Receptor
PDB id Resolution Class Description Source Keywords
2ZFU 2 Å EC: 2.-.-.- STRUCTURE OF THE METHYLTRANSFERASE-LIKE DOMAIN OF NUCLEOMETH HOMO SAPIENS NUCLEOLAR PROTEIN SAM-BINDING PROTEIN PROTEIN STRUCTURE NPHOSPHOPROTEIN NUCLEAR PROTEIN
Ref.: EPIGENETIC CONTROL OF RDNA LOCI IN RESPONSE TO INTR ENERGY STATUS CELL(CAMBRIDGE,MASS.) V. 133 627 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SAH A:900;
B:900;
Valid;
Valid;
none;
none;
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384.411 C14 H20 N6 O5 S c1nc(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2ZFU 2 Å EC: 2.-.-.- STRUCTURE OF THE METHYLTRANSFERASE-LIKE DOMAIN OF NUCLEOMETH HOMO SAPIENS NUCLEOLAR PROTEIN SAM-BINDING PROTEIN PROTEIN STRUCTURE NPHOSPHOPROTEIN NUCLEAR PROTEIN
Ref.: EPIGENETIC CONTROL OF RDNA LOCI IN RESPONSE TO INTR ENERGY STATUS CELL(CAMBRIDGE,MASS.) V. 133 627 2008
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 236 families.
1 2ZFU - 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 211 families.
1 2ZFU - 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 166 families.
1 2ZFU - 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
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2ZFU; Ligand: SAH; Similar sites found: 204
This union binding pocket(no: 1) in the query (biounit: 2zfu.bio2) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3Q87 SAM 0.0006309 0.42688 None
2 3KO0 TFP 0.009802 0.41891 None
3 2YJD YJD 0.004934 0.41778 None
4 1H0A I3P 0.01817 0.41616 None
5 3OLL EST 0.005967 0.41403 None
6 4JWK CTN 0.02239 0.41014 None
7 3QPB URA 0.02898 0.40112 0.930233
8 4C4A SAH 0.00001481 0.51435 1.86047
9 3EVG SAH 0.00002164 0.51288 2.32558
10 4Y2H SAH 0.00009198 0.50404 2.32558
11 4Y2H 49K 0.0001148 0.49971 2.32558
12 3FRH SAH 0.00003518 0.49769 2.32558
13 2P41 SAH 0.00005384 0.49569 2.32558
14 5CUQ NSC 0.00009701 0.49323 2.32558
15 5JJR SAH 0.0001067 0.48278 2.32558
16 1Z3C SA8 0.000004911 0.46393 2.32558
17 4M73 SAH 0.00001102 0.42331 2.32558
18 3TKA SAM 0.004853 0.40402 2.32558
19 1AE1 NAP 0.01226 0.4023 2.32558
20 3G89 SAM 0.000001528 0.58471 2.7907
21 3GU3 SAH 0.00000416 0.58019 2.7907
22 5KOK SAH 0.000002667 0.54602 2.7907
23 5MGZ SAH 0.000008237 0.52519 2.7907
24 1KPG SAH 0.00003021 0.48713 2.7907
25 1KPH SAH 0.00003213 0.48611 2.7907
26 3QOX SAH 0.0001244 0.47456 2.7907
27 4AZW SAM 0.0002737 0.46046 2.7907
28 5GVR LMR 0.005631 0.44115 2.7907
29 5OFW 9TW 0.009845 0.42644 2.7907
30 5KOK R9T 0.00005221 0.41341 2.7907
31 5KOK S9T 0.00005196 0.40899 2.7907
