Receptor
PDB id Resolution Class Description Source Keywords
5N5D 1.55 Å EC: 2.-.-.- CRYSTAL STRUCTURE OF THE O-METHYLTRANSFERASE TOMG FROM STREP ACHROMOGENES INVOLVED IN TOMAYMYCIN SYNTHESIS IN COMPLEX WI STREPTOMYCES REGENSIS O-METHYLTRANSFERASE TOMAYMYCIN ROSSMANN-LIKE FOLD S-ADENOMETHIONINE TRANSFERASE
Ref.: TOTAL BIOSYNTHESIS OF THE PYRROLO[4,2]BENZODIAZEPIN SCAFFOLD TOMAYMYCIN ON AN IN VITRO RECONSTITUTED NR SYSTEM. CELL CHEM BIOL 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 B:304;
B:306;
B:305;
A:308;
A:307;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
GOL A:304;
A:305;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
SAM A:306;
B:303;
Valid;
Valid;
none;
none;
submit data
398.437 C15 H22 N6 O5 S C[S@@...
BU3 A:302;
B:302;
A:303;
A:301;
B:301;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
90.121 C4 H10 O2 C[C@H...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5N5D 1.55 Å EC: 2.-.-.- CRYSTAL STRUCTURE OF THE O-METHYLTRANSFERASE TOMG FROM STREP ACHROMOGENES INVOLVED IN TOMAYMYCIN SYNTHESIS IN COMPLEX WI STREPTOMYCES REGENSIS O-METHYLTRANSFERASE TOMAYMYCIN ROSSMANN-LIKE FOLD S-ADENOMETHIONINE TRANSFERASE
Ref.: TOTAL BIOSYNTHESIS OF THE PYRROLO[4,2]BENZODIAZEPIN SCAFFOLD TOMAYMYCIN ON AN IN VITRO RECONSTITUTED NR SYSTEM. CELL CHEM BIOL 2017
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 236 families.
1 5N5D - SAM C15 H22 N6 O5 S C[S@@+](CC....
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 5N5D - SAM C15 H22 N6 O5 S C[S@@+](CC....
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 5N5D - 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 : 5N5D; Ligand: SAM; Similar sites found: 196
This union binding pocket(no: 1) in the query (biounit: 5n5d.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1QAN SAH 0.0000005849 0.54865 None
2 1IM8 SAI 0.0001682 0.46022 None
3 2FKA BEF 0.008245 0.41338 None
4 4RDN 6MD 0.01723 0.41306 None
5 1FWV SGA MAG FUC 0.01607 0.40951 None
6 2BOS GLA GAL GLC 0.019 0.40743 None
7 2BOS GLA GAL GLC NBU 0.02055 0.40345 None
8 3N7S 3N7 0.03012 0.40107 None
9 4UCI SAM 0.0002217 0.46219 0.884956
10 1EXF GLY 0.003435 0.46185 0.884956
11 2EG5 SAH 0.0001635 0.4883 1.32743
12 3BGD SAH 0.0006581 0.42344 1.32743
13 1WY7 SAH 0.00001747 0.49086 1.44928
14 3FZG SAM 0.009647 0.40278 1.5
15 2XVM SAH 0.00007144 0.5049 1.50754
16 2NXE SAM 0.000055 0.49297 2.21239
17 5L95 AMP 0.0002524 0.45981 2.21239
18 3H8V ATP 0.0004789 0.45238 2.21239
19 3GCZ SAM 0.0006542 0.44653 2.21239
20 5AHO TLA 0.004675 0.43867 2.21239
21 1RJD SAM 0.005724 0.4058 2.21239
22 3FPF TNA 0.00001414 0.40351 2.21239
23 3FPF MTA 0.00001414 0.40351 2.21239
24 1T9D P22 0.02613 0.40126 2.21239
25 3WV8 ATP 0.0008709 0.43706 2.29358
26 1Q0S SAH 0.000005839 0.49378 2.65487
27 4FZV SAM 0.00004257 0.48408 2.65487
28 5KOK SAH 0.00006748 0.48403 2.65487
29 3TLJ SAH 0.00002415 0.47833 2.65487
30 2FK8 SAM 0.0003033 0.4491 2.65487
31 2CDU ADP 0.001033 0.44218 2.65487
32 3O7W SAM 0.002015 0.43793 2.65487
33 1JQ3 AAT 0.0001072 0.40433 2.65487
34 4X7Y SAH 0.000005875 0.40268 2.65487
35 5FTW SAH 0.004389 0.40221 2.65487
36 3X0D SAH 0.00006768 0.48398 3.09735
37 5CUQ NSC 0.0005724 0.46357 3.09735
