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Receptor
PDB id Resolution Class Description Source Keywords
5UL4 1.85 Å NON-ENZYME: OTHER STRUCTURE OF COBALAMIN-DEPENDENT S-ADENOSYLMETHIONINE RADICA OXSB WITH AQUA-COBALAMIN AND S-ADENOSYLMETHIONINE BOUND BACILLUS MEGATERIUM METALLOPROTEIN COBALAMIN RADICAL SAM S-ADENOSYLMETHIONINEOXETANOCIN METAL BINDING PROTEIN
Ref.: A B12-DEPENDENT RADICAL SAM ENZYME INVOLVED IN OXET BIOSYNTHESIS. NATURE V. 544 322 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:817;
A:819;
A:812;
A:807;
A:815;
A:818;
A:811;
A:813;
A:810;
A:809;
A:805;
A:814;
A:808;
A:806;
A:816;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
SAM A:803;
Valid;
Atoms found LESS than expected: % Diff = 0;
submit data
398.437 C15 H22 N6 O5 S C[S@@...
MES A:804;
Invalid;
none;
submit data
195.237 C6 H13 N O4 S C1COC...
SF4 A:801;
Part of Protein;
none;
submit data
351.64 Fe4 S4 [S]12...
B12 A:802;
Part of Protein;
none;
submit data
1330.36 C62 H89 Co N13 O14 P Cc1cc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5UL4 1.85 Å NON-ENZYME: OTHER STRUCTURE OF COBALAMIN-DEPENDENT S-ADENOSYLMETHIONINE RADICA OXSB WITH AQUA-COBALAMIN AND S-ADENOSYLMETHIONINE BOUND BACILLUS MEGATERIUM METALLOPROTEIN COBALAMIN RADICAL SAM S-ADENOSYLMETHIONINEOXETANOCIN METAL BINDING PROTEIN
Ref.: A B12-DEPENDENT RADICAL SAM ENZYME INVOLVED IN OXET BIOSYNTHESIS. NATURE V. 544 322 2017
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 5UL4 - 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 1205 families.
1 5UL4 - 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 1039 families.
1 5UL4 - SAM C15 H22 N6 O5 S C[S@@+](CC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SAM; Similar ligands found: 202
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 ADN 0.565789 0.773333
9 RAB 0.565789 0.773333
10 XYA 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 5AL 0.510417 0.743902
25 54H 0.510204 0.673913
26 VMS 0.510204 0.673913
27 0UM 0.51 0.857143
28 AMP 0.505747 0.707317
29 LMS 0.505747 0.666667
30 A 0.505747 0.707317
31 ABM 0.505618 0.753086
32 A5A 0.505155 0.688889
33 SON 0.5 0.746988
34 SSA 0.5 0.684783
35 6RE 0.5 0.78481
36 K15 0.5 0.883117
37 5AD 0.5 0.75
38 SRP 0.5 0.746988
39 LSS 0.49505 0.706522
40 CA0 0.494624 0.714286
41 A12 0.494505 0.705882
42 AP2 0.494505 0.705882
43 ME8 0.490385 0.841463
44 TSB 0.49 0.681319
45 53H 0.49 0.666667
46 DAL AMP 0.49 0.765432
47 5CA 0.49 0.684783
48 ACP 0.489362 0.694118
49 ADP 0.48913 0.690476
50 5AS 0.48913 0.648936
51 J7C 0.488889 0.772152
52 A2D 0.488889 0.690476
53 ZAS 0.488636 0.769231
54 9ZD 0.485149 0.729412
55 9ZA 0.485149 0.729412
56 8QN 0.485149 0.743902
57 GAP 0.484536 0.73494
