Receptor
PDB id Resolution Class Description Source Keywords
3KRZ 1.8 Å EC: 1.6.99.1 CRYSTAL STRUCTURE OF THE THERMOSTABLE NADH4-BOUND OLD YELLOW FROM THERMOANAEROBACTER PSEUDETHANOLICUS E39 THERMOANAEROBACTER PSEUDETHANOLICUS ATORGANISM_COMMON: CLOSTRIDIUM THERMOHYDROSULFURICUM HOMOTETRAMER DIMER OF DIMERS TIM BARREL THERMOPHILIC OLDENZYME ENE-REDUCTASE ACTIVITY OXIDOREDUCTASE
Ref.: BIOCATALYSIS WITH THERMOSTABLE ENZYMES: STRUCTURE A PROPERTIES OF A THERMOPHILIC 'ENE'-REDUCTASE RELATE YELLOW ENZYME. CHEMBIOCHEM V. 11 197 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FMN A:401;
B:401;
C:401;
D:401;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
456.344 C17 H21 N4 O9 P Cc1cc...
TXD A:402;
B:402;
C:402;
D:402;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
667.457 C21 H31 N7 O14 P2 c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3KRU 1.6 Å EC: 1.6.99.1 CRYSTAL STRUCTURE OF THE THERMOSTABLE OLD YELLOW ENZYME FROM THERMOANAEROBACTER PSEUDETHANOLICUS E39 THERMOANAEROBACTER PSEUDETHANOLICUS ATORGANISM_COMMON: CLOSTRIDIUM THERMOHYDROSULFURICUM HOMOTETRAMER DIMER OF DIMERS TIM BARREL THERMOPHILIC OLDENZYME ENE-REDUCTASE ACTIVITY OXIDOREDUCTASE
Ref.: BIOCATALYSIS WITH THERMOSTABLE ENZYMES: STRUCTURE A PROPERTIES OF A THERMOPHILIC 'ENE'-REDUCTASE RELATE YELLOW ENZYME. CHEMBIOCHEM V. 11 197 2010
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 3KRZ - TXD C21 H31 N7 O14 P2 c1nc(c2c(n....
2 3KRU - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 3KRZ - TXD C21 H31 N7 O14 P2 c1nc(c2c(n....
2 3KRU - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
50% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2H90 Kd = 5 uM COU C9 H6 O2 c1ccc2c(c1....
2 5CPO - XEN C10 H18 N2 O CCCCN1CCCC....
3 3L5M Kd = 8.4 uM COU C9 H6 O2 c1ccc2c(c1....
4 3N14 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
5 3L67 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
6 3L68 Kd = 69.2 uM COU C9 H6 O2 c1ccc2c(c1....
7 5N6Q - 8OZ C9 H8 O2 C=C(c1cccc....
8 5CPN - 531 C14 H19 N O CC(=O)[C@H....
9 5CPM Kd = 27 uM NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
10 3L65 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
11 2H8X - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
12 3L66 Kd = 20.9 uM COU C9 H6 O2 c1ccc2c(c1....
13 3L5L - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
14 3N19 - FNR C17 H23 N4 O9 P Cc1cc2c(cc....
15 2H8Z Kd = 2.5 uM 8CM C9 H6 O3 c1cc2c(c(c....
16 5CPL Kd < 25 uM 536 C13 H16 N2 O c1ccc(cc1)....
17 5OCS - CIT C6 H8 O7 C(C(=O)O)C....
18 3KRZ - TXD C21 H31 N7 O14 P2 c1nc(c2c(n....
19 3KRU - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
20 3HGJ - HBA C7 H6 O2 c1cc(ccc1C....