32 3AQT RCO 0.0261 0.40726 2.7907
33 1V59 NAD 0.01383 0.40461 2.7907
34 3EF0 ALF 0.02136 0.40411 2.7907
35 3X0D SAH 0.000003637 0.54029 3.25581
36 1I1N SAH 0.0002094 0.47228 3.25581
37 4DMG SAM 0.0005943 0.4697 3.25581
38 1U2Z SAH 0.0003287 0.45678 3.25581
39 2PWY SAH 0.0001333 0.45502 3.25581
40 5FTW SAH 0.0003963 0.44941 3.25581
41 4PIO AVI 0.00001547 0.43419 3.25581
42 4PIO SAH 0.00001682 0.4282 3.25581
43 3UCL NAP 0.01785 0.42011 3.25581
44 3UCL FAD 0.01641 0.42011 3.25581
45 3UCL CYH 0.01641 0.42011 3.25581
46 2Q1S NAI 0.01719 0.40556 3.25581
47 3LCC SAH 0.000002135 0.56335 3.72093
48 5M58 SAH 0.0000272 0.50312 3.72093
49 3I53 SAH 0.00002255 0.5013 3.72093
50 5DX8 SFG 0.00003602 0.47647 3.72093
51 1JG3 ADN 0.0001584 0.47534 3.72093
52 5DXA SFG 0.00004371 0.47332 3.72093
53 5DWQ SFG 0.00003924 0.46757 3.72093
54 5DX1 SFG 0.00004397 0.45849 3.72093
55 2NXE SAM 0.0004166 0.45709 3.72093
56 5DX0 SFG 0.00005462 0.45572 3.72093
57 3FUU ADN 0.0006998 0.44312 3.72093
58 2WPF FAD 0.01044 0.44211 3.72093
59 1DL5 SAH 0.0001007 0.4399 3.72093
60 3HVJ 705 0.002451 0.43786 3.72093
61 2WPF WPF 0.01777 0.43191 3.72093
62 3TLJ SAH 0.001261 0.41631 3.72093
63 3LXD FAD 0.007843 0.41314 3.72093
64 3P9C SAH 0.0001274 0.41046 3.72093
65 3R9V DXC 0.02511 0.40533 3.72093
66 2AE2 NAP 0.01634 0.40389 3.72093
67 1KYQ NAD 0.008837 0.40274 3.72093
68 3EGI ADP 0.0001429 0.51919 3.8835
69 4POO SAM 0.001222 0.4107 4
70 2EG5 SAH 0.00000196 0.57969 4.18605
71 2EFJ SAH 0.000002368 0.52017 4.18605
72 2UYQ SAM 0.0001963 0.518 4.18605
73 2BZG SAH 0.00003478 0.50394 4.18605
74 1KYZ SAH 0.00006754 0.49141 4.18605
75 1QAN SAH 0.0001724 0.45705 4.18605
76 2A14 SAH 0.0003222 0.44679 4.18605
77 1R18 SAH 0.0003656 0.4431 4.18605
78 1FEC FAD 0.004543 0.43465 4.18605
79 2JJQ SAH 0.003013 0.43173 4.18605
80 2CBZ ATP 0.02062 0.41391 4.18605
81 3G5K BB2 0.01443 0.40003 4.37158
82 2DPM SAM 0.0001619 0.45759 4.65116
83 1UAY ADN 0.0009277 0.45549 4.65116
84 1YXM ADE 0.004439 0.44757 4.65116
85 4UZI IMD 0.01742 0.41417 4.65116
86 5XLX SAH 0.002124 0.41017 4.65116
87 2VT3 ATP 0.0121 0.40738 4.65116
88 4QTU SAM 0.0000008325 0.56753 4.80769
89 1NV8 SAM 0.0001718 0.41759 4.92958
90 5CLO NS8 0.02282 0.40918 5.08475
91 3G2O SAM 0.00000369 0.54626 5.11628
92 1XDS SAM 0.00003172 0.52356 5.11628
93 2EJU SAH 0.00002623 0.50926 5.11628
94 2WA2 SAM 0.00006311 0.46305 5.11628
95 3A25 SAM 0.0007342 0.4464 5.11628
96 1NW5 SAM 0.000638 0.44482 5.11628
97 5X20 AOT 0.02836 0.40236 5.11628
98 3DXY SAM 0.0000009998 0.60154 5.5814
