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 36 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 26 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: 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
Ligand no: 2; Ligand: ALA ARG THR MLY GLN THR ALA ARG LYS TYR; Similar ligands found: 79
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 ALY GLN THR ALA 0.811111 0.881356
4 ALA ARG THR M3L GLN THR ALA 0.802198 0.967213
5 ALA ARG THR M3L GLN THR ALA ARG LYS SER 0.802198 0.967213
6 ALA ARG THR M3L GLN THR ALA 2MR LYS 0.802198 0.967213
7 ALA ARG THR MLY GLN 0.775281 0.966667
8 ALA ARG THR MLY GLN THR ALA ARG LYS 0.773196 1
9 ALA ARG THR MLY GLN THR ALA ARG MLY SER 0.758242 0.983051
10 ALA ARG THR LYS GLN THR ALA ARG LYS SER 0.747368 0.847458
11 ALA ARG THR M3L GLN THR ALA ARG LYS 0.683673 0.967213
12 ALA ARG THR MLZ GLN THR ALA ARG LYS TYR 0.683673 0.915254
13 ALA ARG THR 4WQ GLN THR ALA ARG LYS SER 0.666667 0.852459
14 ALA ARG THR LYS GLN THR ALA ARG 0.653465 0.847458
15 ALA ARG THR LYS GLN THR ALA ARG LYS 0.653465 0.847458
16 ALA 2MR THR MLY GLN THR ALA ALA 0.62963 0.983333
17 ALA ARG THR MLY GLN THR ALA ARG TYR 0.628319 0.893939
18 ALA ARG THR M3L GLN THR ALA ARG 0.59434 0.951613
19 ALA ARG THR MLY GLN THR ALA ARG LYS SER 0.59375 0.783333
20 ALA ARG THR M3L GLN THR ALA ALA LYS ALA 0.585586 0.951613
21 ALA ALA LEU THR ARG ALA 0.57 0.813559
22 ALA ARG THR MLZ GLN THR ALA ARG LYS 0.567568 0.916667
23 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.546296 0.85
24 THR ARG ARG GLU THR GLN LEU 0.533333 0.85
25 PRO ALA THR ILE MET MET GLN ARG GLY ASN 0.522523 0.83871
26 ALA GLN THR ALA ARG ALY SER THR 0.521739 0.866667
27 LYS ALA ALA ARG ALY SER ALA PRO ALA 0.520408 0.816667
28 ARG ARG ARG GLU THR GLN VAL 0.514852 0.8
29 ALA ARG THR M3L GLN THR ALA DA2 LYS 0.511628 0.967213
30 ILE LYS ARG SER MLZ LYS ASN SER LEU ALA 0.51 0.866667
31 ALA ARG MLY SER THR GLY GLY ALY 0.508333 0.951613
32 ALA DA2 THR M3L GLN THR ALA ARG ALA 0.504065 0.967213
33 GLU ALA GLN THR ARG LEU 0.495495 0.816667
34 ACE GLN THR ALA ARG KCR SER THR 0.479675 0.836066
35 PRO ALA ALA LYS ARG VAL LYS LEU ASP 0.479592 0.728814
36 SAC ARG GLY THR GLN THR GLU 0.474138 0.790323
37 LYS GLN THR SER VAL 0.473684 0.672131
38 LEU GLY GLY ALA LYS GLN ARG GLY ASP VAL 0.473214 0.754098
39 ALA ARG M3L SER 0.465347 0.887097
40 ALA LYS ALA SER GLN ALA ALA 0.460784 0.683333
41 ALA ARG THR GLU LEU TYR ARG SER LEU 0.460317 0.761194
42 PHE ALA GLY LEU ARG GLN ALA VAL THR GLN 0.456897 0.803279
43 ACE ALA ARG THR LYS GLN 0.45283 0.813559
44 GLN THR ALA ARG M3L SER THR GLY 0.443548 0.951613
45 ALA THR ARG ASN PHE SER GLY 0.442623 0.738462
46 ILE LYS ARG SER LYS LYS ASN SER LEU ALA 0.44 0.766667
47 GLN ARG ALA THR LYS MET NH2 0.439655 0.883333
