Receptor
PDB id Resolution Class Description Source Keywords
4C1Q 2.3 Å EC: 2.1.1.43 CRYSTAL STRUCTURE OF THE PRDM9 SET DOMAIN IN COMPLEX WITH H3K4ME2 AND ADOHCY. MUS MUSCULUS TRANSFERASE-PEPTIDE COMPLEX HISTONE METHYLTRANSFERASE SET H3K4ME3
Ref.: MOLECULAR BASIS FOR THE REGULATION OF THE H3K4 METHYLTRANSFERASE ACTIVITY OF PRDM9. CELL REP. V. 5 13 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN B:493;
A:493;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
SAH A:394;
Valid;
none;
submit data
384.411 C14 H20 N6 O5 S c1nc(...
ALA ARG THR MLY GLN THR ALA ARG LYS TYR C:1;
Valid;
none;
submit data
789.957 n/a O=C(N...
GOL B:1358;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4C1Q 2.3 Å EC: 2.1.1.43 CRYSTAL STRUCTURE OF THE PRDM9 SET DOMAIN IN COMPLEX WITH H3K4ME2 AND ADOHCY. MUS MUSCULUS TRANSFERASE-PEPTIDE COMPLEX HISTONE METHYLTRANSFERASE SET H3K4ME3
Ref.: MOLECULAR BASIS FOR THE REGULATION OF THE H3K4 METHYLTRANSFERASE ACTIVITY OF PRDM9. CELL REP. V. 5 13 2013
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 39 families.
1 4C1Q - SAH C14 H20 N6 O5 S c1nc(c2c(n....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 28 families.
1 4C1Q - SAH C14 H20 N6 O5 S c1nc(c2c(n....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 22 families.
1 4C1Q - SAH C14 H20 N6 O5 S c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; 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
Ligand no: 2; Ligand: ALA ARG THR MLY GLN THR ALA ARG LYS TYR; Similar ligands found: 82
No: Ligand ECFP6 Tc MDL keys Tc
1 ALA ARG THR MLY GLN THR ALA ARG LYS TYR 1 1
2 ALA ARG THR MLY GLN THR ALA 1 1
3 ALA ARG THR MLY GLN THR ALA ARG LYS 0.855556 0.983051
4 ALA ARG THR M3L GLN THR ALA 0.802198 0.967213
5 ALA ARG THR ALY GLN THR ALA 0.802198 0.881356
6 ALA ARG THR M3L GLN THR ALA 2MR LYS 0.802198 0.967213
7 ALA ARG THR MLY GLN 0.769231 0.966667
8 ALA ARG THR MLY GLN THR ALA ARG MLY SER 0.76087 0.983051
9 ALA ARG THR M3L GLN THR ALA ARG LYS 0.683673 0.967213
10 ALA ARG THR M3L GLN THR ALA ARG LYS SER 0.683673 0.967213
11 ALA ARG THR MLZ GLN THR ALA ARG LYS TYR 0.67 0.915254
12 ALA ARG THR 4WQ GLN THR ALA ARG LYS SER 0.659574 0.852459
13 ALA ARG THR MLY GLN THR ALA ARG TYR 0.646018 0.893939
14 ARG ARG ARG GLU THR GLN VAL 0.628866 0.833333
15 ALA ARG THR LYS GLN THR ALA ARG LYS 0.628571 0.847458
16 ALA ARG THR ALA ALA THR ALA ARG LYS SER 0.62766 0.79661
17 ALA ARG THR LYS GLN THR ALA ARG 0.622449 0.830508
18 ALA 2MR THR MLY GLN THR ALA ALA 0.613861 1
19 ALA ARG THR MLZ GLN THR ALA ARG LYS 0.605505 0.932203
20 ALA ARG THR MLY GLN THR ALA ARG LYS SER 0.597938 0.783333
21 ALA ARG THR M3L GLN THR ALA ARG 0.588785 0.951613
22 ALA ALA LEU THR ARG ALA 0.564356 0.813559
23 ALA ARG THR M3L GLN THR ALA ALA LYS ALA 0.556522 0.951613
24 ALA ARG 9AT 0.546512 0.779661
25 THR ARG ARG GLU THR GLN LEU 0.537736 0.85
26 PRO ALA THR ILE MET MET GLN ARG GLY ASN 0.536364 0.83871
27 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.531532 0.85
28 ILE LYS ARG SER MLZ LYS ASN SER LEU ALA 0.509804 0.866667
