Receptor
PDB id Resolution Class Description Source Keywords
2ED4 1.85 Å EC: 1.6.8.- CRYSTAL STRUCTURE OF FLAVIN REDUCTASE HPAC COMPLEXED WITH FA THERMUS THERMOPHILUS FLAVIN REDUCTASE FLAVIN DIFFUSIBLE TWO-COMPONENT MONOOXYGEOXIDOREDUCTASE
Ref.: CRYSTAL STRUCTURE OF THE FLAVIN REDUCTASE COMPONENT OF 4-HYDROXYPHENYLACETATE 3-MONOOXYGENASE FROM THER THERMOPHILUS HB8: STRUCTURAL BASIS FOR THE FLAVIN A PROTEINS V. 70 718 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FAD A:400;
B:500;
Valid;
Valid;
none;
none;
submit data
785.55 C27 H33 N9 O15 P2 Cc1cc...
NAD A:401;
B:501;
Valid;
Valid;
none;
none;
submit data
663.425 C21 H27 N7 O14 P2 c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2ED4 1.85 Å EC: 1.6.8.- CRYSTAL STRUCTURE OF FLAVIN REDUCTASE HPAC COMPLEXED WITH FA THERMUS THERMOPHILUS FLAVIN REDUCTASE FLAVIN DIFFUSIBLE TWO-COMPONENT MONOOXYGEOXIDOREDUCTASE
Ref.: CRYSTAL STRUCTURE OF THE FLAVIN REDUCTASE COMPONENT OF 4-HYDROXYPHENYLACETATE 3-MONOOXYGENASE FROM THER THERMOPHILUS HB8: STRUCTURAL BASIS FOR THE FLAVIN A PROTEINS V. 70 718 2008
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2ED4 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2ED4 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2ED4 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: FAD; Similar ligands found: 119
No: Ligand ECFP6 Tc MDL keys Tc
1 FAS 1 1
2 FAD 1 1
3 FAY 0.859259 0.9875
4 RFL 0.852941 0.963855
5 6FA 0.794118 0.987654
6 DAL FAD PER 0.772414 0.951807
7 FAE 0.751773 0.987654
8 SFD 0.651007 0.860215
9 FDA 0.641892 0.906977
10 FNK 0.602564 0.876405
11 62F 0.572327 0.939024
12 F2N 0.566265 0.886364
13 FMN 0.543307 0.876543
14 FA9 0.526316 0.939759
15 6YU 0.516304 0.860215
16 CNV FAD 0.511905 0.908046
17 P6G FDA 0.511628 0.908046
18 FAD NBT 0.508876 0.83871
19 A2D 0.504065 0.875
20 P5F 0.491329 0.941176
21 FAD CNX 0.488506 0.8125
22 APR 0.488372 0.851852
23 AR6 0.488372 0.851852
24 AGS 0.484615 0.811765
25 SAP 0.484615 0.811765
26 M33 0.484375 0.864198
27 BA3 0.484127 0.875
28 FAD NBA 0.480663 0.802083
29 ATP 0.48062 0.851852
30 B4P 0.480315 0.875
31 ADP 0.480315 0.851852
32 AP5 0.480315 0.875
33 ANP 0.477273 0.831325
34 AQP 0.476923 0.851852
35 5FA 0.476923 0.851852
36 48N 0.469388 0.902439
37 OAD 0.467626 0.876543
38 GTA 0.465753 0.892857
39 AN2 0.465116 0.841463
40 AD9 0.462121 0.831325
41 3OD 0.460993 0.876543
42 RBF 0.460938 0.790123
43 FB0 0.460606 0.835165
44 139 0.460526 0.858824
45 AP0 0.46 0.835294
46 A22 0.459854 0.864198
47 ACP 0.458015 0.853659
48 8QN 0.456522 0.864198
49 PRX 0.454545 0.831325
50 A1R 0.453237 0.86747
51 G3A 0.452055 0.902439
52 T5A 0.45098 0.872093
53 G5P 0.44898 0.902439
54 ATF 0.448529 0.821429
55 50T 0.44697 0.819277
56 ACQ 0.444444 0.853659
