Receptor
PDB id Resolution Class Description Source Keywords
4X7Y 1.4 Å EC: 2.1.1.237 MYCF MYCINAMICIN III 3'-O-METHYLTRANSFERASE (E35Q, M56A, E13 VARIANT) IN COMPLEX WITH MG AND SAH MICROMONOSPORA GRISEORUBIDA MACROLIDE METHYLTRANSFERASE ANTIBIOTIC NATURAL PRODUCT TRANSFERASE-ANTIBIOTIC COMPLEX
Ref.: STRUCTURAL BASIS OF SUBSTRATE SPECIFICITY AND REGIO IN THE MYCF/TYLF FAMILY OF SUGAR O-METHYLTRANSFERAS ACS CHEM.BIOL. V. 10 1340 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SAH B:302;
A:302;
Valid;
Valid;
none;
none;
submit data
384.411 C14 H20 N6 O5 S c1nc(...
MG B:301;
A:301;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4X7Y 1.4 Å EC: 2.1.1.237 MYCF MYCINAMICIN III 3'-O-METHYLTRANSFERASE (E35Q, M56A, E13 VARIANT) IN COMPLEX WITH MG AND SAH MICROMONOSPORA GRISEORUBIDA MACROLIDE METHYLTRANSFERASE ANTIBIOTIC NATURAL PRODUCT TRANSFERASE-ANTIBIOTIC COMPLEX
Ref.: STRUCTURAL BASIS OF SUBSTRATE SPECIFICITY AND REGIO IN THE MYCF/TYLF FAMILY OF SUGAR O-METHYLTRANSFERAS ACS CHEM.BIOL. V. 10 1340 2015
Members (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4X81 - MVI C35 H57 N O11 CC[C@@H]1[....
2 4X7X - SAH C14 H20 N6 O5 S c1nc(c2c(n....
3 4X7Z - SAH C14 H20 N6 O5 S c1nc(c2c(n....
4 4X7W - SAH C14 H20 N6 O5 S c1nc(c2c(n....
5 4XVY - SAH C14 H20 N6 O5 S c1nc(c2c(n....
6 4X7U - SAH C14 H20 N6 O5 S c1nc(c2c(n....
7 4X7Y - SAH C14 H20 N6 O5 S c1nc(c2c(n....
8 4X7V - SAH C14 H20 N6 O5 S c1nc(c2c(n....
70% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2WK1 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 4X81 - MVI C35 H57 N O11 CC[C@@H]1[....
3 4X7X - SAH C14 H20 N6 O5 S c1nc(c2c(n....
4 4X7Z - SAH C14 H20 N6 O5 S c1nc(c2c(n....
5 4X7W - SAH C14 H20 N6 O5 S c1nc(c2c(n....
6 4XVY - SAH C14 H20 N6 O5 S c1nc(c2c(n....
7 4X7U - SAH C14 H20 N6 O5 S c1nc(c2c(n....
8 4X7Y - SAH C14 H20 N6 O5 S c1nc(c2c(n....
9 4X7V - SAH C14 H20 N6 O5 S c1nc(c2c(n....
50% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2WK1 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 4X81 - MVI C35 H57 N O11 CC[C@@H]1[....
3 4X7X - SAH C14 H20 N6 O5 S c1nc(c2c(n....
4 4X7Z - SAH C14 H20 N6 O5 S c1nc(c2c(n....
5 4X7W - SAH C14 H20 N6 O5 S c1nc(c2c(n....
6 4XVY - SAH C14 H20 N6 O5 S c1nc(c2c(n....
7 4X7U - SAH C14 H20 N6 O5 S c1nc(c2c(n....
8 4X7Y - SAH C14 H20 N6 O5 S c1nc(c2c(n....