38 4RDH AMP 0.0009641 0.44799 3.09735
39 4IWN GEK 0.0001648 0.44759 3.09735
40 2WA2 SAM 0.0009125 0.44457 3.09735
41 3NJ4 NAD 0.01637 0.44201 3.09735
42 3NJ4 AFX 0.01637 0.44201 3.09735
43 4RDI ATP 0.001671 0.42893 3.09735
44 2BZG SAH 0.001826 0.42727 3.09735
45 1NV8 SAM 0.000178 0.42004 3.09735
46 1NV8 MEQ 0.0002873 0.41462 3.09735
47 3S5W FAD 0.0001136 0.40977 3.09735
48 2AJH MET 0.02592 0.40488 3.09735
49 1X14 NAD 0.001713 0.43249 3.2419
50 2VT3 ATP 0.0008007 0.46152 3.25581
51 2PXX SAH 0.001433 0.42791 3.25581
52 3GU3 SAH 0.00003263 0.53425 3.53982
53 2ZIF SAM 0.000005146 0.53129 3.53982
54 3GRU AMP 0.000003208 0.51192 3.53982
55 5E1M SAH 0.00004399 0.48316 3.53982
56 4YJK URA 0.001066 0.48227 3.53982
57 5DXA SFG 0.00003023 0.47479 3.53982
58 1G60 SAM 0.0001138 0.47444 3.53982
59 5DX8 SFG 0.00003471 0.47213 3.53982
60 5DWQ SFG 0.00004321 0.46219 3.53982
61 5DX0 SFG 0.00005584 0.45145 3.53982
62 4BLW SAH 0.00004183 0.45069 3.53982
63 5DX1 SFG 0.00006262 0.45017 3.53982
64 3VC1 SAH 0.0003398 0.43605 3.53982
65 1KPG SAH 0.0006123 0.43002 3.53982
66 2A14 SAH 0.001804 0.4125 3.53982
67 1Q19 SSC 0.01517 0.41064 3.53982
68 4BLW AMP 0.00006485 0.4084 3.53982
69 2PS1 ORO 0.02094 0.40199 3.53982
70 1Z3C SA8 0.00009706 0.4182 3.69128
71 1R6N 434 0.02853 0.40268 3.79147
72 4QTU SAM 0.00001364 0.51339 3.84615
73 1EJ0 SAM 0.00001766 0.51427 3.88889
74 3EGI ADP 0.00002629 0.55449 3.9823
75 3GDH SAH 0.0000006935 0.52932 3.9823
76 1V59 NAD 0.00005119 0.51798 3.9823
77 5E9W SAH 0.0001505 0.49584 3.9823
78 5HJM MTA 0.0002574 0.45945 3.9823
79 3LCC SAH 0.0005862 0.45305 3.9823
80 2P41 SAH 0.0006101 0.44784 3.9823
81 3EVG SAH 0.001009 0.43839 3.9823
82 1KPH SAH 0.0007455 0.4268 3.9823
83 5MX4 HPA 0.01107 0.4244 3.9823
84 2O07 MTA 0.0001206 0.42495 4.27632
85 2O07 SPD 0.0001436 0.41183 4.27632
86 1G55 SAH 0.000007347 0.52475 4.42478
87 3QOX SAH 0.000002125 0.5206 4.42478
88 2YX1 SFG 0.00004133 0.51587 4.42478
89 5X62 SAH 0.00004561 0.50199 4.42478
90 4DCM SAM 0.0002687 0.47303 4.42478
91 4D79 ATP 0.00166 0.42905 4.42478
92 5D4V SAH 0.001708 0.41378 4.42478
93 5MW4 5JU 0.00007355 0.40632 4.42478
94 1GPM AMP 0.01367 0.40246 4.42478
95 3EGV SAH 0.0002467 0.46964 4.7619
96 3PT9 SAH 0.00000272 0.54936 4.86726
97 2AOT SAH 0.0005215 0.46004 4.86726
98 1P77 ATR 0.003798 0.44425 4.86726
99 4R6W SAH 0.00004001 0.41959 4.86726
100 4M73 SAH 0.00003171 0.41157 4.86726
101 5N53 8NB 0.02036 0.40913 5.12821
102 2DPM SAM 0.000001397 0.53469 5.30973
103 1Y8Q ATP 0.0002149 0.43616 5.30973
104 3ICS ADP 0.003573 0.43079 5.30973
105 3ICT ADP 0.003598 0.43064 5.30973
106 1ZMD NAI 0.0002263 0.42766 5.30973
107 5F7J ADE 0.01586 0.41496 5.30973
108 3QPB URA 0.01855 0.41224 5.30973
109 2HIM ASN 0.02118 0.40685 5.30973
110 3OFK SAH 0.0003052 0.44333 5.55556
111 3Q87 SAM 0.00006858 0.46225 5.6
112 4ONQ SFG 0.0001167 0.47886 5.75221
113 2VDV SAM 0.0004957 0.46605 5.75221
114 3M6W SAM 0.001962 0.43406 5.75221
115 4UP4 GAL NAG 0.01999 0.40412 5.75221
116 2JJQ SAH 0.00003596 0.51866 6.19469
117 3FUU ADN 0.00003363 0.49682 6.19469
118 5THY SAH 0.00007247 0.47479 6.19469
119 3DXY SAM 0.00005834 0.5153 6.42202
120 4DMG SAM 0.0000152 0.5429 6.63717
121 1NW5 SAM 0.0004939 0.44748 6.63717
