Receptor
PDB id Resolution Class Description Source Keywords
5M5G 2.27 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE CHAETOMIUM THERMOPHILUM POLYCOMB RE COMPLEX 2 (PRC2) CHAETOMIUM THERMOPHILUM (STRAIN DSM 14144.50 / IMI 039719) TRANSFERASE REPRESSIVE COMPLEX
Ref.: COMMENT ON "STRUCTURAL BASIS OF HISTONE H3K27 TRIME BY AN ACTIVE POLYCOMB REPRESSIVE COMPLEX 2". SCIENCE V. 354 1543 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN B:8004;
B:8003;
B:8008;
B:8006;
B:8007;
B:8001;
B:8002;
B:8005;
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...
SAH B:8009;
Valid;
none;
submit data
384.411 C14 H20 N6 O5 S c1nc(...
VAL MET LEU PRO GLY ARG GLY VAL PRO E:21;
Valid;
Atoms found LESS than expected: % Diff = 0.016;
submit data
911.184 n/a S(CCC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5M5G 2.27 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE CHAETOMIUM THERMOPHILUM POLYCOMB RE COMPLEX 2 (PRC2) CHAETOMIUM THERMOPHILUM (STRAIN DSM 14144.50 / IMI 039719) TRANSFERASE REPRESSIVE COMPLEX
Ref.: COMMENT ON "STRUCTURAL BASIS OF HISTONE H3K27 TRIME BY AN ACTIVE POLYCOMB REPRESSIVE COMPLEX 2". SCIENCE V. 354 1543 2016
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 5M5G - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 5KJH - SAH C14 H20 N6 O5 S c1nc(c2c(n....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 5M5G - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 5KJH - SAH C14 H20 N6 O5 S c1nc(c2c(n....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 5M5G - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 5KJH - 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: VAL MET LEU PRO GLY ARG GLY VAL PRO; Similar ligands found: 38
No: Ligand ECFP6 Tc MDL keys Tc
1 VAL MET LEU PRO GLY ARG GLY VAL PRO 1 1
2 VAL VAL ARG PRO GLY SER LEU ASP LEU PRO 0.589404 0.842857
3 VAL MET ALA PRO ARG ALA LEU LEU LEU 0.496599 0.909091
4 MET SER LEU PRO GLY ARG TRP LYS PRO LYS 0.485876 0.84
5 VAL MET ALA PRO ARG THR LEU PHE LEU 0.481707 0.821918
6 ARG PRO GLY ASN PHE LEU GLN SER ARG PRO 0.479532 0.808219
7 ARG PRO GLY ASN PHE PHE GLN SER ARG PRO 0.46988 0.746667
8 ARG PRO GLY ASN PHE LEU GLN SER SER PRO 0.465116 0.819444
9 GLY LEU LEU GLY SER PRO VAL ARG ALA 0.460526 0.811594
10 ARG PRO GLN VAL PRO LEU ARG PRO MET 0.45283 0.969231
11 GLY LEU LEU GLY SEP PRO VAL ARG ALA 0.44375 0.77027
12 GLN PRO PRO VAL PRO PRO GLN ARG PRO MET 0.44375 0.969231
13 LEU PRO GLY GLU GLU ASP LEU PRO GLY 0.442177 0.787879
14 ASN PRO ARG ALA MET GLN ALA LEU LEU 0.43949 0.910448
15 ARG PRO MET THR PHE LYS GLY ALA LEU 0.4375 0.835616
16 ALA MET ALA PRO ARG THR LEU LEU LEU 0.435897 0.84507
17 ARG ARG ALA SEP ALA PRO LEU PRO 0.433962 0.783784
18 SER PRO ARG LEU PRO LEU LEU GLU SER 0.432432 0.904762
19 ALA PRO ASP THR ARG PRO 0.432432 0.802817
20 ASP VAL GLN THR GLY ARG ARG PRO TYR GLU 0.430233 0.783784
21 ASN VAL ILE VAL LEU MET LEU PRO MET GLU 0.42953 0.80303
22 VAL ORN LEU DPN PRO VAL ORN LEU DPN PRO 0.429487 0.746269
23 ACE ARG LYS VAL ARG MET 5XU 0.421875 0.730159
24 VAL PRO LEU ARG PRO MET THR TYR 0.420118 0.837838
25 ARG PRO GLY ASN PHE LEU GLN SER ARG LEU 0.418079 0.794521
26 ARG PRO MET THR TYR LYS GLY ALA LEU 0.416667 0.826667
27 PRO ARG ARG PRO VAL ILE MET ARG ARG 0.416149 0.96875
28 GLU PRO GLY GLY SER ARG 0.414966 0.757143
29 LYS GLY PRO PRO LEU PRO ARG PRO ARG VAL 0.412162 0.920635
30 GLY PRO ARG PRO 0.409091 0.857143
31 LEU PRO PHE GLU ARG ALA THR VAL MET 0.407821 0.847222
32 ASN TYR THR PRO GLY PRO GLY THR ARG PHE 0.407821 0.74026
33 ALA PRO ASP THR ARG PRO ALA PRO 0.405229 0.802817
34 ACE ARG THR PRO SEP LEU PRO THR PIP 0.404908 0.75641