9 4X7V - 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 : 4X7Y; Ligand: SAH; Similar sites found: 123
This union binding pocket(no: 1) in the query (biounit: 4x7y.bio1) has 42 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1KPG SAH 0.0123 0.4076 1.45985
2 2BOY BHO 0.03324 0.40808 1.5748
3 4N7C AEF 0.03424 0.41303 1.70455
4 2DPM SAM 0.00251 0.4383 1.82482
5 1KPH SAH 0.01267 0.40704 1.82482
6 3O7W SAM 0.01018 0.43069 2.18978
7 4KRI SAH 0.00633 0.4235 2.18978
8 5A2Z GTP 0.02711 0.42007 2.18978
9 2CHN NGT 0.0188 0.41731 2.18978
10 5GM1 SAH 0.007295 0.41484 2.18978
11 1BW9 NAD 0.01024 0.41116 2.18978
12 1FK8 NAD 0.01123 0.40152 2.33463
13 4DMG SAM 0.0009982 0.48607 2.55474
14 5L95 AMP 0.001069 0.46227 2.55474
15 1O94 ADP 0.00534 0.4179 2.55474
16 1DJN ADP 0.009312 0.41021 2.55474
17 3GFB NAD 0.00769 0.40347 2.55474
18 4IWN GEK 0.01054 0.40785 2.62009
19 5N5D SAM 0.000005875 0.40268 2.65487
20 1X87 NAD 0.001623 0.44331 2.91971
21 5X62 SAH 0.01288 0.41866 2.91971
22 3CHT 4NB 0.03807 0.41382 2.91971
23 4KRG SAH 0.01782 0.41186 2.91971
24 5LD5 NAD 0.01367 0.40291 2.91971
25 3DXY SAM 0.01423 0.42709 3.21101
26 3MQ2 SAH 0.009276 0.42552 3.21101
27 2VDV SAM 0.02572 0.41044 3.25203
28 3GU3 SAH 0.002434 0.47114 3.28467
29 2EJU SAH 0.007915 0.42543 3.28467
30 2UVO NDG 0.0307 0.42481 3.50877
31 4LWP SAH 0.003859 0.4401 3.64964
32 1TUU ADP 0.01753 0.43464 3.64964
33 1KYQ NAD 0.006471 0.43303 3.64964
34 3PT9 SAH 0.0128 0.41559 3.64964
35 1TUU AMP 0.03445 0.41443 3.64964
36 5KOK SAH 0.01408 0.41063 3.64964
37 1L1E SAH 0.01847 0.40238 3.83275
38 3GCZ SAM 0.01032 0.42 4.0146
39 1V59 NAD 0.02198 0.41737 4.0146
40 2XVM SAH 0.00498 0.44623 4.0201
41 5DM1 SAH 0.002092 0.40257 4.11985
42 3OFK SAH 0.001588 0.44712 4.16667
43 5FA5 MTA 0.002159 0.46001 4.37956
44 5IL1 SAM 0.01691 0.40987 4.37956
45 5K7U SAM 0.019 0.40748 4.37956
46 4PIO AVI 0.003906 0.40345 4.37956
47 1P77 ATR 0.03277 0.41958 4.41176
48 1QAN SAH 0.007542 0.41707 4.5082
49 4XUC 43G 0.0000201 0.44437 4.58716
50 4XUC SAM 0.0000201 0.44437 4.58716
51 1YXM ADE 0.01156 0.43973 4.74453
52 5B25 4QJ 0.02448 0.40827 4.74453
53 1XCL SAH 0.00127 0.42436 5.10638
54 4N49 SAM 0.002877 0.43899 5.10949
55 5A0U CHT 0.02947 0.41811 5.10949
56 5JE0 AZ8 0.002871 0.41322 5.26316
57 5JE0 SAH 0.002871 0.41322 5.26316
58 1X14 NAD 0.02242 0.40704 5.47445
59 2DC1 NAD 0.007535 0.40384 5.50847
60 2EG5 SAH 0.003842 0.45187 5.83942
61 5JJR SAH 0.02408 0.4026 5.83942
62 3HVJ 705 0.00002453 0.4731 5.88235
