446602 0.792208
125 ADP ALF 0.445545 0.678161
126 ALF ADP 0.445545 0.678161
127 3AM 0.444444 0.674699
128 MYR AMP 0.444444 0.776471
129 OAD 0.443396 0.73494
130 2VA 0.443299 0.779221
131 S8M 0.442308 0.831169
132 OOB 0.442308 0.722892
133 TYR AMP 0.441441 0.759036
134 6YZ 0.441176 0.694118
135 ADP VO4 0.441176 0.702381
136 VO4 ADP 0.441176 0.702381
137 T99 0.44 0.686047
138 TAT 0.44 0.686047
139 ANP 0.44 0.674419
140 WAQ 0.439252 0.75
141 B5Y 0.436364 0.717647
142 8PZ 0.436364 0.684783
143 F0P 0.435897 0.844156
144 YLC 0.435897 0.755814
145 AAT 0.435644 0.797468
146 1ZZ 0.435185 0.755814
147 9K8 0.435185 0.663158
148 3OD 0.435185 0.73494
149 NVA 2AD 0.434343 0.855263
150 00A 0.433962 0.689655
151 DLL 0.433962 0.722892
152 ARG AMP 0.433628 0.727273
153 7MD 0.433628 0.715909
154 ATF 0.431373 0.666667
155 SO8 0.43 0.792208
156 3UK 0.429907 0.714286
157 A6D 0.429907 0.72619
158 9X8 0.429907 0.717647
159 F2R 0.429752 0.7
160 5SV 0.428571 0.741176
161 AMP DBH 0.428571 0.714286
162 TYM 0.42735 0.746988
163 WSA 0.42735 0.692308
164 9SN 0.427273 0.681818
165 AHZ 0.426087 0.755814
166 P5A 0.425926 0.691489
167 B5V 0.425926 0.705882
168 PR8 0.425926 0.744186
169 A A 0.425926 0.710843
170 3NZ 0.425926 0.807692
171 A1R 0.424528 0.709302
172 2A5 0.424242 0.674419
173 7MC 0.423729 0.719101
174 B5M 0.423423 0.717647
175 7D5 0.422222 0.658824
176 JB6 0.422018 0.709302
177 FYA 0.422018 0.722892
178 AYB 0.421488 0.75
179 A22 0.419048 0.682353
180 MAP 0.419048 0.659091
181 2AM 0.417582 0.666667
182 TAD 0.417391 0.712644
183 A3P 0.416667 0.686747
184 ADP BMA 0.416667 0.714286
185 25A 0.415094 0.690476
186 YLA 0.413223 0.719101
187 8Q2 0.411765 0.663158
188 A3R 0.411215 0.709302
189 ADQ 0.411215 0.694118
190 48N 0.410256 0.72093
191 0XU 0.41 0.824324
192 GA7 0.408696 0.72619
193 7D3 0.40625 0.643678
194 PAP 0.405941 0.678571
195 DQV 0.405172 0.702381
196 OVE 0.404255 0.662791
197 4UV 0.403509 0.697674
198 AF3 ADP 3PG 0.403361 0.712644
199 3AD 0.402299 0.783784
200 CMP 0.402062 0.691358
201 2BA 0.402062 0.682927
202 7C5 0.4 0.731707
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5TUZ; Ligand: 7L6; Similar sites found with APoc: 57
This union binding pocket(no: 1) in the query (biounit: 5tuz.bio1) has 35 residues
No: Leader PDB Ligand Sequence Similarity
1 3GD8 GOL None
2 4KVL PLM 1.91571
3 2YIV YIV 2.29885
4 3F5A SIA GAL NAG 2.43902
5 4CS9 AMP 2.6455
6 2PX8 MGT 2.68199
7 1DKU AP2 2.68199
8 4NOS H4B 2.68199
9 4GN8 ASO 2.68199
10 6C74 PC 2.7027
11 5GQI CTP 2.83401
12 3JWH SAH 3.22581
13 4IA6 EIC 3.44828
14 3B9O FMN 3.44828
15 6MJ7 ARG 3.63636
16 1DTL BEP 3.72671
17 3KIF GDL 3.77358
18 5LFV SIA GAL NAG 3.83142
19 1ISI NCA 3.83142
20 4JGP PYR 4.14747
21 3IT1 TLA 4.21456
22 3N29 GOL 4.21456
23 4LIK CIT 4.5977
24 1TLG GAL 4.8
25 3QXY SAM 4.98084
26 4MDB RLT 5.33333
27 5H4S RAM 5.36398
28 4M3P HCS 5.36398
29 1TL2 NDG 5.9322
30 3BIB PSF 6.03448
31 5CDH TLA 6.13027
32 6GR0 F8W 6.32184
33 3KLL MAL 6.51341
34 5ZHO A2G GLA FUC 6.79012
35 1C5C TK4 6.97674
36 3KPE TM3 7.69231
37 3P4X ADP 8.42912
38 3GUZ PAF 8.52273