57 PAJ 0.442857 0.847059
58 ADQ 0.442857 0.853659
59 5AL 0.441176 0.864198
60 ADX 0.439394 0.775281
61 CA0 0.439394 0.853659
62 A4P 0.437909 0.831461
63 25L 0.4375 0.864198
64 P33 FDA 0.436464 0.817204
65 5SV 0.435714 0.793103
66 TXE 0.434211 0.890244
67 OMR 0.434211 0.818182
68 ABM 0.434109 0.829268
69 A 0.433071 0.82716
70 AMP 0.433071 0.82716
71 4AD 0.432624 0.855422
72 ADJ 0.432258 0.818182
73 BIS 0.430556 0.802326
74 SRA 0.429688 0.788235
75 AFH 0.42953 0.825581
76 TXD 0.427632 0.890244
77 NXX 0.427632 0.865854
78 UP5 0.427632 0.878049
79 DND 0.427632 0.865854
80 6V0 0.427632 0.857143
81 SRP 0.42446 0.843373
82 PR8 0.423611 0.837209
83 TAT 0.423358 0.821429
84 AMO 0.422535 0.865854
85 PTJ 0.42069 0.835294
86 FYA 0.42069 0.864198
87 TXA 0.42069 0.865854
88 CNA 0.420382 0.865854
89 00A 0.41958 0.823529
90 AHX 0.41958 0.835294
91 MAP 0.41844 0.811765
92 NAI 0.418301 0.845238
93 AU1 0.41791 0.831325
94 AP2 0.416667 0.843373
95 A12 0.416667 0.843373
96 25A 0.415493 0.851852
97 AMP MG 0.415385 0.785714
98 COD 0.415094 0.842697
99 ADP BEF 0.414815 0.77907
100 BEF ADP 0.414815 0.77907
101 4TC 0.412903 0.879518
102 APC 0.411765 0.843373
103 NB8 0.410959 0.835294
104 ME8 0.410959 0.806818
105 1ZZ 0.410959 0.806818
106 4UW 0.409091 0.825581
107 NAX 0.409091 0.837209
108 RBY 0.408759 0.843373
109 ADV 0.408759 0.843373
110 ADP MG 0.407407 0.797619
111 P1H 0.405882 0.818182
112 OOB 0.405594 0.864198
113 A A 0.40411 0.829268
114 LAD 0.40411 0.825581
115 UPA 0.403846 0.86747
116 4UU 0.401316 0.833333
117 A3D 0.401235 0.876543
118 DLL 0.4 0.864198
119 XAH 0.4 0.806818
Ligand no: 2; Ligand: NAD; Similar ligands found: 220
No: Ligand ECFP6 Tc MDL keys Tc
1 A3D 0.872727 0.986111
2 NAD IBO 0.845455 0.933333
3 NHD 0.821429 0.972222
4 NAP 0.811966 0.986111
5 NAJ PYZ 0.803419 0.910256
6 NFD 0.791304 0.946667
7 NXX 0.765766 0.972603
8 DND 0.765766 0.972603
9 ZID 0.737705 0.986111
10 NAQ 0.729508 0.934211
11 NAE 0.721311 0.959459
12 NA0 0.712 0.972603
13 TAP 0.704 0.921053
14 AMP NAD 0.696 0.945946
15 NDE 0.689922 0.972603
16 NAJ 0.683333 0.972222
17 NDC 0.679389 0.934211
18 NDO 0.674603 0.958904
19 N01 0.656 0.972222
20 CNA 0.642276 0.972603
21 NBP 0.621212 0.922078
22 NAD BBN 0.609929 0.876543
23 8ID 0.609756 0.922078
24 NAD CJ3 0.601399 0.845238
25 ADP MG 0.579439 0.918919
26 A2D 0.576923 0.958333
27 ADP 0.575472 0.931507
28 NGD 0.574803 0.922078
29 BEF ADP 0.574074 0.894737
30 ADP BEF 0.574074 0.894737
31 BA3 0.566038 0.958333
32 NAD NDT 0.565789 0.755319
33 M33 0.564815 0.918919
34 ADP PO3 0.563636 0.957747
35 B4P 0.560748 0.958333
36 AP5 0.560748 0.958333
37 ATP MG 0.558559 0.918919
38 AN2 0.555556 0.918919
39 GAP 0.553571 0.932432
40 OOB 0.551724 0.972222
41 CA0 0.550459 0.932432