58 AN2 0.483871 0.682353
59 A3S 0.483871 0.813333
60 A7D 0.483871 0.851351
61 GJV 0.483516 0.775
62 SRA 0.483146 0.694118
63 LAD 0.480769 0.752941
64 KAA 0.480769 0.698925
65 GSU 0.480769 0.722222
66 AMO 0.480392 0.746988
67 DSZ 0.480392 0.703297
68 52H 0.48 0.666667
69 M33 0.478723 0.722892
70 BA3 0.478261 0.690476
71 MAO 0.478261 0.82716
72 NEC 0.477778 0.75
73 AOC 0.477778 0.776316
74 DSH 0.477778 0.842105
75 SXZ 0.47619 0.894737
76 AHX 0.475728 0.701149
77 NVA LMS 0.475728 0.736264
78 Y3J 0.47561 0.706667
79 G5A 0.474227 0.684783
80 A3T 0.473684 0.8
81 B4P 0.473118 0.690476
82 AP5 0.473118 0.690476
83 A3N 0.472527 0.766234
84 KB1 0.471698 0.833333
85 PRX 0.46875 0.73494
86 APC 0.46875 0.705882
87 AT4 0.468085 0.686047
88 PAJ 0.466019 0.712644
89 4AD 0.466019 0.759036
90 RBY 0.463918 0.72619
91 ADP PO3 0.463918 0.728395
92 ADV 0.463918 0.72619
93 ADX 0.463158 0.666667
94 MHZ 0.463158 0.82716
95 AU1 0.463158 0.674419
96 YAP 0.462963 0.738095
97 TXA 0.462264 0.72619
98 NB8 0.462264 0.72093
99 A3G 0.461538 0.802632
100 VRT 0.459184 0.842105
101 XAH 0.458716 0.715909
102 YSA 0.458716 0.684783
103 HEJ 0.458333 0.690476
104 50T 0.458333 0.682353
105 ATP 0.458333 0.690476
106 LEU LMS 0.457143 0.717391
107 7D7 0.45679 0.723684
108 KH3 0.455357 0.871795
109 ACQ 0.454545 0.694118
110 AR6 0.453608 0.710843
111 APR 0.453608 0.710843
112 AQP 0.453608 0.690476
113 5FA 0.453608 0.690476
114 NSS 0.451923 0.703297
115 FA5 0.449541 0.746988
116 A5D 0.44898 0.789474
117 AD9 0.44898 0.674419
118 AGS 0.44898 0.678161
119 SAP 0.44898 0.678161
120 PTJ 0.448598 0.72093
121 YLB 0.448276 0.758621
122 YLP 0.447368 0.738636
123 8X1 0.446602 0.680851
124 D3Y 0.446602 0.792208
125 ADP ALF 0.445545 0.678161
126 ALF ADP 0.445545 0.678161
127 3AM 0.444444 0.674699
128 MYR AMP 0.444444 0.776471
129 OAD 0.443396 0.73494
130 2VA 0.443299 0.779221
131 S8M 0.442308 0.831169
132 OOB 0.442308 0.722892
133 TYR AMP 0.441441 0.759036
134 6YZ 0.441176 0.694118
135 ADP VO4 0.441176 0.702381
136 VO4 ADP 0.441176 0.702381
137 T99 0.44 0.686047
138 TAT 0.44 0.686047
139 ANP 0.44 0.674419
140 WAQ 0.439252 0.75
141 B5Y 0.436364 0.717647
142 8PZ 0.436364 0.684783
143 F0P 0.435897 0.844156
144 YLC 0.435897 0.755814
145 AAT 0.435644 0.797468
146 1ZZ 0.435185 0.755814
147 9K8 0.435185 0.663158
148 3OD 0.435185 0.73494
149 NVA 2AD 0.434343 0.855263
150 00A 0.433962 0.689655
151 DLL 0.433962 0.722892
152 ARG AMP 0.433628 0.727273
153 7MD 0.433628 0.715909
154 ATF 0.431373 0.666667
155 SO8 0.43 0.792208
156 3UK 0.429907 0.714286
157 A6D 0.429907 0.72619
158 9X8 0.429907 0.717647
159 F2R 0.429752 0.7
160 5SV 0.428571 0.741176
161 AMP DBH 0.428571 0.714286
162 TYM 0.42735 0.746988
163 WSA 0.42735 0.692308
