Receptor
PDB id Resolution Class Description Source Keywords
3LCV 2 Å EC: 2.-.-.- CRYSTAL STRUCTURE OF ANTIBIOTIC RELATED METHYLTRANSFERASE MICROMONOSPORA ZIONENSIS ANTIBIOTIC RESISTANCE METHYLTRANSFERASE TRANSFERASE
Ref.: STRUCTURAL BASIS FOR THE METHYLATION OF G1405 IN 16 BY AMINOGLYCOSIDE RESISTANCE METHYLTRANSFERASE SGM ANTIBIOTIC PRODUCER: A DIVERSITY OF ACTIVE SITES IN METHYLTRANSFERASES. NUCLEIC ACIDS RES. 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SAM B:301;
Valid;
none;
Kd = 18 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
3LCV 2 Å EC: 2.-.-.- CRYSTAL STRUCTURE OF ANTIBIOTIC RELATED METHYLTRANSFERASE MICROMONOSPORA ZIONENSIS ANTIBIOTIC RESISTANCE METHYLTRANSFERASE TRANSFERASE
Ref.: STRUCTURAL BASIS FOR THE METHYLATION OF G1405 IN 16 BY AMINOGLYCOSIDE RESISTANCE METHYLTRANSFERASE SGM ANTIBIOTIC PRODUCER: A DIVERSITY OF ACTIVE SITES IN METHYLTRANSFERASES. NUCLEIC ACIDS RES. 2010
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 236 families.
1 3LCU Kd = 300 uM SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 3LCV Kd = 18 uM SAM C15 H22 N6 O5 S C[S@@+](CC....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 211 families.
1 3LCU Kd = 300 uM SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 3LCV Kd = 18 uM 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 166 families.
1 3LCU Kd = 300 uM SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 3LCV Kd = 18 uM SAM C15 H22 N6 O5 S C[S@@+](CC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SAM; Similar ligands found: 192
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 ADN 0.565789 0.773333
10 RAB 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 AMP MG 0.511364 0.710843
25 5AL 0.510417 0.743902
26 VMS 0.510204 0.673913
27 54H 0.510204 0.673913
28 0UM 0.51 0.857143
29 A 0.505747 0.707317
30 AMP 0.505747 0.707317
31 ABM 0.505618 0.753086
32 A5A 0.505155 0.688889
33 DAL AMP 0.50505 0.765432
34 NVA LMS 0.504951 0.725275
35 K15 0.5 0.883117
36 6RE 0.5 0.78481
37 5AD 0.5 0.75
38 SSA 0.5 0.684783
39 SON 0.5 0.746988
40 SRP 0.5 0.746988
41 LSS 0.49505 0.706522
42 CA0 0.494624 0.714286
43 A12 0.494505 0.705882
44 AP2 0.494505 0.705882
45 ME8 0.490385 0.841463
46 5CA 0.49 0.684783
47 TSB 0.49 0.681319
48 53H 0.49 0.666667
49 ACP 0.489362 0.694118
50 5AS 0.48913 0.648936
51 ADP 0.48913 0.690476
52 A2D 0.488889 0.690476
53 J7C 0.488889 0.772152
54 ZAS 0.488636 0.769231
55 8QN 0.485149 0.743902
56 GAP 0.484536 0.73494
57 AN2 0.483871 0.682353
58 A3S 0.483871 0.813333
59 A7D 0.483871 0.851351
60 GJV 0.483516 0.775
61 SRA 0.483146 0.694118
62 LAD 0.480769 0.752941
63 KAA 0.480769 0.698925
64 GSU 0.480769 0.722222
65 AMO 0.480392 0.746988
66 DSZ 0.480392 0.703297
67 52H 0.48 0.666667
68 ADP MG 0.478723 0.702381
69 M33 0.478723 0.722892
70 MAO 0.478261 0.82716