42 ATP 0.545455 0.931507
43 ACP 0.545455 0.906667
44 NAD TDB 0.544872 0.70297
45 ADP ALF 0.54386 0.883117
46 ALF ADP 0.54386 0.883117
47 5FA 0.540541 0.931507
48 AQP 0.540541 0.931507
49 APR 0.540541 0.931507
50 AR6 0.540541 0.931507
51 ANP MG 0.53913 0.907895
52 VO4 ADP 0.53913 0.945205
53 ADP VO4 0.53913 0.945205
54 AGS 0.535714 0.883117
55 SAP 0.535714 0.883117
56 AD9 0.535714 0.906667
57 WAQ 0.533333 0.896104
58 ABM 0.53271 0.905405
59 00A 0.529412 0.921053
60 DLL 0.529412 0.972222
61 ANP 0.526316 0.906667
62 NJP 0.526316 0.959459
63 ACQ 0.526316 0.906667
64 OAD 0.525 0.932432
65 AMP MG 0.523364 0.905405
66 ADX 0.522523 0.839506
67 5AL 0.521739 0.945205
68 A1R 0.521008 0.871795
69 9SN 0.520325 0.909091
70 AMP 0.518868 0.930556
71 A 0.518868 0.930556
72 50T 0.517857 0.893333
73 ATF 0.517241 0.894737
74 DAL AMP 0.516949 0.945205
75 3OD 0.516393 0.932432
76 1ZZ 0.516393 0.851852
77 SON 0.513514 0.92
78 PRX 0.513274 0.881579
79 SRP 0.512821 0.92
80 ADP BMA 0.512397 0.932432
81 3UK 0.512397 0.958904
82 MYR AMP 0.512195 0.851852
83 NAJ PZO 0.510949 0.909091
84 NMN 0.509434 0.875
85 AMP DBH 0.507937 0.906667
86 A22 0.504202 0.945205
87 FA5 0.504 0.945946
88 ATP A A A 0.504 0.971831
89 TYR AMP 0.5 0.945946
90 8QN 0.5 0.945205
91 NAX 0.496183 0.886076
92 PR8 0.495935 0.8625
93 PAJ 0.495868 0.873418
94 4AD 0.495868 0.933333
95 AMO 0.495868 0.92
96 ADQ 0.495868 0.932432
97 A12 0.495495 0.894737
98 AP2 0.495495 0.894737
99 ALF ADP 3PG 0.492424 0.873418
100 LA8 ALF 3PG 0.492424 0.873418
101 AHZ 0.492308 0.851852
102 YAP 0.492063 0.933333
103 FYA 0.491935 0.918919
104 AHX 0.491803 0.884615
105 4UU 0.488372 0.933333
106 5SV 0.487603 0.8375
107 TAT 0.487179 0.894737
108 APC 0.486957 0.894737
109 SRA 0.486239 0.881579
110 NAI 0.484848 0.921053
111 6V0 0.484848 0.909091
112 GTA 0.484615 0.898734
113 A A 0.483871 0.958333
114 LAD 0.483871 0.873418
115 AU1 0.482456 0.906667
116 TXE 0.481203 0.921053
117 AF3 ADP 3PG 0.481203 0.873418
118 OMR 0.481203 0.841463
119 LAQ 0.480916 0.851852
120 G3A 0.48062 0.909091
121 TXA 0.48 0.92
122 NB8 0.48 0.884615
123 ME8 0.48 0.851852
124 BIS 0.48 0.871795
125 PTJ 0.48 0.884615
126 139 0.477941 0.886076
127 LPA AMP 0.477273 0.851852
128 AR6 AR6 0.476923 0.958333
129 G5P 0.476923 0.909091
130 AFH 0.476923 0.873418
131 25L 0.47619 0.945205
132 25A 0.47541 0.958333
133 DZD 0.47482 0.897436
134 TXD 0.473684 0.921053
135 4UV 0.472868 0.933333
136 TYM 0.470149 0.945946
137 ADV 0.470085 0.894737
138 RBY 0.470085 0.894737
139 ARG AMP 0.469697 0.841463
140 4TA 0.467626 0.864198
141 48N 0.466165 0.884615
142 XAH 0.465116 0.851852
143 4UW 0.462687 0.897436
144 M24 0.461538 0.886076
145 IOT 0.459854 0.821429
146 T5A 0.456522 0.853659
