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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: 211
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 DSH 0.692308 0.914286
6 SXZ 0.692308 0.916667
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 ADN 0.573333 0.84058
19 RAB 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 SMM 0.536842 0.88
28 SSA 0.536842 0.712644
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 A 0.529412 0.763158
36 LMS 0.529412 0.694118
37 AMP 0.529412 0.763158
38 5CA 0.525773 0.712644
39 ME8 0.524752 0.8125
40 M2T 0.52439 0.821918
41 6RE 0.523256 0.824324
42 GJV 0.522727 0.813333
43 AAT 0.515789 0.863014
44 LSS 0.515152 0.696629
45 KAA 0.514852 0.727273
46 J7C 0.511364 0.835616
47 A5A 0.510417 0.697674
48 SON 0.505495 0.805195
49 SRP 0.505155 0.805195
50 F0P 0.504505 0.915493
51 54H 0.5 0.681818
52 VMS 0.5 0.681818
53 ADX 0.5 0.694118
54 CA0 0.5 0.769231
55 AMO 0.5 0.805195
56 5AL 0.5 0.779221
57 KH3 0.5 0.866667
58 NVA LMS 0.49505 0.707865
59 AHX 0.49505 0.753086
60 TSB 0.494949 0.689655
61 53H 0.494949 0.674157
62 G5A 0.494737 0.712644
63 ABM 0.494382 0.74359
64 A2D 0.494382 0.74359
65 ZAS 0.494253 0.808219
66 A6D 0.490196 0.759494
67 8QN 0.49 0.779221
68 GEK 0.49 0.956522
69 GAP 0.489583 0.769231
70 AN2 0.48913 0.734177
71 A3S 0.48913 0.884058
72 S4M 0.488889 0.831169
73 SRA 0.488636 0.746835
74 LAD 0.485437 0.810127
75 52H 0.484848 0.674157
76 A12 0.483516 0.759494
77 BA3 0.483516 0.74359
78 AP2 0.483516 0.759494
79 NEC 0.483146 0.788732
80 AOC 0.483146 0.842857
81 Y3J 0.481481 0.768116
82 VRT 0.479167 0.861111
83 50T 0.478723 0.734177
84 B4P 0.478261 0.74359
85 ADP 0.478261 0.74359
86 5AS 0.478261 0.655556
87 AP5 0.478261 0.74359
88 A3N 0.477778 0.830986
89 YSA 0.476636 0.712644
90 XAH 0.476636 0.768293
91 0XU 0.473684 0.897059
92 AT4 0.473118 0.7375
93 WAQ 0.471154 0.807692
94 NSS 0.470588 0.712644
95 5AD 0.468354 0.791045
96 AU1 0.468085 0.725
97 M33 0.468085 0.734177
98 MAO 0.467391 0.797468
99 TXA 0.466667 0.759494
100 NB8 0.466667 0.775
101 A3G 0.466667 0.871429
102 3AM 0.465909 0.727273
103 DAL AMP 0.465347 0.779221
104 8X1 0.465347 0.707865
105 A3T 0.463158 0.842857
106 ATP 0.463158 0.74359
107 HEJ 0.463158 0.74359
108 ACP 0.463158 0.746835
109 7D7 0.4625 0.785714
110 LEU LMS 0.461538 0.688889
111 9ZA 0.460784 0.740741
112 9ZD 0.460784 0.740741
113 5FA 0.458333 0.74359
114 AQP 0.458333 0.74359
115 AR6 0.458333 0.766234
116 APC 0.458333 0.759494
117 APR 0.458333 0.766234
118 PRX 0.458333 0.746835
119 F2R 0.457627 0.75
120 IOT 0.456897 0.761905
121 4AD 0.456311 0.794872
122 PAJ 0.456311 0.722892
123 WSA 0.45614 0.72093
124 YAP 0.453704 0.794872
125 8PZ 0.453704 0.712644
126 FA5 0.453704 0.805195
127 ADP PO3 0.453608 0.763158
128 ADV 0.453608 0.782051
129 NVA 2AD 0.453608 0.849315
130 SAP 0.453608 0.728395
131 AGS 0.453608 0.728395