99 3GXO SAH 0.00005851 0.50522 5.5814
100 4DCM SAM 0.00007233 0.50104 5.5814
101 1QZZ SAM 0.0002161 0.48487 5.5814
102 3OFK SAH 0.00007685 0.47202 5.5814
103 3GWZ SAH 0.00006814 0.45042 5.5814
104 3RKR NAP 0.002021 0.44934 5.5814
105 3SSO SAH 0.001924 0.42079 5.5814
106 4USR FAD 0.009262 0.40768 5.5814
107 5N53 8NB 0.009041 0.42951 5.64103
108 5MPT SAH 0.00008841 0.48633 6.04651
109 5HJM MTA 0.0001088 0.47751 6.04651
110 3VSE SAH 0.00003408 0.4506 6.04651
111 2ZIF SAM 0.0009212 0.43804 6.04651
112 2PX8 SAH 0.001152 0.4379 6.04651
113 3CBG SAH 0.003404 0.42118 6.04651
114 4N49 SAM 0.003479 0.41006 6.04651
115 4PZ6 GMP 0.02409 0.40489 6.04651
116 3FZG SAM 0.00003049 0.51807 6.5
117 2FK8 SAM 0.00002044 0.50307 6.51163
118 1L1E SAH 0.00002326 0.50073 6.51163
119 1TPY SAH 0.000027 0.48904 6.51163
120 4R6W SAH 0.0000007119 0.47574 6.51163
121 1G55 SAH 0.0002114 0.46524 6.51163
122 1ELI PYC 0.009601 0.41239 6.51163
123 2F5Z FAD 0.01561 0.40748 6.51163
124 3GRU AMP 0.0006035 0.44565 6.77966
125 1Q0S SAH 0.0007482 0.41839 6.94981
126 3GCZ SAM 0.00002138 0.48857 6.97674
127 3JWH SAH 0.000005615 0.4792 6.97674
128 2AOT SAH 0.0000345 0.46759 6.97674
129 1JQD HSM 0.000261 0.42378 6.97674
130 1NE7 16G 0.01861 0.41054 6.97674
131 1JQD SAH 0.0003184 0.40543 6.97674
132 2ZWA SAH 0.000004671 0.51999 7.44186
133 4M38 SAH 0.0000754 0.47945 7.44186
134 5FA5 MTA 0.0002675 0.47527 7.44186
135 4M37 SAH 0.0001358 0.47341 7.44186
136 4FZV SAM 0.0002511 0.45767 7.44186
137 4GQB 0XU 0.0001505 0.44585 7.44186
138 4ONQ SFG 0.001529 0.43255 7.44186
139 3VYW SAM 0.002164 0.41866 7.44186
140 2YX1 SFG 0.00002681 0.52694 7.90698
141 1N2X SAM 0.0005177 0.43021 7.90698
142 2XYQ SAH 0.001852 0.42893 7.90698
143 1Y8Q ATP 0.002208 0.40222 7.90698
144 3O7W SAM 0.0000002781 0.61905 8.37209
145 5THZ SAH 0.00008188 0.48223 8.37209
146 5THY SAH 0.00007701 0.47906 8.37209
147 3A4T SFG 0.000123 0.46258 8.37209
148 5DM1 SAH 0.000001121 0.43917 8.37209
149 5DM1 5D7 0.000001215 0.43358 8.37209
150 1G0N NDP 0.01443 0.40442 8.37209
151 1G0N PHH 0.02043 0.40039 8.37209
152 1GXU 2HP 0.009118 0.40703 8.79121
153 5E9W SAH 0.000002606 0.58177 8.83721
154 5E8J SAH 0.000002977 0.57126 8.83721
155 3TKY SAH 0.000002983 0.53066 8.83721
156 2PT9 S4M 0.0004784 0.42163 8.83721
157 5L95 AMP 0.002517 0.41945 8.83721
158 1G60 SAM 0.0001715 0.4691 9.30233
159 3GDH SAH 0.0002953 0.43284 9.30233
160 1MFI FHC 0.005607 0.43765 9.64912
161 5X62 SAH 0.000000988 0.5782 9.76744
162 4LH7 1X8 0.0151 0.41497 9.76744
163 4LH7 NMN 0.01908 0.41283 9.76744