29 ALA ARG MLY SER THR GLY GLY ALY 0.508197 0.951613
30 ALA GLN THR ALA ARG ALY SER THR 0.504274 0.866667
31 ALA DA2 THR M3L GLN THR ALA ARG ALA 0.504065 0.967213
32 ALA ARG THR M3L GLN THR ALA DA2 LYS 0.5 0.967213
33 ACE GLN THR ALA ARG PRK SER THR 0.495726 0.806452
34 GLU ALA GLN THR ARG LEU 0.491228 0.816667
35 PRO ALA ALA LYS ARG VAL LYS LEU ASP 0.485149 0.728814
36 ALA ARG M3L SER 0.475248 0.887097
37 ACE GLU ALA GLN THR ARG LEU 0.469565 0.833333
38 ACE GLN THR ALA ARG KCR SER THR 0.467213 0.819672
39 PHE ALA GLY LEU ARG GLN ALA VAL THR GLN 0.466102 0.803279
40 LEU GLY GLY ALA LYS GLN ARG GLY ASP VAL 0.465517 0.754098
41 GLN THR ALA ARG M3L SER 0.462185 0.951613
42 SAC ARG GLY THR GLN THR GLU 0.461538 0.790323
43 ALA ARG THR GLU LEU TYR ARG SER LEU 0.460938 0.761194
44 GLY ARG PHE GLN VAL THR 0.453782 0.730159
45 ACE GLN THR ALA ARG BTK SER THR 0.453782 0.836066
46 ALA THR ARG ASN PHE SER GLY 0.45082 0.738462
47 ALA ARG THR LYS GLN THR ALA ARG LYS SER 0.45 0.711864
48 THR ILE MET MET GLN ARG GLY 0.448276 0.825397
49 GLN THR ALA ARG M3L SER THR GLY 0.448 0.951613
50 ALA LYS ALA SER GLN ALA ALA 0.447619 0.683333
51 GLU THR VAL ARG PHE GLN SER ASP 0.442748 0.75
52 ACE ALA ARG THR LYS GLN 0.440367 0.813559
53 ALA ILE ARG SER 0.436893 0.721311
54 ILE LYS ARG SER LYS LYS ASN SER LEU ALA 0.432692 0.766667
55 ALA MET ARG VAL 0.431373 0.75
56 ACE ARG LYS VAL ARG MET 5XU 0.431373 0.75
57 HIS LYS ILE LEU HIS ARG LEU LEU GLN ASP 0.430657 0.642857
58 GLN ARG ALA THR LYS MET NH2 0.42623 0.883333
59 SER SER ARG LYS GLU TYR TYR ALA 0.425 0.676471
60 LYS GLN THR SER VAL 0.424242 0.672131
61 ALA THR VAL ARG THR TYR SER CYS 0.424 0.705882
62 ILE GLN GLN SER ILE GLU ARG ILE 0.423729 0.774194
63 ARG HIS ARG MLY VAL LEU ARG ASP TYR 0.423611 0.780822
64 ARG HIS ARG MLY VAL LEU ARG ASP ASN 0.423358 0.811594
65 ALA GLN ASP ILE TYR ARG ALA SER TYR 0.421429 0.7
66 ALA ARG LYS SEP THR GLY GLY LYS 0.418605 0.761194
67 ARG GLU ARG SER PRO THR ARG 0.417391 0.7
68 ALA THR ALY ALA ALA ARG ALY SER ALA PRO 0.416667 0.782609
69 LYS GLN THR ALA ARG M3L SER THR GLY 0.416667 0.951613
70 ASN ARG LEU LEU LEU THR GLY 0.411215 0.816667
71 ALA LYS ARG HIS ARG MLY VAL LEU ARG ASP 0.410072 0.764706
72 ALA ARG LYS ILE ASP ASN LEU ASP 0.409449 0.777778
73 ARG ARG ALA THR LYS MET NH2 0.408333 0.883333
74 LYS ALA ALA ARG M3L SER ALA 0.408333 0.919355
75 ALA ARG ALA ALA ALA ALA ALA ALA ALA 0.408163 0.683333
76 ALA ARG M3L SER THR GLY GLY ALY 0.407692 0.921875
77 HIS GLY ALA ALA ARG ALA GLU VAL HIS LEU 0.40678 0.733333
78 ACE ALA ARG THR GLU VAL TYR NH2 0.404762 0.727273
79 GLU ARG THR ILE PRO ILE THR ARG GLU 0.403101 0.768116
80 ARG ILE ALA ALA ALA 0.402062 0.666667
81 GLN LEU ALA THR M3L ALA ALA ARG LYS SER 0.401639 0.95082
82 PRO PRO LYS LYS LYS ARG LYS VAL 0.4 0.728814
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4C1Q; 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: 4c1q.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
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