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Receptor
PDB id Resolution Class Description Source Keywords
3IIZ 1.62 Å EC: 7.-.-.- X-RAY STRUCTURE OF THE FEFE-HYDROGENASE MATURASE HYDE FROM T IN COMPLEX WITH S-ADENOSYL-L-METHIONINE THERMOTOGA MARITIMA ADOMET RADICAL SAM RADICAL HYDE HYDROGENASE FE4S4 CLUSTECLEAVAGE MATURATION ADENOSYLMETHIONINE ADOMET BINDING PR
Ref.: UNEXPECTED ELECTRON TRANSFER MECHANISM UPON ADOMET IN RADICAL SAM PROTEINS PROC.NATL.ACAD.SCI.USA 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL A:349;
A:350;
Invalid;
Invalid;
none;
none;
submit data
35.453 Cl [Cl-]
CO3 A:351;
Invalid;
none;
submit data
60.009 C O3 C(=O)...
CPS A:1701;
A:1702;
A:1703;
A:1704;
A:1705;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
614.877 C32 H58 N2 O7 S C[C@H...
FES A:2648;
Part of Protein;
none;
submit data
175.82 Fe2 S2 S1[Fe...
H2S A:2649;
A:2650;
Invalid;
Invalid;
none;
none;
submit data
34.081 H2 S S
SAM A:1501;
Valid;
none;
submit data
398.437 C15 H22 N6 O5 S C[S@@...
SF4 A:2460;
Part of Protein;
none;
submit data
351.64 Fe4 S4 [S]12...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4JYD 1.71 Å EC: 7.-.-.- X-RAY SNAPSHOTS OF POSSIBLE INTERMEDIATES IN THE TIME COURSE SYNTHESIS AND DEGRADATION OF PROTEIN-BOUND FE4S4 CLUSTERS. THERMOTOGA MARITIMA RADICAL SAM PROTEIN FEFE-HYDROGENASE ACTIVE SITE ASSEMBLY CLUSTER S-ADENOSYL-L-METHIONINE OXIDOREDUCTASE
Ref.: X-RAY SNAPSHOTS OF POSSIBLE INTERMEDIATES IN THE TI OF SYNTHESIS AND DEGRADATION OF PROTEIN-BOUND FE4S4 CLUSTERS. PROC.NATL.ACAD.SCI.USA V. 110 7188 2013
Members (18)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 293 families.
1 3CIW - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 4JYE - SAH C14 H20 N6 O5 S c1nc(c2c(n....
3 3CIX - SAH C14 H20 N6 O5 S c1nc(c2c(n....
4 5FEX - 5AD SEC n/a n/a
5 5FF3 - PRS C4 H7 N O2 S C1[C@H](NC....
6 5FEP - SAM C15 H22 N6 O5 S C[S@@+](CC....
7 3IIZ - SAM C15 H22 N6 O5 S C[S@@+](CC....
8 5FES - SAM C15 H22 N6 O5 S C[S@@+](CC....
9 5FF0 - 5X8 C13 H18 N6 O5 S c1nc(c2c(n....
10 4JXC - SAM C15 H22 N6 O5 S C[S@@+](CC....
11 4JY9 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
12 4JYF - SAH C14 H20 N6 O5 S c1nc(c2c(n....
13 5FF4 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
14 3IIX - MET C5 H11 N O2 S CSCC[C@@H]....
15 4JYD - SAH C14 H20 N6 O5 S c1nc(c2c(n....
16 5FEW - SAH C14 H20 N6 O5 S c1nc(c2c(n....
17 5FF2 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
18 5FEZ - 9SE C6 H9 N O4 Se C[C@]1(N[C....
70% Homology Family (18)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 250 families.
1 3CIW - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 4JYE - SAH C14 H20 N6 O5 S c1nc(c2c(n....
3 3CIX - SAH C14 H20 N6 O5 S c1nc(c2c(n....
4 5FEX - 5AD SEC n/a n/a
5 5FF3 - PRS C4 H7 N O2 S C1[C@H](NC....
6 5FEP - SAM C15 H22 N6 O5 S C[S@@+](CC....
7 3IIZ - SAM C15 H22 N6 O5 S C[S@@+](CC....
8 5FES - SAM C15 H22 N6 O5 S C[S@@+](CC....
9 5FF0 - 5X8 C13 H18 N6 O5 S c1nc(c2c(n....
10 4JXC - SAM C15 H22 N6 O5 S C[S@@+](CC....
11 4JY9 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
12 4JYF - SAH C14 H20 N6 O5 S c1nc(c2c(n....
13 5FF4 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
14 3IIX - MET C5 H11 N O2 S CSCC[C@@H]....
15 4JYD - SAH C14 H20 N6 O5 S c1nc(c2c(n....