21 3HF3 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: FMN; Similar ligands found: 16
No: Ligand ECFP6 Tc MDL keys Tc
1 FMN 1 1
2 RBF 0.75641 0.876712
3 RS3 0.571429 0.831169
4 FAS 0.543307 0.876543
5 FAD 0.543307 0.876543
6 FAE 0.539062 0.865854
7 DAL FAD PER 0.5 0.833333
8 LFN 0.475 0.643836
9 C3F 0.473684 0.74359
10 CF4 0.463918 0.734177
11 FAY 0.446043 0.864198
12 FNR 0.444444 0.909091
13 RFL 0.442857 0.845238
14 4LS 0.411215 0.875
15 1VY 0.406593 0.769231
16 DLZ 0.404494 0.782051
Ligand no: 2; Ligand: TXD; Similar ligands found: 237
No: Ligand ECFP6 Tc MDL keys Tc
1 TXD 1 1
2 TXP 0.796296 0.986842
3 TXE 0.6875 0.973684
4 A2D 0.659574 0.933333
5 6V0 0.649123 0.935897
6 BA3 0.628866 0.933333
7 AP5 0.622449 0.933333
8 B4P 0.622449 0.933333
9 ADJ 0.621849 0.91358
10 NAI 0.62069 0.923077
11 APR 0.613861 0.907895
12 AR6 0.613861 0.907895
13 NAX 0.606838 0.888889
14 ADP 0.606061 0.907895
15 ACP 0.60396 0.884615
16 ATP 0.60396 0.907895
17 AN2 0.6 0.896104
18 AQP 0.598039 0.907895
19 5FA 0.598039 0.907895
20 AP0 0.596639 0.8875
21 ACQ 0.596154 0.884615
22 M33 0.594059 0.896104
23 CA0 0.594059 0.909091
24 AD9 0.592233 0.884615
25 AGS 0.592233 0.8625
26 SAP 0.592233 0.8625
27 A22 0.583333 0.921053
28 3OD 0.580357 0.909091
29 OAD 0.576577 0.909091
30 5AL 0.575472 0.896104
31 A1R 0.572727 0.898734
32 ANP 0.566038 0.884615
33 SRP 0.564815 0.873418
34 ADX 0.563107 0.821429
35 A 0.561224 0.881579
36 AMP 0.561224 0.881579
37 ADQ 0.558559 0.909091
38 4AD 0.558559 0.886076
39 50T 0.557692 0.871795
40 4TC 0.557377 0.911392
41 ATF 0.555556 0.873418
42 UP5 0.553719 0.935065
43 APC 0.552381 0.873418
44 PRX 0.552381 0.860759
45 AMP MG 0.55 0.835443
46 8QN 0.54955 0.896104
47 48N 0.545455 0.864198
48 AMO 0.544643 0.897436
49 PAJ 0.544643 0.853659
50 ABM 0.544554 0.858974
51 PR8 0.54386 0.865854
52 00A 0.539823 0.875
53 AHX 0.539823 0.864198
54 ME8 0.53913 0.833333
55 EAD 0.537313 0.888889
56 OOB 0.535714 0.921053
57 25L 0.534483 0.921053
58 A12 0.533981 0.873418
59 AP2 0.533981 0.873418
60 AFH 0.533333 0.853659
61 LAD 0.530435 0.853659
62 WAQ 0.530435 0.875
63 9SN 0.529915 0.864198
64 DND 0.528455 0.922078
65 NXX 0.528455 0.922078
66 CNA 0.527559 0.922078
67 DLL 0.526316 0.921053
68 PTJ 0.525862 0.841463
69 NB8 0.525862 0.864198
70 BIS 0.525862 0.851852
71 TXA 0.525862 0.897436
72 SRA 0.524752 0.8375
73 TAT 0.522936 0.873418
74 25A 0.522124 0.907895
75 3UK 0.521739 0.909091
76 ADP MG 0.518868 0.848101
77 AU1 0.518868 0.884615
78 ADV 0.518519 0.873418
79 RBY 0.518519 0.873418
80 ADP BEF 0.514019 0.82716
81 BEF ADP 0.514019 0.82716
82 1ZZ 0.512821 0.833333
83 FA5 0.512605 0.897436