71 BA3 0.478261 0.690476
72 AOC 0.477778 0.776316
73 DSH 0.477778 0.842105
74 NEC 0.477778 0.75
75 SXZ 0.47619 0.894737
76 AHX 0.475728 0.701149
77 Y3J 0.47561 0.706667
78 G5A 0.474227 0.684783
79 A3T 0.473684 0.8
80 ADP BEF 0.473684 0.686047
81 BEF ADP 0.473684 0.686047
82 B4P 0.473118 0.690476
83 AP5 0.473118 0.690476
84 A3N 0.472527 0.766234
85 KB1 0.471698 0.833333
86 LEU LMS 0.471154 0.706522
87 APC 0.46875 0.705882
88 PRX 0.46875 0.73494
89 PAJ 0.466019 0.712644
90 4AD 0.466019 0.759036
91 RBY 0.463918 0.72619
92 ADP PO3 0.463918 0.728395
93 ADV 0.463918 0.72619
94 ADX 0.463158 0.666667
95 MHZ 0.463158 0.82716
96 AU1 0.463158 0.674419
97 YAP 0.462963 0.738095
98 TXA 0.462264 0.72619
99 NB8 0.462264 0.72093
100 A3G 0.461538 0.802632
101 VRT 0.459184 0.842105
102 ATP MG 0.459184 0.702381
103 YSA 0.458716 0.684783
104 XAH 0.458716 0.715909
105 50T 0.458333 0.682353
106 ATP 0.458333 0.690476
107 7D7 0.45679 0.723684
108 ANP MG 0.455446 0.678161
109 KH3 0.455357 0.871795
110 ACQ 0.454545 0.694118
111 AQP 0.453608 0.690476
112 5FA 0.453608 0.690476
113 AR6 0.453608 0.710843
114 APR 0.453608 0.710843
115 NSS 0.451923 0.703297
116 FA5 0.449541 0.746988
117 AGS 0.44898 0.678161
118 SAP 0.44898 0.678161
119 A5D 0.44898 0.789474
120 AD9 0.44898 0.674419
121 PTJ 0.448598 0.72093
122 YLB 0.448276 0.758621
123 YLP 0.447368 0.738636
124 D3Y 0.446602 0.792208
125 ADP ALF 0.445545 0.678161
126 ALF ADP 0.445545 0.678161
127 TYR AMP 0.445455 0.746988
128 MYR AMP 0.444444 0.776471
129 3AM 0.444444 0.674699
130 OAD 0.443396 0.73494
131 2VA 0.443299 0.779221
132 OOB 0.442308 0.722892
133 S8M 0.442308 0.831169
134 ADP VO4 0.441176 0.702381
135 VO4 ADP 0.441176 0.702381
136 ANP 0.44 0.674419
137 TAT 0.44 0.686047
138 WAQ 0.439252 0.75
139 ARG AMP 0.438596 0.727273
140 YLC 0.435897 0.755814
141 AAT 0.435644 0.797468
142 3OD 0.435185 0.73494
143 1ZZ 0.435185 0.755814
144 NVA 2AD 0.434343 0.815789
145 DLL 0.433962 0.722892
146 00A 0.433962 0.689655
147 7MD 0.433628 0.715909
148 ATF 0.431373 0.666667
149 SO8 0.43 0.792208
150 3UK 0.429907 0.714286
151 A6D 0.429907 0.72619
152 5SV 0.428571 0.741176
153 AMP DBH 0.428571 0.714286
154 WSA 0.42735 0.692308
155 TYM 0.42735 0.746988
156 9SN 0.427273 0.681818
157 AHZ 0.426087 0.755814
158 A A 0.425926 0.710843
159 3NZ 0.425926 0.807692
160 P5A 0.425926 0.691489
161 PR8 0.425926 0.744186
162 A1R 0.424528 0.709302
163 2A5 0.424242 0.674419
164 7MC 0.423729 0.719101
165 7D5 0.422222 0.658824
166 FYA 0.422018 0.722892
167 JB6 0.422018 0.709302
168 AYB 0.421488 0.75
169 PLP AAD 0.419355 0.764045
170 A22 0.419048 0.682353
171 MAP 0.419048 0.659091
172 2AM 0.417582 0.666667
173 TAD 0.417391 0.712644
174 A3P 0.416667 0.686747
175 ADP BMA 0.416667 0.714286
176 25A 0.415094 0.690476
177 YLA 0.413223 0.719101