132 RBY 0.453608 0.782051
133 AD9 0.453608 0.725
134 PTJ 0.45283 0.731707
135 MHZ 0.452632 0.797468
136 00A 0.451923 0.740741
137 A3P 0.451613 0.74026
138 YLP 0.451327 0.771084
139 7MD 0.45045 0.768293
140 ALF ADP 0.45 0.707317
141 ADP ALF 0.45 0.707317
142 2VA 0.447917 0.819444
143 OOB 0.446602 0.779221
144 ANP 0.444444 0.725
145 T99 0.444444 0.7375
146 ACQ 0.444444 0.746835
147 TAT 0.444444 0.7375
148 P5A 0.443396 0.719101
149 7D5 0.443182 0.708861
150 A1R 0.442308 0.7625
151 YLC 0.439655 0.790123
152 2AM 0.438202 0.717949
153 DLL 0.438095 0.779221
154 ARG AMP 0.4375 0.759036
155 A22 0.436893 0.734177
156 D3Y 0.436893 0.859155
157 ATF 0.435644 0.716049
158 MYR AMP 0.435185 0.746988
159 80F 0.434426 0.75
160 SO8 0.434343 0.808219
161 OAD 0.433962 0.769231
162 3UK 0.433962 0.769231
163 TAD 0.433628 0.765432
164 25A 0.432692 0.74359
165 6YZ 0.431373 0.746835
166 VO4 ADP 0.431373 0.734177
167 ADP VO4 0.431373 0.734177
168 9SN 0.431193 0.731707
169 TYM 0.431034 0.805195
170 B5V 0.429907 0.759494
171 PR8 0.429907 0.8
172 ADQ 0.428571 0.746835
173 YLB 0.42735 0.771084
174 9K8 0.425926 0.67033
175 1ZZ 0.425926 0.746988
176 FYA 0.425926 0.779221
177 3OD 0.425926 0.769231
178 PPS 0.425743 0.674419
179 MAP 0.423077 0.707317
180 A2P 0.421053 0.727273
181 4YB 0.421053 0.735632
182 9X8 0.420561 0.75
183 ADP BMA 0.420561 0.746835
184 TYR AMP 0.419643 0.794872
185 5SV 0.419048 0.731707
186 3NZ 0.416667 0.824324
187 YLA 0.416667 0.771084
188 8Q2 0.415254 0.688889
189 A3R 0.415094 0.7625
190 B5Y 0.414414 0.75
191 B5M 0.414414 0.75
192 48N 0.413793 0.753086
193 LPA AMP 0.413793 0.768293
194 AYB 0.413223 0.761905
195 ACK 0.413043 0.710526
196 QQY 0.413043 0.696203
197 BIS 0.412844 0.719512
198 JB6 0.412844 0.7625
199 PAP 0.41 0.730769
200 DQV 0.408696 0.75641
201 OVE 0.408602 0.7125
202 AMP DBH 0.40708 0.746835
203 4UV 0.40708 0.75
204 3AD 0.406977 0.852941
205 AF3 ADP 3PG 0.40678 0.743902
206 OMR 0.40678 0.738095
207 LAQ 0.405172 0.768293
208 A A 0.40367 0.74359
209 7C5 0.403509 0.789474
210 7MC 0.403361 0.75
211 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 with APoc: 271
This union binding pocket(no: 1) in the query (biounit: 4x7y.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
1 6FDF SAH 1.45985
2 1O68 KIV 1.45985
3 1KPG SAH 1.45985
4 2VYN NAD 1.45985
5 1RKX NAD 1.45985
6 2BOY BHO 1.5748
7 4N7C AEF 1.70455
8 2DPM SAM 1.82482
9 3TKY SAH 1.82482
10 1KPH SAH 1.82482
11 1BW9 NAD 2.18978
12 3MAG SAH 2.18978
13 3MCT SAH 2.18978
14 5OJ7 AR6 2.18978
15 3O7W SAM 2.18978
16 4KRI SAH 2.18978
17 5A2Z GTP 2.18978
18 2CHN NGT 2.18978
19 5GM1 SAH 2.18978
20 2WA2 SAM 2.18978
21 1VI2 NAD 2.18978
22 1NPD NAD 2.18978
23 3RIY NAD 2.1978
24 1GXS BEZ 2.22222
25 1Q0S SAH 2.3166
26 1FK8 NAD 2.33463
27 4DMG SAM 2.55474
28 5L95 AMP 2.55474
29 6C8R SAH 2.55474
30 4DCM SAM 2.55474
31 2EFJ SAH 2.55474
32 1FP1 SAH 2.55474
33 2CDU ADP 2.55474