63 3H2B SAH 0.01776 0.40595 5.91133
64 1M2K APR 0.008515 0.40167 6.0241
65 1IM8 SAI 0.01445 0.40723 6.14754
66 3VSE SAH 0.007351 0.44179 6.20438
67 5MF6 7M2 0.003895 0.40808 6.20438
68 5MF6 AR6 0.003895 0.40808 6.20438
69 2SIM DAN 0.02174 0.41761 6.56934
70 4BUZ NAD 0.00274 0.42174 6.91057
71 1YC5 NCA 0.004554 0.41275 6.91057
72 4BUZ OAD 0.004015 0.40757 6.91057
73 4BUZ OCZ 0.004123 0.40712 6.91057
74 4RDH AMP 0.009433 0.42866 6.93431
75 4D79 ATP 0.01787 0.40874 6.93431
76 5W0N 2KH 0.02564 0.40728 6.93431
77 3GWZ SAH 0.01376 0.42412 7.29927
78 1KK8 BEF ADP 0.01983 0.40962 7.29927
79 3GXO SAH 0.02406 0.40865 7.29927
80 2JJQ SAH 0.006985 0.43888 7.66423
81 3GRU AMP 0.005171 0.42137 7.66423
82 3VC1 SAH 0.005314 0.42085 7.66423
83 4II2 ATP 0.01119 0.41228 7.66423
84 2ZWA SAH 0.01536 0.4033 7.66423
85 5LOG SAH 0.00001356 0.54954 7.72532
86 1WY7 SAH 0.003911 0.42974 7.72947
87 2HNK SAH 0.000007669 0.55523 8.0292
88 4OUJ LBT 0.022 0.44137 8.0292
89 5F8F SFG 0.01028 0.42683 8.0292
90 4AZT SAM 0.01378 0.41407 8.0292
91 5TUK FAD 0.007366 0.40424 8.0292
92 1O5I NAD 0.01611 0.40791 8.03213
93 4EJ1 FOL 0.0274 0.40905 8.20895
94 4NEC SAH 0.01339 0.42119 8.33333
95 4UXM BE7 0.002173 0.42095 8.33333
96 3BGD PM6 0.007925 0.40294 8.46154
97 1TPY SAH 0.01463 0.40424 8.75912
98 3R4S SIA 0.03829 0.40259 8.75912
99 2VT3 ATP 0.006192 0.4456 9.30233
100 3VYW SAM 0.001007 0.4596 9.41558
101 1KYZ SAH 0.002865 0.45 9.48905
102 3G89 SAM 0.01628 0.42044 9.63855
103 4QTU SAM 0.01779 0.40591 9.85401
104 1F3L SAH 0.003202 0.4336 10.219
105 4JBL MET 0.04324 0.41286 10.219
106 2P41 SAH 0.02474 0.40204 10.5839
107 5FAW CHT 0.02948 0.42213 10.9489
108 1Y8Q ATP 0.007693 0.4111 10.9489
109 3EGI ADP 0.005941 0.4605 11.165
110 3LU1 NAD 0.00373 0.41122 11.3139
111 5ULP KB1 0.003122 0.42789 12.3134
112 1XDS SAM 0.01772 0.41859 12.7737
113 3LQV ADE 0.02264 0.41905 12.8205
114 1LSS NAD 0.001924 0.44689 12.8571
115 5FA8 SAM 0.01111 0.40685 13.0435
116 1G55 SAH 0.007726 0.42268 13.5036
117 4YMH SAH 0.00002711 0.53048 14.5833
118 3GDH SAH 0.009431 0.4073 15.7676
119 5E8J SAH 0.001102 0.47896 15.9091
120 3LKZ SFG 0.01499 0.40936 23.7226
121 1L3I SAH 0.000683 0.45274 29.6875
122 5DX8 SFG 0.006043 0.41842 36.8421
123 5DXA SFG 0.006434 0.41722 36.8421
Pocket No.: 2; Query (leader) PDB : 4X7Y; 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: 4x7y.bio1) has 41 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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