Receptor
PDB id Resolution Class Description Source Keywords
4K39 1.78 Å EC: 1.8.98.- NATIVE ANSMECPE WITH BOUND ADOMET AND CP18CYS PEPTIDE CLOSTRIDIUM PERFRINGENS ADOMET RADICAL FOLD OXIDOREDUCTASE
Ref.: X-RAY STRUCTURE OF AN ADOMET RADICAL ACTIVASE REVEA ANAEROBIC SOLUTION FOR FORMYLGLYCINE POSTTRANSLATIO MODIFICATION. PROC.NATL.ACAD.SCI.USA V. 110 8519 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SF4 B:501;
B:502;
A:503;
A:502;
A:501;
B:503;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
submit data
351.64 Fe4 S4 [S]12...
CL B:504;
Invalid;
none;
submit data
35.453 Cl [Cl-]
GOL B:505;
A:506;
A:505;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
SAM A:504;
Valid;
none;
submit data
398.437 C15 H22 N6 O5 S C[S@@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4K39 1.78 Å EC: 1.8.98.- NATIVE ANSMECPE WITH BOUND ADOMET AND CP18CYS PEPTIDE CLOSTRIDIUM PERFRINGENS ADOMET RADICAL FOLD OXIDOREDUCTASE
Ref.: X-RAY STRUCTURE OF AN ADOMET RADICAL ACTIVASE REVEA ANAEROBIC SOLUTION FOR FORMYLGLYCINE POSTTRANSLATIO MODIFICATION. PROC.NATL.ACAD.SCI.USA V. 110 8519 2013
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4K39 - 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 3 families.
1 4K39 - 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 2 families.
1 4K38 - SAM C15 H22 N6 O5 S C[S@@+](CC....
2 4K39 - 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 : 4K39; Ligand: SAM; Similar sites found: 72
This union binding pocket(no: 1) in the query (biounit: 4k39.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4X7Q 3YR 0.007935 0.40659 1.28205
2 1NJJ GET 0.0128 0.42199 1.35135
3 4LH7 1X8 0.004174 0.44597 1.54799
4 2QX0 PH2 0.01172 0.41766 1.88679
5 1Q19 SSC 0.01807 0.40628 2.16216
6 4XH0 ADP 0.0258 0.40181 2.16216
7 3HAV ATP 0.009425 0.42288 2.67559
8 4FHD EEM 0.000007764 0.44342 2.7027
9 4FHD 0TT 0.000007764 0.44342 2.7027
10 1I1N SAH 0.01165 0.40638 3.09735
11 2F67 12B 0.01664 0.4038 3.10559
12 2F62 12M 0.01727 0.40271 3.10559
13 4CC6 L5Y 0.009964 0.4144 3.14465
14 2WQN ADP 0.009871 0.40612 3.22581
15 1GU3 BGC BGC BGC BGC BGC 0.01761 0.4065 3.3557
16 4R33 SAH 0.003327 0.43802 3.51351
17 4R33 TRP 0.003327 0.43802 3.51351
18 3VSV XYS 0.0111 0.42277 3.51351
19 5LKC FUC GLA A2G 0.01497 0.40973 3.57143
20 1KTG AMP 0.003806 0.44685 3.62319
21 3RFA SAM 0.00000007493 0.61831 3.78378
22 1JPA ANP 0.02559 0.4075 3.84615
23 2XUA SHF 0.02046 0.40335 4.13534
24 1SGJ OAA 0.01252 0.41253 4.22535
25 5DBX ANP 0.01317 0.40024 4.26829
26 2VN9 GVD 0.02196 0.40162 4.31894
27 3V8S 0HD 0.008603 0.40126 4.32432
28 2IF8 ADP 0.02202 0.40155 4.40771
29 1Z82 G3P 0.01736 0.40682 4.47761
30 1Z82 G3H 0.02238 0.40119 4.47761
31 3EXS 5RP 0.01456 0.4021 4.52489
32 3I9U DTU 0.01124 0.41296 4.94297
33 2ET1 GLV 0.02643 0.4002 4.97512
34 1TZD ADP 0.03477 0.40177 5.09091
35 5L8L ADP 0.01381 0.4032 5.12821
36 2XOC ADP 0.001395 0.47136 5.36398
37 1MID LAP 0.005803 0.42132 5.49451
38 5UL4 SAM 0.01045 0.40112 5.67568
39 1T36 ORN 0.01335 0.41262 6.21622
40 4WCX SAM 0.0002201 0.44378 6.48649
41 4LRJ ANP 0.005395 0.41032 6.50888
42 3LQV ADE 0.02095 0.40519 6.95652
43 5J6Y BGC 0.009372 0.41457 7.44681
44 5J6Y GLC 0.009372 0.41457 7.44681
45 1FUT 2GP 0.02186 0.40202 7.54717
46 3M2W L8I 0.00934 0.40725 8.02676
47 1QKQ MAN 0.02176 0.4126 8.4507
48 4R78 AMP 0.008032 0.41902 9.06149
49 2GOO NDG 0.01874 0.4111 9.16031
50 1OLT SAM 0.000002216 0.54362 10
51 1UPR 4IP 0.00235 0.46672 10.5691
52 4NJH SAM 0.000001032 0.47372 10.8696
53 4NJH 2K8 0.000001032 0.47372 10.8696
54 5DZT AMP 0.001893 0.45826 11.3514
55 5EXK 5AD 0.0001015 0.52302 12.3867
56 2QK4 ATP 0.008174 0.41865 13.2432
57 3T7V SAM 0.0001263 0.45258 15.4286
58 5TH5 MET 0.0000263 0.54933 17.1103
59 5TH5 7C5 0.0006346 0.40893 17.1103
60 4M7T SAM 0.00001402 0.5193 17.7778
61 1O9U ADZ 0.01256 0.42309 22.2222
62 5VSM MET 0.00000000003017 0.72569 25.4717
63 5VSM 5AD 0.00000000009169 0.70576 25.4717
64 5KOD IAC 0.02702 0.41586 27.7778
65 3LAD FAD 0.02976 0.40193 33.3333
66 3C8F MT2 0.0003054 0.49746 33.4694
67 2FB3 5AD 0.00000008683 0.5923 36.1765
68 2FB3 GTP 0.000001117 0.5923 36.1765
69 2FB3 MET 0.00000008293 0.57988 36.1765
70 1OBD ATP 0.009166 0.40763 38.8889
71 5WGG SAM 0.0000000005129 0.72334 39.4595
72 3JUC PCA 0.02333 0.40392 44.4444
Feedback