34 2ZIF SAM 2.55474
35 6MFL OPV 2.55474
36 1GY8 NAD 2.55474
37 1O94 ADP 2.55474
38 4UCI SAM 2.55474
39 1DJN ADP 2.55474
40 6C8R EQV 2.55474
41 3GFB NAD 2.55474
42 4IWN GEK 2.62009
43 5N5D SAM 2.65487
44 3WV8 ATP 2.75229
45 1EJ0 SAM 2.77778
46 1UAY ADN 2.89256
47 3L9W AMP 2.91971
48 1X87 NAD 2.91971
49 5X62 SAH 2.91971
50 5OCS CIT 2.91971
51 3CHT 4NB 2.91971
52 5FYR INS 2.91971
53 4KRG SAH 2.91971
54 3X0D SAH 2.91971
55 5LD5 NAD 2.91971
56 5M58 SAH 3.04348
57 2V5K OXM 3.13589
58 6DUB SAH 3.15315
59 1S7G NAD 3.16206
60 1S7G APR 3.16206
61 5BSZ SAH 3.2
62 3DXY SAM 3.21101
63 3MQ2 SAH 3.21101
64 2VDV SAM 3.25203
65 3GU3 SAH 3.28467
66 1ZGA SAH 3.28467
67 1ZQ9 SAM 3.28467
68 2JHP SAH 3.28467
69 1FP2 SAH 3.28467
70 2EJU SAH 3.28467
71 3SRV S19 3.28467
72 5F2K SAH 3.28467
73 5F2K OCA 3.28467
74 5DNK SAH 3.28467
75 1NVT NAP 3.28467
76 2UVO NDG 3.50877
77 4LWP SAH 3.64964
78 1TUU ADP 3.64964
79 1KYQ NAD 3.64964
80 3P2E SAH 3.64964
81 3PT9 SAH 3.64964
82 1TUU AMP 3.64964
83 5WP4 SAH 3.64964
84 5KOK SAH 3.64964
85 6B9T 2HE 3.64964
86 3QOX SAH 3.75587
87 1L1E SAH 3.83275
88 1V59 NAD 4.0146
89 1I9G SAM 4.0146
90 5WP5 SAH 4.0146
91 2IZ1 ATR 4.0146
92 3GCZ SAM 4.0146
93 4D52 GXL 4.0146
94 5EY0 ILE 4.0146
95 5YF1 SFG 4.0146
96 4I5I NAD 4.0146
97 3LST SAH 4.0146
98 2YX1 SFG 4.0146
99 3B20 NAD 4.0146
100 4Y9D NAI 4.0146
101 2XVM SAH 4.0201
102 5DM1 SAH 4.11985
103 3OFK SAH 4.16667
104 3CBG SAH 4.31034
105 5FA5 MTA 4.37956
106 2Q28 ADP 4.37956
107 4GQB 0XU 4.37956
108 5IL1 SAM 4.37956
109 5K7U SAM 4.37956
110 1HYH NAD 4.37956
111 4PIO AVI 4.37956
112 4PIO SAH 4.37956
113 1P77 ATR 4.41176
114 2VWT PYR 4.49438
115 1QAN SAH 4.5082
116 4XUC 43G 4.58716
117 4XUC SAM 4.58716
118 5KVA SAM 4.74453
119 1PJS NAD 4.74453
120 1YXM ADE 4.74453
121 4M73 SAH 4.74453
122 4M73 M72 4.74453
123 5B25 4QJ 4.74453
124 3C3Y SAH 5.06329
125 1XCL SAH 5.10638
126 1V6A TRE 5.10949
127 5A0U CHT 5.10949
128 4N49 SAM 5.10949
129 1LVL NAD 5.10949
130 4C4A SAH 5.10949
131 1CER NAD 5.10949
132 1BXK NAD 5.10949
133 3HJ1 UTP 5.10949
134 4YLZ LAT NAG GAL 5.22876
135 3W6X HZP 5.24017
136 5JE0 SAH 5.26316
137 5JE0 AZ8 5.26316
138 3BXO SAM 5.43933
139 5E9W SAH 5.47445
140 5ERG SAM 5.47445
141 1U2Z SAH 5.47445
142 1X14 NAD 5.47445
143 5EO8 TFU 5.47445
144 1Z45 NAD 5.47445
145 1W7J ADP BEF 5.47445
146 2DC1 NAD 5.50847
147 2PX8 SAH 5.57621
148 1M3U KPL 5.68182
149 2EG5 SAH 5.83942
150 3JWH SAH 5.83942
151 6GKV SAH 5.83942
152 1WG8 SAM 5.83942
153 5JJR SAH 5.83942
154 3HVJ 705 5.88235
155 3H2B SAH 5.91133
156 1M2K APR 6.0241
157 1P1C SAH 6.03015
158 1IM8 SAI 6.14754
159 3VSE SAH 6.20438
160 3ZG6 APR 6.20438
161 6B9R 2HE 6.20438
162 6C5B SAH 6.20438
163 5FUB SAH 6.20438
164 6BQ6 TER 6.20438
165 1RJD SAM 6.20438
166 5JE8 NAD 6.20438
167 1JQN DCO 6.20438
168 6HOY AR6 6.20438
169 5BW4 SAM 6.36704
170 2AG8 NAP 6.46388
171 2SIM DAN 6.56934
172 6I6X H6B 6.56934