147 EAD 0.455782 0.886076
148 MAP 0.455285 0.883117
149 BT5 0.453901 0.821429
150 A4P 0.452555 0.833333
151 UP5 0.451852 0.933333
152 PAP 0.445378 0.917808
153 AP0 0.445255 0.884615
154 4TC 0.445255 0.909091
155 YLP 0.444444 0.831325
156 P1H 0.443709 0.864198
157 AOC 0.442478 0.810811
158 Z5A 0.439189 0.833333
159 2A5 0.436975 0.857143
160 G A A A 0.43662 0.909091
161 COD 0.43662 0.802326
162 ADJ 0.435714 0.841463
163 YLC 0.434783 0.851852
164 YLB 0.434783 0.831325
165 U A G G 0.433566 0.921053
166 ATR 0.433333 0.90411
167 7MD 0.432836 0.851852
168 G5A 0.429752 0.790698
169 PO4 PO4 A A A A PO4 0.429688 0.943662
170 TAD 0.42963 0.873418
171 5AS 0.42735 0.770115
172 BTX 0.426573 0.831325
173 YLA 0.425532 0.831325
174 DSZ 0.425197 0.790698
175 NCN 0.424779 0.805556
176 UPA 0.42446 0.921053
177 VMS 0.424 0.8
178 54H 0.424 0.8
179 N0B 0.422819 0.853659
180 6AD 0.422764 0.85
181 AYB 0.422535 0.821429
182 7D3 0.422414 0.844156
183 YLY 0.421769 0.821429
184 TSB 0.420635 0.809524
185 ODP 0.41958 0.922078
186 AV2 0.419355 0.855263
187 FB0 0.419355 0.775281
188 A5A 0.419355 0.819277
189 NNR 0.419048 0.739726
190 A A A 0.418605 0.918919
191 LEU LMS 0.418605 0.793103
192 649 0.417266 0.775281
193 NMN AMP PO4 0.416667 0.933333
194 SSA 0.416 0.790698
195 P5A 0.415385 0.755556
196 LSS 0.414062 0.772727
197 A2R 0.412698 0.918919
198 52H 0.412698 0.790698
199 JB6 0.412214 0.896104
200 5N5 0.411215 0.783784
201 YSA 0.410448 0.811765
202 5CA 0.409449 0.790698
203 53H 0.409449 0.790698
204 ITT 0.408333 0.878378
205 7D4 0.408333 0.844156
206 NA7 0.407692 0.894737
207 5CD 0.407407 0.794521
208 0WD 0.406897 0.909091
209 A3P 0.40678 0.930556
210 AVV 0.40625 0.860759
211 RAB 0.40566 0.808219
212 ADN 0.40566 0.808219
213 XYA 0.40566 0.808219
214 FDA 0.405063 0.823529
215 GSU 0.40458 0.790698
216 7MC 0.404255 0.831325
217 NSS 0.403101 0.811765
218 6FA 0.402516 0.853659
219 NVA LMS 0.4 0.793103
220 PPS 0.4 0.817073
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2ED4; Ligand: FAD; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 2ed4.bio1) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2ED4; Ligand: NAD; Similar sites found: 13
This union binding pocket(no: 2) in the query (biounit: 2ed4.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5DP2 NAP 0.02233 0.41734 3.3557
2 3SRV S19 0.01192 0.41362 3.3557
3 2XK9 XK9 0.03332 0.41284 3.3557
4 4OYA 1VE 0.02536 0.43998 4.02685
5 1R37 NAD 0.03755 0.41066 4.02685
6 3L4S 3PG 0.03492 0.41061 4.69799
7 3L4S NAD 0.0334 0.41061 4.69799
8 1VG0 GER 0.01857 0.40206 4.69799
9 1WDK NAD 0.02026 0.41326 5.36913
10 5CEO 50D 0.01757 0.40627 5.36913
11 1Q19 APC 0.02069 0.41015 6.04027
12 12AS AMP 0.03502 0.40652 6.04027
13 3K87 FAD 0.0000007271 0.66492 47.651
