Receptor
PDB id Resolution Class Description Source Keywords
5DNK 1.9 Å EC: 2.-.-.- THE STRUCTURE OF PKMT1 FROM RICKETTSIA PROWAZEKII IN COMPLEX ADOHCY RICKETTSIA PROWAZEKII (STRAIN MADRID EORGANISM_TAXID: 272947 METHYLTRANSFERASE ROSSMAN FOLD SAM BINDING PROTEIN METHYLTRANSFERASE
Ref.: STRUCTURAL INSIGHTS INTO SUBSTRATE RECOGNITION AND IN OUTER MEMBRANE PROTEIN B (OMPB) BY PROTEIN-LYSIN METHYLTRANSFERASES FROM RICKETTSIA. J.BIOL.CHEM. V. 291 19962 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SAH A:601;
B:601;
Valid;
Valid;
none;
none;
submit data
384.411 C14 H20 N6 O5 S c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5DNK 1.9 Å EC: 2.-.-.- THE STRUCTURE OF PKMT1 FROM RICKETTSIA PROWAZEKII IN COMPLEX ADOHCY RICKETTSIA PROWAZEKII (STRAIN MADRID EORGANISM_TAXID: 272947 METHYLTRANSFERASE ROSSMAN FOLD SAM BINDING PROTEIN METHYLTRANSFERASE
Ref.: STRUCTURAL INSIGHTS INTO SUBSTRATE RECOGNITION AND IN OUTER MEMBRANE PROTEIN B (OMPB) BY PROTEIN-LYSIN METHYLTRANSFERASES FROM RICKETTSIA. J.BIOL.CHEM. V. 291 19962 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 236 families.
1 5DNK - 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 5DNK - 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 5DNK - 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 : 5DNK; Ligand: SAH; Similar sites found: 187
This union binding pocket(no: 1) in the query (biounit: 5dnk.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3TKY SAH 0.000003652 0.58032 1.3587
2 1U2Z SAH 0.00001089 0.56452 1.38568
3 3NTD FAD 0.002001 0.47238 1.41593
4 3X0D SAH 0.000002448 0.49695 1.44404
5 1PJS NAD 0.01129 0.40741 1.53173
6 2UYQ SAM 0.00003885 0.53505 1.6129
7 3ICT ADP 0.003477 0.41459 1.62455
8 3ICS ADP 0.00595 0.40461 1.62455
9 5JJR SAH 0.0001027 0.44331 1.80505
10 2ZWA SAH 0.0001073 0.42374 1.80505
11 2WA2 SAM 0.0006576 0.46667 1.81159
12 1NW5 SAM 0.0002268 0.42431 1.88088
13 1V59 NAD 0.0000789 0.48787 1.88285
14 2B9W FAD 0.008058 0.45467 1.88679
15 1LDN NAD 0.03333 0.40167 1.89873
16 4MIG G3F 0.0003656 0.52143 1.98556
17 3PT9 SAH 0.0001273 0.44138 1.98556
18 2ZIF SAM 0.00008523 0.44007 2.0202
19 1ZMD NAI 0.0001117 0.40336 2.1097
20 4PIO SAH 0.00002174 0.40696 2.16718
21 4PIO AVI 0.00003828 0.40191 2.16718
22 1ELI PYC 0.0009624 0.48884 2.31362
23 4M38 SAH 0.000004158 0.48015 2.33236
24 1G55 SAH 0.00006744 0.44343 2.33236
25 3S1S SAH 0.00008055 0.42462 2.34657
26 3GWZ SAH 0.0001111 0.4705 2.43902
27 3GXO SAH 0.0003337 0.4427 2.43902
28 4TM3 FAD 0.00402 0.47851 2.48307
29 3BGD SAH 0.000002757 0.46675 2.69231
30 3BGD PM6 0.000004069 0.43356 2.69231
31 3G89 SAM 0.0000001114 0.59337 2.81124
32 4CNK FAD 0.002354 0.46872 2.8133
33 2FK8 SAM 0.00002412 0.4525 2.83019
34 3GCZ SAM 0.00007955 0.44806 2.83688
35 1Y8Q ATP 0.00006986 0.41691 2.89017
36 2EJU SAH 0.000006698 0.48841 2.91005
37 2P41 SAH 0.00004266 0.45688 2.95082
38 2PX8 SAH 0.0005893 0.40929 2.97398
39 2YX1 SFG 0.00001924 0.50321 2.97619