164 4II2 ATP 0.003222 0.41145 9.76744
165 2YLD CMO 0.01923 0.41383 10.2362
166 3H8V ATP 0.003521 0.4168 10.6164
167 1VE3 SAM 0.00000204 0.55744 10.6977
168 5XVK SAH 0.0002189 0.44663 10.6977
169 3A27 SAM 0.001562 0.43215 10.6977
170 3EGV SAH 0.0002509 0.47147 10.8844
171 5E1M SAH 0.00009344 0.47556 11.1628
172 3DUW SAH 0.00211 0.42272 11.1628
173 1ZQ9 SAM 0.002859 0.42073 11.1628
174 4BLW SAH 0.0003431 0.42177 11.6279
175 2VDV SAM 0.000003953 0.56554 12.093
176 5OCA 9QZ 0.02568 0.42114 12.1849
177 1EJ0 SAM 0.0009071 0.44241 12.2222
178 1IM8 SAI 0.00000003022 0.62103 12.5581
179 3MB5 SAM 0.00005667 0.46932 12.5581
180 3C3Y SAH 0.001415 0.4301 12.5581
181 2JHP SAH 0.005538 0.41178 12.5581
182 1WY7 SAH 0.0001702 0.45682 12.5604
183 4OBW SAM 0.00005447 0.49547 13.0233
184 1RJD SAM 0.000002691 0.53977 13.4884
185 1BZL FAD 0.01232 0.43899 14.4186
186 3S1S SAH 0.000475 0.43269 14.4186
187 2PXX SAH 0.00001102 0.51982 14.8837
188 4A6D SAM 0.00002262 0.50652 14.8837
189 1N13 AG2 0.02071 0.4107 15.0442
190 2XVM SAH 0.0000006919 0.52166 16.0804
191 3LAD FAD 0.008991 0.41752 16.7442
192 4TM3 FAD 0.01402 0.42517 18.6047
193 3BGD SAH 0.00002627 0.48295 19.0698
194 3BGD PM6 0.00004037 0.44987 19.0698
195 3PT9 SAH 0.0003322 0.46136 20
196 4IWN GEK 0.0000007269 0.56872 21.3953
197 3AD8 FAD 0.005587 0.44308 22.2222
198 3DMH SAM 0.00003362 0.49407 24.186
199 3DMH GMP 0.00005811 0.44009 24.186
200 3VC1 SAH 0.000001062 0.42648 25.5814
201 3VC1 GST 0.000001062 0.42648 25.5814
202 4RZB NFQ 0.01688 0.40837 26.0465
203 1WG8 SAM 0.000439 0.45332 28.8372
204 1LSS NAD 0.0009724 0.43316 38.5714
Pocket No.: 2; Query (leader) PDB : 2ZFU; Ligand: SAH; Similar sites found: 20
This union binding pocket(no: 2) in the query (biounit: 2zfu.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3UU7 2OH 0.02266 0.40446 1.39535
2 2V57 PRL 0.01603 0.41682 1.57895
3 3HP9 CF1 0.0317 0.40166 1.86047
4 3ICR FAD 0.01681 0.40327 2.7907
5 3W54 RNB 0.01217 0.40178 2.7907
6 2XRH NIO 0.02283 0.40598 3
7 1EJH M7G 0.0321 0.40556 3.15789
8 3BJE URA 0.0227 0.40193 3.25581
9 1MO9 FAD 0.04241 0.40891 4.18605
10 4OUJ LBT 0.02414 0.40187 4.18605
11 5K7U SAM 0.007401 0.40097 6.51163
12 2G3F IZC 0.01778 0.41175 6.97674
13 1W6F ISZ 0.02171 0.40581 6.97674
14 5DLY SAH 0.00002058 0.40141 6.97674
15 2QCX PF1 0.01736 0.41268 7.44186
16 1T0S BML 0.02393 0.40139 8.83721
17 3NTD FAD 0.01463 0.40702 9.30233
18 5LX9 OLB 0.01169 0.40257 12.093
19 2BP1 FLC 0.0404 0.40076 15.3488
20 3AD8 NAD 0.01401 0.40374 22.2222
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