35 LEU PRO PHE ASP ARG THR THR ILE MET 0.403409 0.849315
36 ARG PRO PRO GLY PHE SER PRO PHE ALA 0.402367 0.777778
37 ARG ARG LEU PRO ILE PHE SER ARG LEU 0.402367 0.780822
38 ASP LEU THR ARG PRO 0.401361 0.814286
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5M5G; Ligand: SAH; Similar sites found: 38
This union binding pocket(no: 1) in the query (biounit: 5m5g.bio2) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2H21 SAM 0.0002381 0.43239 4.09091
2 3QXY SAM 0.00001168 0.49848 7.34967
3 3N71 SFG 0.00003344 0.45961 7.7551
4 4LH7 1X8 0.01715 0.41126 8.35913
5 3S7D SAH 0.0001529 0.45605 8.54503
6 5HQ8 SAH 0.000003918 0.51437 8.56481
7 5KJK 6T1 0.001346 0.46264 8.62471
8 5KJK SAM 0.001346 0.46264 8.62471
9 5CCM SAM 0.0004879 0.47999 8.64486
10 5CCM 4ZX 0.0006378 0.47999 8.64486
11 5CPR SAM 0.0003111 0.47202 8.95522
12 1MT6 SAH 0.0000004053 0.63341 20.3571
13 5AYF C7H 0.00001241 0.54524 20.9125
14 5AYF SAM 0.00001886 0.53362 20.9125
15 4J8O SAH 0.0000003713 0.54103 21.0728
16 2F69 SAH 0.0000004939 0.53684 21.0728
17 3M54 SAH 0.00000008113 0.57802 21.8391
18 4AU7 SAH 0.00003669 0.50957 22.6721
19 5V22 SAH 0.00000003318 0.6287 23.2323
20 2CHT TSA 0.02114 0.40428 23.622
21 4FMU 0UM 0.0000004977 0.58677 24.8201
22 2R3A SAM 0.000002704 0.53831 26
23 4C1Q SAH 0.0000000985 0.58734 26.8571
24 4YNM SAM 0.00000004005 0.6146 29.646
25 4NVQ SAH 0.000003912 0.44371 30.5263
26 4NVQ 2OD 0.000004275 0.4371 30.5263
27 3HNA SAH 0.00000005104 0.64689 30.662
28 3SWC SAH 0.00000001069 0.66814 30.8772
29 2RFI SAH 0.00000005835 0.59608 30.8772
30 5T0K SAM 0.0000001768 0.58805 30.9609
31 5JIY SAM 0.0000006126 0.55554 31.7518
32 5TUZ 7L6 0.0000007664 0.60581 33.7165
33 5TUZ SAM 0.0000007664 0.60581 33.7165
34 3OOI SAM 0.00000004059 0.62821 34.0517
35 3F9W SAH 0.000002357 0.50677 36.747
36 2W5Z SAH 0.0000008743 0.52854 40.625
37 5JLB SAH 0.00000003409 0.64555 42.8571
38 4Z4P SAH 0.000001114 0.57764 49.3976
Pocket No.: 2; Query (leader) PDB : 5M5G; Ligand: VAL MET LEU PRO GLY ARG GLY VAL PRO; Similar sites found: 36
This union binding pocket(no: 2) in the query (biounit: 5m5g.bio2) has 38 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2YJP CYS 0.01694 0.43511 2.64463
2 4PW3 MSS 0.01666 0.40344 2.98103
3 1DDG FAD 0.01692 0.40313 3.47594
4 2H21 SAM 0.00001955 0.52138 4.09091
5 2VHL GLP 0.04893 0.40259 4.29293
6 3VO1 FAD 0.01707 0.41221 4.77707
7 5KJK SAM 0.00003128 0.47062 8.62471
8 5KJK 6T1 0.00003128 0.47062 8.62471
9 5CCM 4ZX 0.00002086 0.47936 8.64486
10 5CCM SAM 0.00001518 0.47778 8.64486
11 1ECM TSA 0.03163 0.41281 9.17431
12 4ZVF GAV 0.01533 0.42161 11.6279
13 3SJK LYS PRO VAL LEU ARG THR ALA 0.04691 0.41022 12.1053
14 2BVE PH5 0.006627 0.42138 16.8067
15 1MT6 SAH 0.000001015 0.65059 20.3571
16 5AYF C7H 0.000000594 0.5076 20.9125
17 5AYF SAM 0.0000004466 0.50259 20.9125
18 4J8O SAH 0.000000949 0.40349 21.0728
19 4AU7 SAH 0.0001546 0.511 22.6721
20 5V22 SAH 0.0000001378 0.45353 23.2323
21 4FMU 0UM 0.00000008266 0.48094 24.8201
22 4C1Q SAH 0.0000006752 0.42077 26.8571
23 4YNM SAM 0.0000003302 0.43666 29.646
24 4NVQ 2OD 0.00000001068 0.60521 30.5263
25 4NVQ SAH 0.00000003143 0.59306 30.5263
26 3HNA SAH 0.0000003638 0.64615 30.662
27 3SWC SAH 0.0000003102 0.64119 30.8772
28 2RFI SAH 0.0000003994 0.42597 30.8772
29 5T0K SAM 0.000003524 0.41341 30.9609
30 5JIY SAM 0.000003578 0.40628 31.7518
31 5TUZ SAM 0.0000000224 0.56923 33.7165
32 5TUZ 7L6 0.0000000224 0.56923 33.7165
33 3OOI SAM 0.000000108 0.46361 34.0517
34 3F9W SAH 0.00001938 0.52155 36.747
35 5JLB SAH 0.0000002519 0.64555 42.8571
36 4Z4P SAH 0.000006431 0.57764 49.3976
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