40 4N49 SAM 0.0007581 0.40139 3.03738
41 3QOX SAH 0.000004139 0.58518 3.05164
42 1QZZ SAM 0.00007798 0.47914 3.20856
43 4C4A SAH 0.000001948 0.49898 3.2491
44 3VSE SAH 0.00003058 0.50569 3.26633
45 3EVG SAH 0.00004023 0.45795 3.27273
46 1AE1 NAP 0.02547 0.4099 3.2967
47 4FZV SAM 0.0001938 0.42233 3.34262
48 1MFI FHC 0.01977 0.40114 3.50877
49 2DPM SAM 0.0002756 0.41073 3.52113
50 2WSB NAD 0.001333 0.48373 3.54331
51 3VYW SAM 0.0004402 0.41457 3.57143
52 4II2 ATP 0.0006791 0.40727 3.61446
53 1YXM ADE 0.01213 0.40549 3.63036
54 3A27 SAM 0.0001552 0.43991 3.67647
55 2VT3 ATP 0.005302 0.4087 3.72093
56 5CUQ NSC 0.00005277 0.54534 3.74532
57 3C3Y SAH 0.000693 0.40863 3.79747
58 4ZGS NAD 0.02299 0.40224 3.88601
59 3UCL FAD 0.0009252 0.51138 3.97112
60 3UCL CYH 0.0009252 0.51138 3.97112
61 3UCL NAP 0.001011 0.51138 3.97112
62 3GRU AMP 0.00001317 0.44456 4.0678
63 4GLL NAD 0.01501 0.42058 4.1543
64 2YY7 NAD 0.00249 0.45902 4.16667
65 2PXX SAH 0.000002154 0.49705 4.18605
66 1ZQ9 SAM 0.0006362 0.41992 4.21053
67 5K7U SAM 0.0009703 0.4152 4.29799
68 4LH7 1X8 0.005801 0.43124 4.33437
69 4IWN GEK 0.0000001737 0.49989 4.36681
70 1R18 SAH 0.0002617 0.40841 4.40529
71 1EJ0 SAM 0.0002947 0.4295 4.44444
72 5EB4 FAD 0.001256 0.48506 4.51128
73 4DMG SAM 0.00124 0.43401 4.58015
74 3A25 SAM 0.0001178 0.44486 4.65116
75 2PT9 S4M 0.00004477 0.41536 4.6729
76 4JCA CIT 0.007337 0.41427 4.79042
77 2AOT SAH 0.000003424 0.5226 4.79452
78 1JQD SAH 0.00001087 0.40917 4.79452
79 1JQD HSM 0.0000704 0.4008 4.79452
80 1UP7 NAD 0.0008905 0.47394 4.79616
81 5HJM MTA 0.00004466 0.44823 4.82955
82 2WPF FAD 0.005903 0.48054 4.84848
83 2WPF WPF 0.01224 0.46393 4.84848
84 5DXA SFG 0.00001198 0.44707 4.87106
85 5DX8 SFG 0.00001209 0.44673 4.87106
86 5DWQ SFG 0.000009384 0.4427 4.87106
87 5DX1 SFG 0.000008935 0.43598 4.87106
88 5DX0 SFG 0.00002296 0.42714 4.87106
89 1PS9 FAD 0.01281 0.4334 4.87365
90 1L1E SAH 0.00000861 0.46805 4.87805
91 5XVK SAH 0.000346 0.4047 4.92958
92 1XDS SAM 0.00001938 0.50308 5.08021
93 1FEC FAD 0.006965 0.45178 5.30612
94 4AZW SAM 0.00001387 0.47021 5.30786
95 5MPT SAH 0.00009517 0.44919 5.31401
96 1WY7 SAH 0.00006825 0.42982 5.31401
97 5X62 SAH 0.000001434 0.52323 5.41872
98 2FKA BEF 0.003446 0.44485 5.42636
99 1KYQ NAD 0.002061 0.40421 5.47445
100 3FUU ADN 0.0001258 0.43692 5.53506
101 3TLJ SAH 0.0003565 0.40065 5.59567
102 4J1Q NDP 0.01598 0.41428 5.60345
103 1NV8 SAM 0.000008131 0.41626 5.6338
104 1N2X SAM 0.0001521 0.4171 5.64784
105 1RJD SAM 0.00003404 0.45081 5.68862
106 1KYZ SAH 0.0002973 0.43613 5.75342
107 2PZM UDP 0.001403 0.48568 5.75758
108 2PZM NAD 0.001403 0.48568 5.75758
109 5THQ NDP 0.01956 0.41234 5.88235
110 4Y2H SAH 0.00002853 0.56927 5.96591
111 4Y2H 49K 0.00003982 0.56176 5.96591
112 1JNR FAD 0.008017 0.46494 6
113 1G60 SAM 0.0001904 0.42768 6.15385
114 4RDH AMP 0.0001572 0.45588 6.25
115 4RDI ATP 0.000183 0.43704 6.25
116 3G2O SAM 0.000002743 0.50983 6.35452
117 5E9W SAH 0.000004007 0.54568 6.41026