178 ADQ 0.411215 0.694118
179 48N 0.410256 0.72093
180 0XU 0.41 0.824324
181 NAD IBO 0.406504 0.717647
182 7D3 0.40625 0.643678
183 PAP 0.405941 0.678571
184 OVE 0.404255 0.662791
185 4UV 0.403509 0.697674
186 ALF ADP 3PG 0.403361 0.712644
187 AF3 ADP 3PG 0.403361 0.712644
188 LA8 ALF 3PG 0.403361 0.712644
189 3AD 0.402299 0.783784
190 CMP 0.402062 0.691358
191 2BA 0.402062 0.682927
192 7C5 0.4 0.731707
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3LCV; Ligand: SAM; Similar sites found: 202
This union binding pocket(no: 1) in the query (biounit: 3lcv.bio1) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1L0I PSR 0.01538 0.41545 None
2 4R6W SAH 0.0003821 0.40743 None
3 1RJD SAM 0.0000001975 0.59258 0.711744
4 2WA2 SAM 0.00142 0.44172 1.08696
5 1J1R ADE 0.009299 0.431 1.14943
6 2QES ADE 0.002664 0.46387 1.53257
7 1IM8 SAI 0.00001261 0.51648 1.63934
8 2BZG SAH 0.00002844 0.51223 1.72414
9 5X62 SAH 0.0000299 0.51695 1.77936
10 3TKY SAH 0.000005978 0.50093 1.77936
11 4ONQ SFG 0.0004287 0.46047 1.77936
12 3GCZ SAM 0.001228 0.4404 1.77936
13 3P9C SAH 0.0003611 0.40728 1.92308
14 3KP6 SAL 0.01308 0.42553 1.98676
15 3G89 SAM 0.00003123 0.52835 2.00803
16 3I53 SAH 0.00003096 0.50003 2.13523
17 1G55 SAH 0.0003741 0.45864 2.13523
18 1NV8 MEQ 0.0004173 0.42287 2.13523
19 1NV8 SAM 0.0004701 0.41622 2.13523
20 4RPL 3UC 0.02708 0.40588 2.13523
21 4RPL FAD 0.02586 0.40508 2.13523
22 2EJU SAH 0.008018 0.40454 2.13523
23 3EZ2 ADP 0.02825 0.40013 2.13523
24 2PZE ATP 0.01064 0.43043 2.18341
25 2PXX SAH 0.000002537 0.55194 2.32558
26 3KU0 ADE 0.001951 0.47017 2.39044
27 3O7W SAM 0.0000007206 0.60511 2.4911
28 2EFJ SAH 0.000004702 0.553 2.4911
29 5DX1 SFG 0.0002189 0.45965 2.4911
30 5GWX SAM 0.00006684 0.45653 2.4911
31 5GWX SAR 0.00006684 0.45653 2.4911
32 5DX0 SFG 0.0003211 0.45283 2.4911
33 5DX8 SFG 0.0002865 0.45116 2.4911
34 5DXA SFG 0.0003513 0.44757 2.4911
35 5DWQ SFG 0.0004246 0.44608 2.4911
36 2YX1 SFG 0.002697 0.4375 2.4911
37 4PIO SAH 0.00007492 0.43192 2.4911
38 5J60 FAD 0.004133 0.42462 2.4911
39 4PIO AVI 0.0003438 0.41472 2.4911
40 3ZUY TCH 0.01903 0.40486 2.4911
41 4X9M FAD 0.01463 0.40069 2.4911
42 2PX8 SAH 0.003198 0.42212 2.60223
43 2A14 SAH 0.00006066 0.48301 2.6616
44 3MB5 SAM 0.0001162 0.46705 2.7451
45 4ZA2 NAD 0.004254 0.41116 2.7668
46 3FJG 3PG 0.03665 0.40031 2.78884
47 2VDV SAM 0.000003216 0.57465 2.84553
48 3GWZ SAH 0.000002828 0.57726 2.84698
49 3GU3 SAH 0.000006331 0.57611 2.84698
50 3GXO SAH 0.000002148 0.57537 2.84698
51 1XDS SAM 0.000007526 0.55733 2.84698
52 1QZZ SAM 0.00001846 0.53905 2.84698
53 2AOT SAH 0.00001924 0.53171 2.84698
54 3VC1 SAH 0.0002284 0.47923 2.84698
55 5IL1 SAM 0.001342 0.4387 2.84698
56 2P41 SAH 0.002031 0.43079 2.84698
57 5K7U SAM 0.002139 0.42981 2.84698
58 1JQD HSM 0.0005369 0.42147 2.84698
