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Receptor
PDB id Resolution Class Description Source Keywords
2R3A 2 Å EC: 2.1.1.43 METHYLTRANSFERASE DOMAIN OF HUMAN SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG 2 HOMO SAPIENS HISTONE H3-K9 METHYLTRANSFERASE 2 HISTONE-LYSINE N- METHYLTRANSFERASE H3 LYSINE-9 SPECIFIC 2 ALTERNATIVE SPLICING CELL CYCLE CHROMATIN REGULATOR CHROMOSOMAL PROTEIN DIFFERENTIATION NUCLEUS REPRESSOR S-ADENOSYL-L-METHIONINE TELOMERE TRANSCRIPTION TRANSCRIPTION REGULATION STRUCTURAL GENOMICS STRUCTURAL GENOMICS CONSORTIUM SGC TRANSFERASE
Ref.: STRUCTURAL BIOLOGY OF HUMAN H3K9 METHYLTRANSFERASES PLOS ONE V. 5 E8570 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SAM A:304;
Valid;
none;
submit data
398.437 C15 H22 N6 O5 S C[S@@...
ZN A:300;
A:301;
A:302;
A:303;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2R3A 2 Å EC: 2.1.1.43 METHYLTRANSFERASE DOMAIN OF HUMAN SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG 2 HOMO SAPIENS HISTONE H3-K9 METHYLTRANSFERASE 2 HISTONE-LYSINE N- METHYLTRANSFERASE H3 LYSINE-9 SPECIFIC 2 ALTERNATIVE SPLICING CELL CYCLE CHROMATIN REGULATOR CHROMOSOMAL PROTEIN DIFFERENTIATION NUCLEUS REPRESSOR S-ADENOSYL-L-METHIONINE TELOMERE TRANSCRIPTION TRANSCRIPTION REGULATION STRUCTURAL GENOMICS STRUCTURAL GENOMICS CONSORTIUM SGC TRANSFERASE
Ref.: STRUCTURAL BIOLOGY OF HUMAN H3K9 METHYLTRANSFERASES PLOS ONE V. 5 E8570 2010
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 39 families.
1 2R3A - SAM C15 H22 N6 O5 S C[S@@+](CC....
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 2R3A - SAM C15 H22 N6 O5 S C[S@@+](CC....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 22 families.
1 6BOX - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 2R3A - SAM C15 H22 N6 O5 S C[S@@+](CC....
Polypharmacology
Similar Ligands
Ligand no: 1; 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 : 2R3A; Ligand: SAM; Similar sites found with APoc: 100
This union binding pocket(no: 1) in the query (biounit: 2r3a.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 2VZ6 FEF 1.66667
2 2PUL ACP 1.66667
3 2V7O DRN 1.66667
4 3UYK 0CX 1.66667
5 3M2W L8I 1.67224
6 2AF6 BRU 1.93798
7 5HCY 60D 2
8 4LH7 1X8 2
9 4RUS NAG 2.10084
10 4P86 5GP 2.18579
11 3WVR AMP 2.33333
12 2CHT TSA 2.3622
13 1TZD ADP 2.54545
14 1ZX5 LFR 2.66667
15 3X01 AMP 2.66667
16 4PZ6 GMP 2.66667
17 2IF8 ADP 2.66667
18 4IDT T28 2.66667
19 4GYI ADP 2.66667
20 3MGB GHP 3MY 3FG GHP GHP OMY 3FG 2.66667
21 5XVG 8FX 2.73038
22 3DAK ANP 2.75862
23 3C3N FMN 3
24 3FSY SCA 3
25 1SVK ALF GDP 3
26 5VN0 NAI 3
27 3S6X SIA GAL BGC 3
28 2QLU ADE 3.33333
29 4K33 ACP 3.33333
30 2YIV NBN 3.33333
31 5NJI 8Z2 3.66667
32 1XF1 CIT 3.66667
33 3IUY AMP 3.94737
34 5HVJ ANP 4
35 1F76 ORO 4
36 2PVF ACP 4
37 4FL3 ANP 4
38 2IRY DGT 4
39 3DGY 2GP 4.12371
40 4NFE BEN 4.21941
41 1S9D AFB 4.26829
42 2RIO ADP 4.33333
43 5OC1 ANN 4.33333
44 2QX0 PH2 4.40252
45 5H4S RAM 4.57746
46 3KN5 ANP 4.66667
47 6E8I PTR 4.73373
48 1K7U NAG NAG 4.83871
49 2RIF AMP 4.96454
50 2ODE ALF GDP 4.96454
51 1D4D SIN 5
52 4UX9 ANP 5
53 2A19 ANP 5.14286
54 1ZDQ MSM 5.33333
55 6CI9 F3V 5.40541
56 1FUT 2GP 5.66038
57 5AWM ANP 5.66667
58 1FDJ 13P 6
59 2XIG CIT 6
60 2BIF SIN 6
61 1SQL GUN 6.16438
62 5KK4 44E 6.25
63 3QXY SAM 6.33333
64 2H21 SAM 6.33333
65 6CGN DA 6.33333
66 3ISN EDM 6.66667
67 1TAD GDP 6.66667
68 1TAD ALF 6.66667
69 4PTN PYR 6.66667
70 1YFZ IMP 6.82927
71 3VSV XYS 7
72 6AC9 ANP 7.02703
73 4XCP PLM 7.05882
74 4GDX GLU 7.17949
75 1RGE 2GP 7.29167
76 3GNI ATP 7.33333
77 4ARE FLC 7.33333
78 3N71 SFG 7.66667
79 6C0B PAM 7.69231
80 3ALN ANP 7.95107
81 2FSH ANP 8
82 4I94 ANP 9
83 5JZJ AN2 9.09091
84 5WHU SIA GAL 9.39597
85 2JHP GUN 9.66667
86 1O9U ADZ 11
87 3UG4 AHR 11.3333
88 4TVD BGC 12
89 2O0J ADP 12
90 3HAV ATP 12.3746
91 6CWH 6LA 14.2857
92 4MDB RLT 14.6667
93 3KIF GDL 16.0377
94 5UKL SIX 17.7419
95 5CZY SAM 19.3333
96 6C74 PC 25.2252
97 5WF7 A9G 26
98 3KMT SAH 26.0504
99 4CS9 AMP 33.3333
100 5T0K SAM 48.7544
101 5JIY SAM 50
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