Receptor
PDB id Resolution Class Description Source Keywords
2ZIF 2.4 Å EC: 7.-.-.- CRYSTAL STRUCTURE OF TTHA0409, PUTATIVE DNA MODIFICATION MET FROM THERMUS THERMOPHILUS HB8- COMPLEXED WITH S-ADENOSYL-L- THERMUS THERMOPHILUS MODIFICATION METHYLASE METHYLTRANSFERASE S-ADENOSYLMETHIONTHERMUS THERMOPHILUS STRUCTURAL GENOMICS NPPSFA NATIONALON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES RIKEN STRUCTGENOMICS/PROTEOMICS INITIATIVE RSGI TRANSFERASE
Ref.: CRYSTAL STRUCTURE OF A PUTATIVE DNA METHYLASE TTHA0 THERMUS THERMOPHILUS HB8 PROTEINS V. 73 259 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SAM A:298;
B:298;
Valid;
Valid;
none;
none;
Kd = 43 uM
398.437 C15 H22 N6 O5 S C[S@@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2ZIF 2.4 Å EC: 7.-.-.- CRYSTAL STRUCTURE OF TTHA0409, PUTATIVE DNA MODIFICATION MET FROM THERMUS THERMOPHILUS HB8- COMPLEXED WITH S-ADENOSYL-L- THERMUS THERMOPHILUS MODIFICATION METHYLASE METHYLTRANSFERASE S-ADENOSYLMETHIONTHERMUS THERMOPHILUS STRUCTURAL GENOMICS NPPSFA NATIONALON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES RIKEN STRUCTGENOMICS/PROTEOMICS INITIATIVE RSGI TRANSFERASE
Ref.: CRYSTAL STRUCTURE OF A PUTATIVE DNA METHYLASE TTHA0 THERMUS THERMOPHILUS HB8 PROTEINS V. 73 259 2008
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 311 families.
1 2ZIF Kd = 43 uM 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 266 families.
1 2ZIF Kd = 43 uM SAM C15 H22 N6 O5 S C[S@@+](CC....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 218 families.
1 2ZIF Kd = 43 uM SAM C15 H22 N6 O5 S C[S@@+](CC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SAM; Similar ligands found: 221
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 XYA 0.565789 0.773333
9 RAB 0.565789 0.773333
10 ADN 0.565789 0.773333
11 5CD 0.564103 0.783784
12 EP4 0.5625 0.826667
13 SA8 0.56044 0.945205
14 5X8 0.555556 0.888889
15 SFG 0.555556 0.875
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 VMS 0.510204 0.673913
26 54H 0.510204 0.673913
27 0UM 0.51 0.857143
28 A 0.505747 0.707317
29 AMP 0.505747 0.707317
30 LMS 0.505747 0.666667
31 ABM 0.505618 0.753086
32 45A 0.505618 0.753086
33 A5A 0.505155 0.688889
34 SRP 0.5 0.746988
35 K15 0.5 0.883117
36 SON 0.5 0.746988
37 6RE 0.5 0.78481
38 SSA 0.5 0.684783
39 5AD 0.5 0.75
40 LSS 0.49505 0.706522
41 CA0 0.494624 0.714286
42 A12 0.494505 0.705882
43 AP2 0.494505 0.705882
44 ME8 0.490385 0.841463
45 53H 0.49 0.666667
46 5CA 0.49 0.684783
47 DAL AMP 0.49 0.765432
48 TSB 0.49 0.681319
49 ACP 0.489362 0.694118
50 KG4 0.489362 0.714286
51 5AS 0.48913 0.648936
52 ADP 0.48913 0.690476
53 J7C 0.488889 0.772152
54 A2D 0.488889 0.690476
55 ZAS 0.488636 0.769231
56 9ZA 0.485149 0.729412
57 9ZD 0.485149 0.729412
58 8QN 0.485149 0.743902
59 8LH 0.484848 0.746988
60 GAP 0.484536 0.73494
61 AN2 0.483871 0.682353
62 ADP MG 0.483871 0.728395
63 A7D 0.483871 0.851351
64 A3S 0.483871 0.813333
65 GJV 0.483516 0.775
66 SRA 0.483146 0.694118
67 KAA 0.480769 0.698925
68 LAD 0.480769 0.752941
69 GSU 0.480769 0.722222
70 DSZ 0.480392 0.703297
71 AMO 0.480392 0.746988
72 52H 0.48 0.666667
73 8LE 0.479592 0.717647
74 APC MG 0.479167 0.731707
75 M33 0.478723 0.722892
76 MAO 0.478261 0.82716
77 BA3 0.478261 0.690476
78 AOC 0.477778 0.776316
79 NEC 0.477778 0.75
80 DSH 0.477778 0.842105
81 SXZ 0.47619 0.894737
82 AHX 0.475728 0.701149
83 NVA LMS 0.475728 0.736264
84 Y3J 0.47561 0.706667
85 8LQ 0.475248 0.768293
86 G5A 0.474227 0.684783
87 A3T 0.473684 0.8
88 AP5 0.473118 0.690476
89 B4P 0.473118 0.690476
90 A3N 0.472527 0.766234
91 KB1 0.471698 0.833333
92 APC 0.46875 0.705882
93 PRX 0.46875 0.73494
94 AT4 0.468085 0.686047
95 PAJ 0.466019 0.712644
96 4AD 0.466019 0.759036
97 ADP PO3 0.463918 0.728395
98 RBY 0.463918 0.72619
99 ADV 0.463918 0.72619
100 ATP MG 0.463918 0.728395
101 MHZ 0.463158 0.82716
102 ADX 0.463158 0.666667