164 9SN 0.427273 0.681818
165 AHZ 0.426087 0.755814
166 P5A 0.425926 0.691489
167 B5V 0.425926 0.705882
168 PR8 0.425926 0.744186
169 A A 0.425926 0.710843
170 3NZ 0.425926 0.807692
171 A1R 0.424528 0.709302
172 2A5 0.424242 0.674419
173 7MC 0.423729 0.719101
174 B5M 0.423423 0.717647
175 7D5 0.422222 0.658824
176 JB6 0.422018 0.709302
177 FYA 0.422018 0.722892
178 AYB 0.421488 0.75
179 A22 0.419048 0.682353
180 MAP 0.419048 0.659091
181 2AM 0.417582 0.666667
182 TAD 0.417391 0.712644
183 A3P 0.416667 0.686747
184 ADP BMA 0.416667 0.714286
185 25A 0.415094 0.690476
186 YLA 0.413223 0.719101
187 8Q2 0.411765 0.663158
188 A3R 0.411215 0.709302
189 ADQ 0.411215 0.694118
190 48N 0.410256 0.72093
191 0XU 0.41 0.824324
192 GA7 0.408696 0.72619
193 7D3 0.40625 0.643678
194 PAP 0.405941 0.678571
195 DQV 0.405172 0.702381
196 OVE 0.404255 0.662791
197 4UV 0.403509 0.697674
198 AF3 ADP 3PG 0.403361 0.712644
199 3AD 0.402299 0.783784
200 CMP 0.402062 0.691358
201 2BA 0.402062 0.682927
202 7C5 0.4 0.731707
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5UL4; Ligand: SAM; Similar sites found with APoc: 70
This union binding pocket(no: 1) in the query (biounit: 5ul4.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 5LRT ADP 1.1811
2 5EXK 5AD 1.20846
3 3VSV XYP 2.03762
4 6EK3 OUL 2.26244
5 5NUE NAD 2.40964
6 5NUF NAD 2.40964
7 5X8G S0N 2.47423
8 4RF7 ARG 2.50696
9 4NJH 2K8 2.6087
10 4NJH SAM 2.6087
11 1RSG FAD 2.71318
12 4IV9 FAD 2.87253
13 4ZRN UPG 2.88462
14 4ZRN NAD 2.88462
15 1C0I FAD 3.0303
16 1C0I BE2 3.0303
17 5C5H 4YB 3.09051
18 1OC2 TDX 3.16092
19 1OC2 NAD 3.16092
20 1GPM AMP 3.2381
21 4B0T ADP 3.24544
22 2QHV OC9 3.33333
23 3NZ1 3NY 3.44828
24 5KJW 53C 3.51288
25 2RKV COA 3.54767
26 3LL5 ATP 3.61446
27 4U0O MTA 3.71622
28 1OLT SAM 3.71991
29 1F9V ADP 3.7464
30 4NMC 2OP 3.78109
31 4NMC FAD 3.78109
32 5WKC FAD 3.84047
33 6F5W KG1 4.06504
34 4B2Z P5S 4.24107
35 5X1M THG 4.43038
36 5X1M DHB 4.43038
37 5FUI APY 4.54545
38 1SB8 NAD 4.54545
39 4ITH RCM 4.7619
40 1ELI PYC 4.88432
41 4WOE ADP 5.02793
42 2Q1W NAD 5.1051
43 2HO2 PRO PRO PRO PRO PRO PRO PRO PRO PRO LEU 5.26316
44 1KEW NAD 5.26316
45 1KEW TYD 5.26316
46 6A3J NAI 5.36585
47 1U29 I3P 5.42636
48 1OUK 084 5.46448
49 4K37 SAM 5.67568
50 4K38 SAM 5.67568
51 4K39 SAM 5.67568
52 4X6F 3XU 5.71429
53 5Y72 DST 5.97015
54 3GE7 AFQ 6.21762
55 3ESS 18N 6.52174
56 1QSM ACO 6.57895
57 6FA4 D1W 6.93642
58 5OCG 9R5 8.46561
59 3T7V SAM 8.57143
60 2Q0L FAD 8.68167
61 4FK7 P34 9.17031
62 1FHX 4IP 9.30233
63 3IWD M2T 9.67742
64 1L3I SAH 10.4167
65 4JYD SAH 10.9195
66 3WDM ADN 11.8774
67 3T4L ZEA 12.963
68 4GUS FAD 19.0476
69 2CNT COA 20.625
70 3H0L ADP 23.4043
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