59 3GQT UFO 0.009508 0.41566 2.84698
60 1JQD SAH 0.0004494 0.41064 2.84698
61 3GRU AMP 0.003327 0.40795 2.84698
62 2DPY ADP 0.02708 0.40515 2.84698
63 5E1M SAH 0.0001189 0.48357 2.90456
64 5E1M PRO PRO LYS ARG ILE ALA 0.0001189 0.48357 2.90456
65 2VWA PTY 0.0226 0.41044 2.9703
66 3LCC SAH 0.000001511 0.57512 2.97872
67 3JWH SAH 0.0000009771 0.60721 3.20285
68 3X0D SAH 0.0004532 0.45506 3.20285
69 1MRH FMC 0.007809 0.43332 3.20285
70 1CT9 GLN 0.01101 0.42095 3.20285
71 3S1S SAH 0.001803 0.41876 3.20285
72 4DO1 ANN 0.02736 0.40388 3.20285
73 3DXY SAM 0.00003152 0.53479 3.21101
74 1QAN SAH 0.00167 0.42349 3.27869
75 3A4T SFG 0.001216 0.42918 3.28467
76 1EJ0 SAM 0.002712 0.42527 3.33333
77 1MZV AMP 0.01674 0.40763 3.40426
78 5FA5 MTA 0.0001908 0.48602 3.55872
79 1TPY SAH 0.00006984 0.48048 3.55872
80 4GQB 0XU 0.0001394 0.45729 3.55872
81 3VSE SAH 0.004354 0.432 3.55872
82 1WG8 SAM 0.004277 0.40514 3.55872
83 3VYW SAM 0.005748 0.40433 3.55872
84 3EVG SAH 0.00141 0.43776 3.63636
85 1UAY ADN 0.003458 0.43243 3.71901
86 3GDH SAH 0.00004047 0.47829 3.73444
87 3BGD SAH 0.00004815 0.48257 3.84615
88 3BGD PM6 0.0001624 0.43881 3.84615
89 1Q0S SAH 0.0001135 0.46094 3.861
90 2JJQ SAH 0.00007303 0.51104 3.91459
91 5XVK SAH 0.00002927 0.49133 3.91459
92 2JHP SAH 0.0007118 0.45519 3.91459
93 5JJR SAH 0.001298 0.43934 3.91459
94 3BP1 GUN 0.01622 0.42561 3.91459
95 1O5I NAD 0.002926 0.42019 4.01606
96 5CUQ NSC 0.005748 0.40958 4.11985
97 2HMT NAI 0.003828 0.40857 4.16667
98 5C2N NAG 0.02993 0.40296 4.16667
99 3RKR NAP 0.001789 0.45555 4.19847
100 4CS9 AMP 0.04364 0.40429 4.2328
101 5E8J SAH 0.0000656 0.51323 4.27046
102 1NW5 SAM 0.00004265 0.49921 4.27046
103 5HJM MTA 0.0001675 0.47365 4.27046
104 5E9W SAH 0.00005498 0.43762 4.27046
105 3A25 SAM 0.006997 0.40715 4.31894
106 3EGI ADP 0.00594 0.43949 4.36893
107 1JJV ATP 0.006407 0.43879 4.36893
108 3FUU ADN 0.001301 0.43535 4.42804
109 4FZV SAM 0.003359 0.4142 4.60251
110 5THY SAH 0.000002243 0.54809 4.62633
111 5THZ SAH 0.000002321 0.53596 4.62633
112 1KYZ SAH 0.00001939 0.51953 4.62633
113 4A6D SAM 0.00001543 0.51821 4.62633
114 1KYZ FER 0.000493 0.41914 4.62633
115 3OFK SAH 0.0003392 0.45211 4.62963
116 3KIF GDL 0.01676 0.41605 4.71698
117 3LE7 ADE 0.01789 0.41479 4.98084
118 2FK8 SAM 0.00006749 0.48576 4.98221
119 1J78 OLA 0.0004111 0.45379 4.98221
120 1N2X SAM 0.003059 0.40944 4.98221
121 3RLF MAL 0.02111 0.40658 4.98221
122 1Z3C SA8 0.0007241 0.4029 4.98221
123 5M58 SAH 0.000002098 0.51872 5.21739
124 1UZN NAP 0.003615 0.42741 5.26316
125 1VE3 SAM 0.000004891 0.5458 5.28634
126 4AZW SAM 0.00000898 0.52832 5.33808
127 4R84 CSF 0.01243 0.40273 5.33808
128 5MGZ SAH 0.00000549 0.53751 5.50847
129 5AAV GW5 0.0112 0.41575 5.55556
130 3ZVS MLI 0.01869 0.40918 5.625
131 2DPM SAM 0.000249 0.45766 5.69395