103 AU1 0.463158 0.674419
104 YAP 0.462963 0.738095
105 TXA 0.462264 0.72619
106 NB8 0.462264 0.72093
107 A3G 0.461538 0.802632
108 VRT 0.459184 0.842105
109 YSA 0.458716 0.684783
110 XAH 0.458716 0.715909
111 H1Q 0.458333 0.719512
112 50T 0.458333 0.682353
113 HEJ 0.458333 0.690476
114 ATP 0.458333 0.690476
115 LEU LMS 0.457143 0.717391
116 7D7 0.45679 0.723684
117 KH3 0.455357 0.871795
118 ACQ 0.454545 0.694118
119 AQP 0.453608 0.690476
120 AR6 0.453608 0.710843
121 5FA 0.453608 0.690476
122 APR 0.453608 0.710843
123 NSS 0.451923 0.703297
124 FA5 0.449541 0.746988
125 A5D 0.44898 0.789474
126 AGS 0.44898 0.678161
127 SAP 0.44898 0.678161
128 AD9 0.44898 0.674419
129 PTJ 0.448598 0.72093
130 YLB 0.448276 0.758621
131 YLP 0.447368 0.738636
132 OZP 0.447368 0.844156
133 8X1 0.446602 0.680851
134 D3Y 0.446602 0.792208
135 N5O 0.445652 0.789474
136 ADP ALF 0.445545 0.678161
137 ALF ADP 0.445545 0.678161
138 MYR AMP 0.444444 0.776471
139 3AM 0.444444 0.674699
140 HY8 0.443478 0.822785
141 OAD 0.443396 0.73494
142 2VA 0.443299 0.779221
143 OOB 0.442308 0.722892
144 S8M 0.442308 0.831169
145 TYR AMP 0.441441 0.759036
146 6YZ 0.441176 0.694118
147 VO4 ADP 0.441176 0.702381
148 ADP VO4 0.441176 0.702381
149 ANP 0.44 0.674419
150 T99 0.44 0.686047
151 TAT 0.44 0.686047
152 N37 0.439655 0.828947
153 WAQ 0.439252 0.75
154 HZ2 0.438596 0.822785
155 8PZ 0.436364 0.684783
156 B5Y 0.436364 0.717647
157 N5A 0.43617 0.786667
158 F0P 0.435897 0.844156
159 YLC 0.435897 0.755814
160 AAT 0.435644 0.797468
161 1ZZ 0.435185 0.755814
162 9K8 0.435185 0.663158
163 3OD 0.435185 0.73494
164 NVA 2AD 0.434343 0.855263
165 00A 0.433962 0.689655
166 DLL 0.433962 0.722892
167 ARG AMP 0.433628 0.727273
168 7MD 0.433628 0.715909
169 ATF 0.431373 0.666667
170 SO8 0.43 0.792208
171 3UK 0.429907 0.714286
172 A6D 0.429907 0.72619
173 9X8 0.429907 0.717647
174 F2R 0.429752 0.7
175 AMP DBH 0.428571 0.714286
176 5SV 0.428571 0.741176
177 OZV 0.428571 0.690476
178 TYM 0.42735 0.746988
179 WSA 0.42735 0.692308
180 9SN 0.427273 0.681818
181 AHZ 0.426087 0.755814
182 P5A 0.425926 0.691489
183 J4G 0.425926 0.759036
184 PR8 0.425926 0.744186
185 A A 0.425926 0.710843
186 3NZ 0.425926 0.807692
187 B5V 0.425926 0.705882
188 A1R 0.424528 0.709302
189 2A5 0.424242 0.674419
190 7MC 0.423729 0.719101
191 B5M 0.423423 0.717647
192 HQG 0.423077 0.702381
193 7D5 0.422222 0.658824
194 JB6 0.422018 0.709302
195 FYA 0.422018 0.722892
196 AYB 0.421488 0.75
197 B1U 0.419643 0.632653
198 A22 0.419048 0.682353
199 MAP 0.419048 0.659091
200 2AM 0.417582 0.666667
201 TAD 0.417391 0.712644
202 ADP BMA 0.416667 0.714286
203 A3P 0.416667 0.686747
204 25A 0.415094 0.690476
205 YLA 0.413223 0.719101
206 8Q2 0.411765 0.663158
207 ADQ 0.411215 0.694118
208 A3R 0.411215 0.709302
209 48N 0.410256 0.72093
210 0XU 0.41 0.824324
211 GA7 0.408696 0.72619
212 7D3 0.40625 0.643678
213 PAP 0.405941 0.678571
214 DQV 0.405172 0.702381
215 OVE 0.404255 0.662791
216 4UV 0.403509 0.697674
217 AF3 ADP 3PG 0.403361 0.712644
218 3AD 0.402299 0.783784
219 CMP 0.402062 0.691358
220 2BA 0.402062 0.682927
221 7C5 0.4 0.731707
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2ZIF; Ligand: SAM; Similar sites found with APoc: 8
This union binding pocket(no: 1) in the query (biounit: 2zif.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 3TLJ SAH 9.09091
2 3TLJ SAH 9.09091
3 3GDH SAH 15.3527
4 3GDH SAH 15.3527
5 3EGI ADP 17.9612
6 3EGI ADP 17.9612
7 1G60 SAM 39.2308
8 1G60 SAM 39.2308
Pocket No.: 2; Query (leader) PDB : 2ZIF; Ligand: SAM; Similar sites found with APoc: 6
This union binding pocket(no: 2) in the query (biounit: 2zif.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 3TLJ SAH 9.09091
2 3TLJ SAH 9.09091
3 3EGI ADP 17.9612
4 3EGI ADP 17.9612
5 3EGI ADP 17.9612
6 3EGI ADP 17.9612
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