84 YAP 0.512605 0.886076
85 G3A 0.512397 0.8875
86 OMR 0.512 0.845238
87 P1H 0.510791 0.86747
88 SON 0.509434 0.873418
89 GAP 0.509091 0.884615
90 5SV 0.508772 0.819277
91 XAH 0.508333 0.833333
92 G5P 0.508197 0.8875
93 T5A 0.507812 0.879518
94 0WD 0.507692 0.911392
95 ADP PO3 0.504587 0.881579
96 GTA 0.504065 0.855422
97 FYA 0.5 0.896104
98 ATP MG 0.5 0.848101
99 LAQ 0.5 0.833333
100 DAL AMP 0.5 0.871795
101 NAJ PZO 0.496241 0.864198
102 COD 0.496183 0.827586
103 NDP 0.496124 0.911392
104 4UU 0.495935 0.910256
105 ADP VO4 0.495575 0.871795
106 VO4 ADP 0.495575 0.871795
107 A4P 0.492188 0.858824
108 4UV 0.491803 0.910256
109 TYM 0.488189 0.897436
110 MAP 0.486957 0.8625
111 ALF ADP 0.486726 0.817073
112 ADP ALF 0.486726 0.817073
113 139 0.484615 0.9125
114 NPW 0.484615 0.878049
115 UPA 0.484375 0.923077
116 YLP 0.484127 0.835294
117 ANP MG 0.482456 0.839506
118 DZD 0.481203 0.948718
119 NZQ 0.480916 0.9
120 4UW 0.480315 0.876543
121 A2R 0.478261 0.896104
122 A3D 0.477612 0.909091
123 IOT 0.476923 0.825581
124 ALF ADP 3PG 0.476562 0.809524
125 LA8 ALF 3PG 0.476562 0.809524
126 NAD 0.473684 0.921053
127 XNP 0.473684 0.865854
128 YLA 0.473282 0.857143
129 YLB 0.472868 0.835294
130 YLC 0.472868 0.855422
131 ADP BMA 0.470588 0.884615
132 AYB 0.469697 0.825581
133 2A5 0.468468 0.860759
134 AF3 ADP 3PG 0.465116 0.809524
135 ATR 0.464286 0.881579
136 ITT 0.463636 0.857143
137 FB0 0.462069 0.820225
138 A5A 0.46087 0.781609
139 7MD 0.460317 0.878049
140 TYR AMP 0.459677 0.873418
141 BT5 0.459259 0.804598
142 MYR AMP 0.459016 0.811765
143 5AS 0.458716 0.775281
144 NA7 0.458333 0.897436
145 AVV 0.457627 0.864198
146 TAD 0.456693 0.853659
147 NJP 0.455224 0.910256
148 A A 0.454545 0.883117
149 AHZ 0.453125 0.790698
150 VMS 0.452991 0.764045
151 54H 0.452991 0.764045
152 PAP 0.451327 0.894737
153 JB6 0.45082 0.875
154 7D4 0.45045 0.825
155 NAQ 0.45 0.864198
156 LPA AMP 0.449612 0.811765
157 TSB 0.449153 0.793103
158 AOC 0.448598 0.815789
159 G5A 0.447368 0.775281
160 N0B 0.446809 0.879518
161 M24 0.446043 0.843373
162 YLY 0.446043 0.825581
163 SSA 0.444444 0.775281
164 62F 0.444444 0.878049
165 AMP DBH 0.444444 0.860759
166 1DG 0.443662 0.911392
167 DG1 0.443662 0.911392
168 NAE 0.442857 0.886076
169 ARG AMP 0.44186 0.802326
170 DSZ 0.441667 0.775281
171 NSS 0.441667 0.775281
172 BTX 0.441176 0.813953
173 4TA 0.441176 0.845238
174 52H 0.440678 0.755556
175 7D3 0.440367 0.825
176 5CD 0.44 0.753247
177 ATP A A A 0.44 0.894737
178 6AD 0.439655 0.831325
179 7MC 0.439394 0.857143
180 XYA 0.438776 0.789474
181 ADN 0.438776 0.789474
182 RAB 0.438776 0.789474
183 53H 0.436975 0.755556