16 5FEW - SAH C14 H20 N6 O5 S c1nc(c2c(n....
17 5FF2 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
18 5FEZ - 9SE C6 H9 N O4 Se C[C@]1(N[C....
50% Homology Family (18)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 204 families.
1 3CIW - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 4JYE - SAH C14 H20 N6 O5 S c1nc(c2c(n....
3 3CIX - SAH C14 H20 N6 O5 S c1nc(c2c(n....
4 5FEX - 5AD SEC n/a n/a
5 5FF3 - PRS C4 H7 N O2 S C1[C@H](NC....
6 5FEP - SAM C15 H22 N6 O5 S C[S@@+](CC....
7 3IIZ - SAM C15 H22 N6 O5 S C[S@@+](CC....
8 5FES - SAM C15 H22 N6 O5 S C[S@@+](CC....
9 5FF0 - 5X8 C13 H18 N6 O5 S c1nc(c2c(n....
10 4JXC - SAM C15 H22 N6 O5 S C[S@@+](CC....
11 4JY9 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
12 4JYF - SAH C14 H20 N6 O5 S c1nc(c2c(n....
13 5FF4 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
14 3IIX - MET C5 H11 N O2 S CSCC[C@@H]....
15 4JYD - SAH C14 H20 N6 O5 S c1nc(c2c(n....
16 5FEW - SAH C14 H20 N6 O5 S c1nc(c2c(n....
17 5FF2 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
18 5FEZ - 9SE C6 H9 N O4 Se C[C@]1(N[C....
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 : 4JYD; Ligand: SAH; Similar sites found with APoc: 79
This union binding pocket(no: 1) in the query (biounit: 4jyd.bio1) has 33 residues
No: Leader PDB Ligand Sequence Similarity
1 3C3N FMN 1.60256
2 5V8E CIT 1.61812
3 2JBM SRT 2.00669
4 6C4A PYR 2.01149
5 5W0N UPU 2.01149
6 1QPR PHT 2.11268
7 1TIQ COA 2.22222
8 1ZLQ EDT 2.29885
9 3NB0 G6P 2.29885
10 2OVW CBI 2.29885
11 4JR7 GNP 2.29885
12 3N2O AG2 2.29885
13 2ZE3 AKG 2.54545
14 5E9G GLV 2.58621
15 3GD8 GOL 2.69058
16 5H4S RAM 2.8169
17 1S5O 152 2.87356
18 5VLQ ANP 2.87356
19 1IGW PYR 3.16092
20 2P7Q GG6 3.16092
21 1AUX AGS 3.21543
22 4MIX UD1 3.27381
23 1O9U ADZ 3.44828
24 5JWP AKG 3.44828
25 1UJP CIT 3.69004
26 2B7N NTM 3.73563
27 1LNM DTX 3.80435
28 2TPS TPS 3.96476
29 5VSM 5AD 4.08805
30 5VSM MET 4.08805
31 1WK9 TSB 4.10959
32 3RFA SAM 4.31034
33 3PGU OLA 4.31034
34 4NJH 2K8 4.34783
35 4NJH SAM 4.34783
36 1Y7P RIP 4.4843
37 2AJH MET 4.59184
38 5WGG SAM 4.88506
39 5TCI MLI 4.88506
40 2ZI8 SDT 4.88506
41 5OSW DIU 5.17241
42 2QLX RM4 5.55556
43 4JGT PYR 5.68562
44 5TH5 7C5 5.70342
45 2Z6I FMN 5.72289
46 3JQQ A2P 6.01266
47 5O6Y 5YA 6.07477
48 6F9G PUT 6.32184
49 3SUT OAN 6.32184
50 2A19 ANP 7.42857
51 4K37 SAM 7.47126
52 4K38 SAM 7.47126
53 4K39 SAM 7.47126
54 3BIB PSF 7.75862
55 4YEE 4CQ 7.77778
56 3UPY FOM 8.04598
57 3KYF 5GP 5GP 8.22511
58 1Q6O LG6 8.33333
59 4CM9 YGL 9.72222
60 4CME KTZ 9.72222
61 5JDI 6JO 9.72222
62 1O5Q PYR 10.4918
63 5UL4 SAM 10.9195
64 5L8N 6RQ 10.9375
65 2F6U CIT 11.9658
66 6HTO 5AD 12.069
67 6HTO MET 12.069
68 3EXS 5RP 13.1222
69 4U0O MTA 13.1757
70 6DZN AE3 14.0845
71 2FB3 MET 15
72 2FB3 5AD 15
73 1OLT SAM 21.5517
74 5EXK 5AD 24.1692
75 5EXK MET 24.1692
76 4WCX SAM 37.931
77 4WCX MET 37.931
78 3T7V SAM 45.6897
79 3T7V MD0 45.6897
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