173 4OM8 NAD 6.56934
174 4BH1 SIA GAL NAG 6.62651
175 3DUW SAH 6.72646
176 4BUZ NAD 6.91057
177 1YC5 NCA 6.91057
178 4BUZ OAD 6.91057
179 4BUZ OCZ 6.91057
180 4RDH AMP 6.93431
181 5DWQ SFG 6.93431
182 5DX0 SFG 6.93431
183 4RDI ATP 6.93431
184 5E9G GLV 6.93431
185 4D79 ATP 6.93431
186 5W0N 2KH 6.93431
187 4NKT 2KH 6.93431
188 6ECW SAH 6.93431
189 5FWA J7C 6.93431
190 2HMT NAI 6.94444
191 3MB5 SAM 7.05882
192 3GWZ SAH 7.29927
193 6GVZ CHO 7.29927
194 1KK8 BEF ADP 7.29927
195 3GXO SAH 7.29927
196 3H8V ATP 7.66423
197 2JJQ SAH 7.66423
198 2OOR NAD 7.66423
199 3TKA SAM 7.66423
200 3GRU AMP 7.66423
201 3VC1 SAH 7.66423
202 1F8G NAD 7.66423
203 4II2 ATP 7.66423
204 2ZWA SAH 7.66423
205 5LOG SAH 7.72532
206 1WY7 SAH 7.72947
207 2HNK SAH 8.0292
208 4OUJ LBT 8.0292
209 5F8F SFG 8.0292
210 4AZW SAM 8.0292
211 4PNE SAH 8.0292
212 3B1F NAD 8.0292
213 5TUK FAD 8.0292
214 1O5I NAD 8.03213
215 4EJ1 FOL 8.20895
216 4NEC SAH 8.33333
217 4UXM BE7 8.33333
218 3SSO SAH 8.39416
219 3TTY GLA 8.39416
220 3BGD PM6 8.46154
221 1TPY SAH 8.75912
222 3R4S SIA 8.75912
223 3Q87 SAM 8.82353
224 4CQM NAP 9.1954
225 5YEC ATP 9.2437
226 2VT3 ATP 9.30233
227 3VYW SAM 9.41558
228 1KYZ SAH 9.48905
229 5HZ9 5M8 9.62963
230 3G89 SAM 9.63855
231 6D3U 83Y BDP 83Y GCD 9.85401
232 4QTU SAM 9.85401
233 1F3L SAH 10.219
234 4JBL MET 10.219
235 2P41 SAH 10.5839
236 2XYQ SAH 10.6557
237 5FAW CHT 10.9489
238 1Y8Q ATP 10.9489
239 3EGI ADP 11.165
240 3LU1 NAD 11.3139
241 1T0S BML 11.6279
242 6DNT NAD 12.0438
243 2VB6 ADP BEF 12.0805
244 3QV1 NAD 12.1951
245 5ULP KB1 12.3134
246 2PWY SAH 12.4031
247 1XDS SAM 12.7737
248 3LQV ADE 12.8205
249 1LSS NAD 12.8571
250 5FA8 SAM 13.0435
251 1G55 SAH 13.5036
252 4YMH SAH 14.5833
253 4KIB SAH 14.5985
254 2Q1W NAD 14.5985
255 3V1Y NAD 14.9635
256 3GDH SAH 15.7676
257 5E8J SAH 15.9091
258 4KXQ APR 16.6667
259 5UMY TNN 17.1429
260 1D6Z HY1 19.708
261 1MEX RAC 20.1878
262 5ZW3 SAH 21.3333
263 3LKZ SFG 23.7226
264 1J5P NAD 24.9012
265 6F5Z SAH 27.8689
266 1L3I SAH 29.6875
267 5ZCO CHD 32.8767
268 5Z84 CHD 32.8767
269 5DX8 SFG 36.8421
270 5DXA SFG 36.8421
271 5DX1 SFG 42.1053
Pocket No.: 2; Query (leader) PDB : 4X7Y; Ligand: SAH; Similar sites found with APoc: 25
This union binding pocket(no: 2) in the query (biounit: 4x7y.bio1) has 41 residues
No: Leader PDB Ligand Sequence Similarity
1 1VC9 ATP None
2 5D4Y BXP 1.82482
3 6CS8 F9Y 1.82482
4 1U26 IHS 2.18978
5 1BXG NAD 2.18978
6 2P3V SRT 2.34375
7 1H0A I3P 3.16456
8 1D2E GDP 3.28467
9 2QJT AMP 3.64964
10 6C4N NAP 4.37956
11 4B5W PYR 4.6875
12 2Z48 A2G 4.74453
13 1V0L XIF XYP 4.79233
14 1TDU DUR 5.47445
15 1J71 THR ILE THR SER 5.83942
16 3I53 SAH 5.83942
17 1W85 TDP 5.83942
18 4D1J DGJ 6.93431
19 5N69 ADP 7.29927
20 5D6T NGA 7.72059
21 3U31 NAD 8.0292
22 2FK8 SAM 8.0292
23 4XWM CBK 8.75912
24 2R4V GSH 8.75912
25 5A6B OAN 9.12409
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