132 3NDJ JHZ 0.001417 0.45084 5.69395
133 4C4A SAH 0.001682 0.43054 5.69395
134 4DMG SAM 0.005837 0.42587 5.69395
135 1UCD U5P 0.01845 0.41496 5.78947
136 4XUC SAM 0.007185 0.40783 5.9633
137 4XUC 43G 0.007185 0.40783 5.9633
138 3TLJ SAH 0.00006241 0.478 6.04982
139 2XRH NIO 0.002144 0.4638 6.04982
140 4OBW SAM 0.00008578 0.49117 6.22568
141 4M73 SAH 0.0000543 0.50093 6.40569
142 4M73 M72 0.00005134 0.41236 6.40569
143 3SZB I1E 0.02575 0.40328 6.40569
144 3H8V ATP 0.009578 0.40114 6.40569
145 2VDJ HSE 0.003712 0.4579 6.76157
146 1Y8Q ATP 0.004537 0.40248 6.76157
147 3WMX NAD 0.001843 0.4014 6.76157
148 1BC5 SAH 0.000002974 0.5316 7.43494
149 5MPT SAH 0.000005308 0.54424 7.82918
150 1YXM ADE 0.0008763 0.486 7.82918
151 2ZIF SAM 0.00218 0.4257 7.82918
152 1Q7L GLY 0.01216 0.4042 7.95455
153 3C3Y SAH 0.006602 0.40495 8.01688
154 4Y2H SAH 0.001593 0.44153 8.18505
155 4Y2H 49K 0.002111 0.43623 8.18505
156 3DMH SAM 0.00577 0.40427 8.18505
157 4YNU FAD 0.01648 0.40196 8.18505
158 4YNU LGC 0.01946 0.40196 8.18505
159 1I1N SAH 0.001601 0.40159 8.40708
160 1KPH SAH 0.000084 0.47717 8.54093
161 1KPG SAH 0.0001097 0.47238 8.54093
162 1U2Z SAH 0.0001878 0.4586 8.54093
163 4IWN GEK 0.00003028 0.49073 8.8968
164 4DCM SAM 0.002761 0.43278 8.8968
165 1UWK NAD 0.01522 0.40434 8.8968
166 1SQL GUN 0.01529 0.423 8.90411
167 4UP5 94W 0.01785 0.41529 9.09091
168 4YMU ARG 0.0338 0.40036 9.09091
169 5XLX SAH 0.000007706 0.48991 9.60854
170 3QOX SAH 0.00003423 0.48857 9.60854
171 5MW4 5JU 0.00169 0.44149 9.60854
172 4A91 GLU 0.01882 0.41735 9.60854
173 1JG3 ADN 0.004251 0.41668 9.60854
174 4N49 SAM 0.005491 0.40517 9.60854
175 5N53 8NB 0.01146 0.42725 9.74359
176 1L1E SAH 0.00008053 0.48253 9.96441
177 3PT9 SAH 0.001999 0.4311 10.3203
178 1G60 SAM 0.00009122 0.48501 10.3846
179 3Q87 SAM 0.0006377 0.43707 11.1765
180 5KOK SAH 0.000001843 0.52043 11.3879
181 5KOK S9T 0.0000167 0.51979 11.3879
182 5KOK R9T 0.00001652 0.51839 11.3879
183 3EGV SAH 0.002628 0.42972 11.4173
184 2NXE SAM 0.002907 0.42395 11.4173
185 1QCI ADE 0.02038 0.41161 11.4504
186 1R18 SAH 0.00186 0.42154 11.8943
187 4II2 ATP 0.00627 0.40274 12.0482
188 2ZWA SAH 0.0000005272 0.5682 12.0996
189 4QTU SAM 0.00003478 0.50303 12.5926
190 3G2O SAM 0.000001889 0.56394 13.1673
191 4M37 SAH 0.002033 0.427 13.1673
192 4M38 SAH 0.004021 0.41089 13.1673
193 2ZWI C5P 0.01607 0.40851 13.1673
194 2UYQ SAM 0.000005482 0.59995 14.2349
195 2PWY SAH 0.0007758 0.43361 17.0543
196 3PMA SCR 0.008208 0.41305 17.2414
197 5KAX RHQ 0.02788 0.40449 17.4699
198 5FTW SAH 0.0000006763 0.57004 17.9688
199 1WY7 SAH 0.004343 0.4063 19.8068
200 2XVM SAH 0.0000006976 0.60577 20.2847
201 2EG5 SAH 0.00001306 0.54609 20.2847
202 3KO0 TFP 0.03027 0.40619 26.7327
203 3FZG SAM 0.0000000001426 0.76695 50
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