39 2Y69 CHD 8.57143
40 5ZJ5 GDP 8.64198
41 1R1Q ACE ARG GLU PTR VAL ASN VAL 10
42 3FIU POP 10.0402
43 2H21 SAM 10.3448
44 2X1L ADN 10.3448
45 4DDY DN6 11.1111
46 5KK4 44E 12.5
47 3N71 SFG 12.6437
48 3IWD M2T 13.2353
49 2HPL ASP ASP LEU TYR GLY 14
50 3KIH GDL 14.433
51 1ECM TSA 14.6789
52 1J78 OLA 18.0077
53 2BVE PH5 18.4874
54 5CZY SAM 20.6897
55 5WFC A97 32.5671
56 5WF7 A9G 33.7165
57 3KMT SAH 36.9748
Pocket No.: 2; Query (leader) PDB : 5TUZ; Ligand: 7L6; Similar sites found with APoc: 19
This union binding pocket(no: 2) in the query (biounit: 5tuz.bio1) has 37 residues
No: Leader PDB Ligand Sequence Similarity
1 2W58 ADP None
2 5C2N NAG None
3 5NM7 GLY 2.68199
4 4Z3E GAL NGA GLA BGC GAL 3.0303
5 4CJN QNZ 3.06513
6 1SJD NPG 3.83142
7 3WR7 SPD 4.70588
8 4CR6 MAN 5.74713
9 2V7O DRN 6.13027
10 4TVD BGC 7.27969
11 5TQZ GLC 7.33333
12 2H8Z 8CM 7.66284
13 2V8L GLC GLC GLC GLC GLC GLC GLC 8.49057
14 5A4W QCT 8.49057
15 2XG5 EC5 10.9827
16 2XG5 EC2 10.9827
17 5WHT SIA 19.5652
18 5WHT SIA GAL 19.5652
19 4MPO AMP 19.6078
Pocket No.: 3; Query (leader) PDB : 5TUZ; Ligand: SAM; Similar sites found with APoc: 58
This union binding pocket(no: 3) in the query (biounit: 5tuz.bio1) has 37 residues
No: Leader PDB Ligand Sequence Similarity
1 2W58 ADP None
2 5C2N NAG None
3 2YIV YIV 2.29885
4 4CS9 AMP 2.6455
5 2PX8 MGT 2.68199
6 5NM7 GLY 2.68199
7 1DKU AP2 2.68199
8 4Z3E GAL NGA GLA BGC GAL 3.0303
9 4CJN QNZ 3.06513
10 3JWH SAH 3.22581
11 4IA6 EIC 3.44828
12 3B9O FMN 3.44828
13 1DTL BEP 3.72671
14 3KIF GDL 3.77358
15 5LFV SIA GAL NAG 3.83142
16 1SJD NPG 3.83142
17 4JGP PYR 4.14747
18 3IT1 TLA 4.21456
19 3N29 GOL 4.21456
20 4LIK CIT 4.5977
21 3WR7 SPD 4.70588
22 1TLG GAL 4.8
23 3QXY SAM 4.98084
24 4MDB RLT 5.33333
25 5H4S RAM 5.36398
26 4CR6 MAN 5.74713
27 1TL2 NDG 5.9322
28 5CDH TLA 6.13027
29 2V7O DRN 6.13027
30 6GR0 F8W 6.32184
31 3KLL MAL 6.51341
32 1C5C TK4 6.97674
33 4TVD BGC 7.27969
34 5TQZ GLC 7.33333
35 2H8Z 8CM 7.66284
36 3KPE TM3 7.69231
37 3P4X ADP 8.42912
38 2V8L GLC GLC GLC GLC GLC GLC GLC 8.49057
39 5A4W QCT 8.49057
40 2Y69 CHD 8.57143
41 5ZJ5 GDP 8.64198
42 1R1Q ACE ARG GLU PTR VAL ASN VAL 10
43 2H21 SAM 10.3448
44 2XG5 EC2 10.9827
45 2XG5 EC5 10.9827
46 4DDY DN6 11.1111
47 3N71 SFG 12.6437
48 3IWD M2T 13.2353
49 2HPL ASP ASP LEU TYR GLY 14
50 3KIH GDL 14.433
51 1ECM TSA 14.6789
52 1J78 OLA 18.0077
53 2BVE PH5 18.4874
54 5WHT SIA 19.5652
55 5WHT SIA GAL 19.5652
56 4MPO AMP 19.6078
57 5CZY SAM 20.6897
58 3KMT SAH 36.9748
Pocket No.: 4; Query (leader) PDB : 5TUZ; Ligand: SAM; Similar sites found with APoc: 18
This union binding pocket(no: 4) in the query (biounit: 5tuz.bio1) has 35 residues
No: Leader PDB Ligand Sequence Similarity
1 3GD8 GOL None
2 4KVL PLM 1.91571
3 3F5A SIA GAL NAG 2.43902
4 4NOS H4B 2.68199
5 4GN8 ASO 2.68199
6 6C74 PC 2.7027
7 5GQI CTP 2.83401
8 6MJ7 ARG 3.63636
9 1ISI NCA 3.83142
10 4M3P HCS 5.36398
11 3BIB PSF 6.03448
12 5ZHO A2G GLA FUC 6.79012
13 3GUZ PAF 8.52273
14 3FIU POP 10.0402
15 2X1L ADN 10.3448
16 5KK4 44E 12.5
17 5WFC A97 32.5671
18 5WF7 A9G 33.7165
APoc FAQ
Feedback