122 1N2X SAM 0.0002635 0.43759 6.63717
123 1U2Z SAH 0.000002222 0.51947 7.07965
124 3DMH SAM 0.000006389 0.51742 7.07965
125 1P1C SAH 0.000002709 0.51261 7.07965
126 1XCL SAH 0.0000002874 0.48234 7.07965
127 3DMH GMP 0.00001226 0.45969 7.07965
128 2PT9 S4M 0.0002026 0.43125 7.07965
129 5K7U SAM 0.002766 0.41947 7.07965
130 4XFR CIT 0.01711 0.41651 7.07965
131 3TKY SAH 0.005867 0.40198 7.07965
132 1X87 NAD 0.00004056 0.4699 7.52212
133 1KYQ NAD 0.002679 0.42391 7.52212
134 1I7M CG 0.01675 0.40685 7.52212
135 5M58 SAH 0.004737 0.40592 7.52212
136 1XDS SAM 0.008105 0.40996 7.75401
137 5TVF CGQ 0.003798 0.42953 7.9646
138 5MGZ SAH 0.002003 0.42175 7.9646
139 3VSE SAH 0.00004084 0.52262 8.40708
140 3G2O SAM 0.00002636 0.50676 8.40708
141 5IL1 SAM 0.001745 0.42812 8.40708
142 1TLG GAL 0.01278 0.4263 8.40708
143 2PX8 SAH 0.002242 0.42342 8.40708
144 1WG8 SAM 0.00003947 0.50274 8.84956
145 3A25 SAM 0.0002132 0.46756 8.84956
146 3L9W GSH 0.00001141 0.45296 8.84956
147 3L9W AMP 0.00001216 0.44052 8.84956
148 4POO SAM 0.000355 0.42594 9
149 4M38 SAH 0.000009286 0.51072 9.29204
150 5XVK SAH 0.001898 0.40632 9.29204
151 1KYZ SAH 0.003189 0.42057 9.73451
152 2XYQ SAH 0.000004529 0.53979 9.83607
153 5G3L SIA 0.02275 0.42998 10.101
154 2EJU SAH 0.00001067 0.52373 10.177
155 4EUE NAI 0.0001354 0.40246 10.177
156 3VYW SAM 0.0000006194 0.55844 10.6195
157 5MPT SAH 0.0001121 0.47962 10.6195
158 1KK8 BEF ADP 0.0066 0.40659 10.6195
159 1LSS NAD 0.00002424 0.49386 10.7143
160 1VE3 SAM 0.002143 0.42427 11.0619
161 3G89 SAM 0.00002984 0.5224 11.5044
162 5GWX SAM 0.000113 0.42995 11.5044
163 5GWX SAR 0.000113 0.42995 11.5044
164 2WR9 MAN MAN 0.00496 0.44041 11.7188
165 3A27 SAM 0.00006798 0.48899 12.3894
166 3S1S SAH 0.00005389 0.46401 12.3894
167 4N49 SAM 0.001014 0.42849 12.3894
168 2HK9 ATR 0.002542 0.44258 12.8319
169 4II2 ATP 0.003754 0.40561 13.4969
170 5E8J SAH 0.0001408 0.49129 13.6364
171 4AZW SAM 0.0006068 0.4437 13.7168
172 5THZ SAH 0.00006378 0.46228 14.1593
173 4OBW SAM 0.001137 0.43616 14.1593
174 4TXI FAD 0.0001035 0.4053 14.6018
175 5FA5 MTA 0.0008959 0.44943 15.0442
176 4C4A SAH 0.00001294 0.51436 15.9292
177 3BJE URA 0.006088 0.43585 15.9292
178 1L1E SAH 0.0005059 0.4351 15.9292
179 1TPY SAH 0.0007723 0.42632 15.9292
180 3ZFD ANP 0.01235 0.40147 15.9292
181 3A4T SFG 0.000007322 0.50519 16.8142
182 3IWD M2T 0.02512 0.40214 19.1176
183 1ZQ9 SAM 0.000002199 0.55334 19.469
184 5JJR SAH 0.001064 0.43741 19.9115
185 3SSO SAH 0.000001709 0.42044 23.4513
186 1DL5 SAH 0.0000004135 0.51924 26.1062
187 1JG3 ADN 0.00000932 0.52626 27.8761
188 1I1N SAH 0.00004251 0.44417 27.8761
189 3JWH SAH 0.00004307 0.52153 28.1106
190 3HVJ 705 0.00000000001971 0.56314 29.646
191 4XUC 43G 0.00000000000812 0.59479 30.0885
192 4XUC SAM 0.00000000000812 0.59479 30.0885
193 1R18 SAH 0.000008861 0.50404 32.7434
194 3R75 PYR 0.02588 0.40028 33.6283
195 3C3Y SAH 0.000000000008922 0.77488 37.1681
196 3CBG SAH 0.000002844 0.41055 46.0177
Pocket No.: 2; Query (leader) PDB : 5N5D; Ligand: SAM; 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: 5n5d.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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