48 GLU THR VAL ARG PHE GLN SER ASP 0.439394 0.765625
49 ALA LYS ARG HIS ARG MLY VAL LEU ARG ASP 0.4375 0.797101
50 ALA ILE ARG SER 0.431373 0.721311
51 GLU ARG THR ILE PRO ILE THR ARG GLU 0.429688 0.771429
52 GLN LEU ALA THR M3L ALA ALA ARG LYS SER 0.426357 0.967213
53 ALA MET ARG VAL 0.425743 0.75
54 ARG HIS ARG MLY VAL LEU ARG ASP ASN 0.425373 0.811594
55 ALA ARG LYS SEP THR GLY GLY LYS 0.424 0.761194
56 ARG HIS ARG MLY VAL LEU ARG ASP TYR 0.422535 0.780822
57 SER SER ARG LYS GLU TYR TYR ALA 0.422414 0.676471
58 ACE ARG LYS VAL ARG MET 5XU 0.421569 0.75
59 ALA ARG ALA ALA ALA ALA ALA ALA ALA 0.421053 0.683333
60 LYS ARG ARG LYS SEP VAL 0.420561 0.716418
61 ALA ASN SER ARG TRP ALY THR SER ILE ILE 0.41958 0.69863
62 ALA THR VAL ARG THR TYR SER CYS 0.419355 0.705882
63 GLN ARG SER THR SEP THR 0.418803 0.731343
64 HIS GLY ALA ALA ARG ALA GLU VAL HIS LEU 0.417391 0.733333
65 ALA PRO ALA LEU ARG VAL VAL LYS 0.416667 0.75
66 ARG GLU ARG SER PRO THR ARG 0.415929 0.7
67 ILE GLN GLN SER ILE GLU ARG ILE 0.415254 0.774194
68 THR ILE MET MET GLN ARG GLY 0.415254 0.825397
69 ALA ARG LYS ILE ASP ASN LEU ASP 0.414634 0.777778
70 THR ALA ARG M3L SER THR GLY GLY LYS ALA 0.409091 0.951613
71 ALA ASN SER ARG TRP GLN ASP THR ARG LEU 0.408759 0.71831
72 LYS ALA ALA ARG M3L SER ALA 0.40678 0.919355
73 ACE ALA ARG THR GLU VAL TYR NH2 0.406504 0.727273
74 ASN ARG LEU LEU LEU THR GLY 0.40566 0.833333
75 LYS GLN THR ALA ARG M3L SER THR GLY 0.404959 0.951613
76 ALA ARG M3L SER THR GLY GLY ALY 0.403101 0.921875
77 LYS ILE LEU HIS ARG LEU LEU GLN ASP 0.403101 0.642857
78 ARG ARG ALA THR LYS MET NH2 0.401709 0.883333
79 ALA ASN SER ARG TRP GLN THR SER ILE ILE 0.4 0.671233
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4C1Q; Ligand: SAH; Similar sites found: 22
This union binding pocket(no: 1) in the query (biounit: 4c1q.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3KMT SAH 0.00000125 0.57696 None
2 2Y7P SAL 0.02154 0.40013 None
3 3W5J GDP 0.01062 0.41783 2.28571
4 4WEI GLC GAL 0.02708 0.40851 2.85714
5 4PPF FLC 0.02469 0.40283 2.85714
6 3QXY SAM 0.000006764 0.52811 3.42857
7 2H21 SAM 0.00001235 0.46306 3.42857
8 3N71 SFG 0.000001968 0.52729 5.71429
9 1R6D NAD 0.03054 0.41198 6.28571
10 1XE7 GUN 0.007798 0.40522 6.28571
11 3BIB PSF 0.007348 0.4358 6.89655
12 4MDB RLT 0.01091 0.42417 8.57143
13 2R5N R5P 0.01758 0.40738 11.4286
14 2R5N RP5 0.01886 0.40701 11.4286
15 2R5N TPP 0.02288 0.40188 11.4286
16 1H8P PC 0.01315 0.40511 15.5963
17 3F8D FAD 0.01513 0.43641 18.2857
18 5CZY SAM 0.000002484 0.51276 24
19 5M5G SAH 0.0000000985 0.58734 26.8571
20 5M5G VAL MET LEU PRO GLY ARG GLY VAL PRO 0.0000006752 0.42077 26.8571
21 5JIY SAM 0.0000007186 0.57987 30.2857
22 5T0K SAM 0.0000009784 0.55947 30.2857
Feedback