118 5E8J SAH 0.000002386 0.54144 6.41026
119 3I53 SAH 0.000002451 0.48746 6.62651
120 2EG5 SAH 0.00001777 0.50697 6.72043
121 4D79 ATP 0.0004106 0.42311 6.88406
122 2BZG SAH 0.000002743 0.50268 6.89655
123 4POO SAM 0.00008845 0.41373 7
124 5DLY SAH 0.0000004889 0.40083 7.14286
125 2FAV APR 0.003781 0.44275 7.22222
126 1TPY SAH 0.00001855 0.44987 7.31707
127 1QAN SAH 0.000004506 0.46762 7.37705
128 1BC5 SAH 0.000154 0.41671 7.43494
129 3O7W SAM 0.000007133 0.52321 7.48299
130 3FRH SAH 0.0003006 0.49366 7.50988
131 2XYQ SAH 0.0002498 0.43652 7.58621
132 1PR9 NAP 0.001139 0.47893 7.78689
133 3VC1 SAH 0.0000002083 0.50403 8.01282
134 3VC1 GST 0.0000006994 0.40235 8.01282
135 3OFK SAH 0.000006419 0.46829 8.33333
136 2WDQ TEO 0.005769 0.42204 8.40336
137 3DUW SAH 0.0003425 0.42464 8.52018
138 1DL5 SAH 0.00000815 0.43379 8.83281
139 5DM1 SAH 0.0000001188 0.41475 8.98876
140 5DM1 5D7 0.0000001281 0.40955 8.98876
141 5IL1 SAM 0.0007852 0.41839 9
142 2F5Z FAD 0.002859 0.46946 9.375
143 3FZG SAM 0.00003687 0.47956 9.5
144 3LCC SAH 0.000002829 0.51424 9.78723
145 5XLX SAH 0.0004567 0.47654 9.92908
146 3U31 NAD 0.0005451 0.40168 10
147 4M73 SAH 0.0000008061 0.40877 10.089
148 4OBW SAM 0.0001765 0.43705 10.1167
149 5THZ SAH 0.0002583 0.4969 10.1235
150 5THY SAH 0.0001482 0.43383 10.1235
151 1WG8 SAM 0.000297 0.4958 10.1754
152 2JJQ SAH 0.000722 0.43513 10.5882
153 3DMH SAM 0.000002868 0.48274 11.0236
154 3DMH GMP 0.000005417 0.4292 11.0236
155 5KOK SAH 0.00001184 0.4718 11.0831
156 5FA5 MTA 0.000008202 0.50718 11.4441
157 5FTW SAH 0.00003356 0.44701 11.7188
158 2H88 TEO 0.006903 0.41331 11.9048
159 4ONQ SFG 0.00008567 0.44629 12.3249
160 1LSS NAD 0.00008348 0.43035 12.8571
161 3GU3 SAH 0.00001827 0.52894 13.0282
162 2ALG DAO 0.01501 0.40334 13.0435
163 3EGV SAH 0.00001935 0.47979 13.3858
164 2NXE SAM 0.00001473 0.47478 13.3858
165 5CLO NS8 0.003849 0.43898 13.5593
166 1KPG SAH 0.00001832 0.45022 13.5889
167 1NFQ NAI 0.002798 0.45776 13.8462
168 4DCM SAM 0.00009036 0.46428 14.1333
169 1KPH SAH 0.00002023 0.44863 14.2857
170 1JG3 ADN 0.0000774 0.44735 14.8936
171 1IM8 SAI 0.00000005631 0.54045 15.1639
172 4QTU SAM 0.0000001725 0.53413 16.3462
173 5E1M SAH 0.000002859 0.48406 16.5975
174 2VDV SAM 0.000002962 0.53648 16.6667
175 5M58 SAH 0.00003218 0.45679 16.9565
176 5MGZ SAH 0.000001484 0.50068 17.3729
177 3JWH SAH 0.0000003818 0.61115 17.5115
178 3DXY SAM 0.0000004046 0.58878 17.8899
179 4R6W SAH 0.0000001544 0.44275 18.2171
180 3GDH SAH 0.00009184 0.41342 18.6722
181 3Q87 SAM 0.0000229 0.4376 19.2
182 3A4T SFG 0.00002845 0.44301 20.8029
183 3EGI ADP 0.0000402 0.5282 21.8447
184 1KQN NAD 0.03183 0.40381 22.2222
185 1VE3 SAM 0.000001754 0.50946 22.467
186 1Z3C SA8 0.000002502 0.42667 23.1544
187 2XVM SAH 0.000001033 0.5557 24.6231
Pocket No.: 2; Query (leader) PDB : 5DNK; Ligand: SAH; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5dnk.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Feedback