Pocket No.: 3; Query (leader) PDB : 2ED4; Ligand: NAD; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 2ed4.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2ED4; Ligand: FAD; Similar sites found: 60
This union binding pocket(no: 4) in the query (biounit: 2ed4.bio1) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5U75 SIA GAL NDG FUC 0.02588 0.41036 None
2 1SQS TLA 0.02978 0.40952 None
3 4QVB F42 0.007284 0.40592 None
4 3GFS FMN 0.02564 0.40028 None
5 1QSC ACE TYR PRO ILE GLN GLU THR 0.006973 0.42024 1.34228
6 2ZL4 ALA ALA ALA ALA 0.02163 0.41813 2.01342
7 1G27 BB1 0.009787 0.40655 2.01342
8 2GMP NAG MAN 0.02945 0.41083 2.38095
9 2GMM MAN MAN 0.0343 0.40827 2.38095
10 2AWN ADP 0.02093 0.42458 2.68456
11 2AJH MET 0.03058 0.40999 2.68456
12 1JJ7 ADP 0.03567 0.40675 2.68456
13 1WOQ BGC 0.02357 0.40575 2.68456
14 2JLD ALA GLY GLY ALA ALA ALA ALA ALA 0.003265 0.46518 3.3557
15 5JH2 A2P 0.01701 0.41698 3.3557
16 4U60 SIA 0.02984 0.41269 3.3557
17 4U60 SIA GAL NGA 0.03459 0.40934 3.3557
18 3I6B KDO 0.03267 0.40624 3.3557
19 5O0X FAD 0.007669 0.43032 4.02685
20 2Z9I GLY ALA THR VAL 0.02092 0.42235 4.02685
21 4DR9 BB2 0.01654 0.40263 4.02685
22 1P77 ATR 0.04019 0.40142 4.02685
23 5KJW 53C 0.04645 0.40132 4.02685
24 3R6K FUC GAL GLA 0.01201 0.43889 4.69799
25 1XPJ TLA 0.001068 0.50123 4.7619
26 3UEC ALA ARG TPO LYS 0.03184 0.41115 4.79452
27 4X1Z FUC GAL NDG 0.02166 0.40428 5.36913
28 3B9Q MLI 0.04994 0.40397 5.36913
29 3HUN ZZ7 0.03495 0.40074 5.36913
30 5EOO CIT 0.02282 0.42318 6.04027
31 4XFR CIT 0.03261 0.40829 6.04027
32 4USS GSH 0.03432 0.4051 6.71141
33 1DNP MHF 0.04429 0.4002 6.71141
34 1A5Z FBP 0.01684 0.42652 8.05369
35 5MUL BDP 0.02193 0.41655 8.05369
36 2BVE PH5 0.01631 0.41184 8.40336
37 3IT7 TLA 0.01927 0.42381 8.72483
38 1G6H ADP 0.02189 0.4196 8.72483
39 5X2N ALA 0.03481 0.40522 8.72483
40 3CV2 COA 0.01776 0.42299 9.39597
41 5IUC SIA GAL A2G 0.02837 0.40546 10.2362
42 1UGX GAL MGC 0.00963 0.42973 10.5263
43 1FLM FMN 0.0126 0.40161 10.6557
44 2WHX ADP 0.02699 0.41288 10.7383
45 1RL4 BRR 0.01733 0.42091 11.4094
46 3I7V B4P 0.003945 0.45667 11.9403
47 2IZ1 ATR 0.02348 0.41467 12.0805
48 3A3B RBF 0.000989 0.48052 12.7517
49 3A3B FMN 0.001116 0.47782 12.7517
50 4C2C ALA ALA ALA 0.02946 0.40176 14.094
51 3BNK FMN 0.00000007364 0.59408 28.1879
52 1EJE FMN 0.000001666 0.5754 32.2148
53 3ZOD HQE 0.00000003674 0.58684 34.2282
54 1USF FMN 0.0000002221 0.56367 38.255
55 1USF NAP 0.0000003256 0.53294 38.255
56 1I0S FMN 0.00000008895 0.54488 40.9396
57 1I0S NAP 0.000000749 0.54333 40.9396
58 1YOA FAD 0.000001076 0.56461 44.2953
59 3CB0 FMN 0.000000001925 0.53035 46.9799
60 3K87 FAD 0.00000001706 0.61597 47.651
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