184 5CA 0.436975 0.775281
185 ZID 0.43662 0.909091
186 FDA 0.436242 0.870588
187 FNK 0.435065 0.840909
188 NAD IBO 0.433824 0.8625
189 ODP 0.433824 0.9
190 6FA 0.433333 0.879518
191 MTA 0.432692 0.746835
192 P5A 0.430894 0.76087
193 NMN AMP PO4 0.430657 0.886076
194 5N5 0.43 0.789474
195 LSS 0.429752 0.73913
196 NDE 0.428571 0.897436
197 FAD 0.427632 0.890244
198 FAS 0.427632 0.890244
199 SFD 0.427632 0.768421
200 EP4 0.427184 0.75
201 AR6 AR6 0.426357 0.883117
202 NVA LMS 0.42623 0.73913
203 A4D 0.425743 0.766234
204 A2P 0.423423 0.868421
205 A3P 0.423423 0.881579
206 DTA 0.423077 0.759494
207 NDC 0.422819 0.8875
208 LEU LMS 0.422764 0.73913
209 5X8 0.421053 0.759494
210 NAJ PYZ 0.41958 0.843373
211 KAA 0.419355 0.75
212 GSU 0.419355 0.755556
213 3AT 0.418803 0.883117
214 DTP 0.418803 0.848101
215 PPS 0.415254 0.8
216 7D5 0.415094 0.8
217 ARU 0.414634 0.831325
218 YSA 0.414062 0.775281
219 FAY 0.414013 0.901235
220 6RE 0.412844 0.714286
221 AV2 0.411765 0.835443
222 RFL 0.411392 0.880952
223 3DH 0.411215 0.746835
224 SAI 0.410256 0.731707
225 M2T 0.409524 0.710843
226 SFG 0.408696 0.725
227 DAT 0.408696 0.848101
228 F2N 0.408537 0.850575
229 3AM 0.407407 0.844156
230 AMP NAD 0.406897 0.873418
231 IMO 0.405405 0.844156
232 J7C 0.405405 0.722892
233 P5F 0.404908 0.860465
234 A U 0.404412 0.886076
235 Z5A 0.40411 0.816092
236 SA8 0.401709 0.72619
237 WSA 0.4 0.784091
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3KRU; Ligand: FMN; 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: 3kru.bio1) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3KRU; Ligand: FMN; Similar sites found: 125
This union binding pocket(no: 2) in the query (biounit: 3kru.bio1) has 33 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1TB3 FMN 0.0000212 0.47101 1.74927
2 2Z9V PXM 0.02528 0.41695 1.74927
3 3TTN SPD 0.03517 0.41015 1.76471
4 1W8S FBP 0.02185 0.40503 1.90114
5 4WZH FMN 0.0001019 0.47526 2.04082
6 1TV5 FMN 0.0001941 0.46022 2.04082
7 1EIX BMQ 0.01665 0.40414 2.04082
8 2JE7 XMM 0.03989 0.40621 2.09205
9 3NZ1 3NY 0.01092 0.44246 2.29885
10 1KBJ FMN 0.000007932 0.52034 2.33236
11 1KBI PYR 0.00001669 0.50279 2.33236
12 2ZRU FMN 0.00002729 0.45421 2.33236
13 2BTM PGA 0.0009437 0.48739 2.38095
14 1F76 FMN 0.00009873 0.47582 2.67857
15 2YPI PGA 0.001018 0.48007 2.83401
16 2B1Q TRE 0.04854 0.40155 2.86885
17 5TCI MLI 0.00399 0.46182 2.91545
18 1DQX BMP 0.01013 0.40479 2.99625
19 5CSS G3P 0.01369 0.42681 3.09735
20 4BI7 PGA 0.001035 0.4853 3.11284
21 2GNM MAN 0.02566 0.41569 3.1746
22 4YMZ 13P 0.001147 0.48298 3.18725
23 4ORM FMN 0.001005 0.445 3.207
24 4ORM ORO 0.001005 0.445 3.207
25 4ORM 2V6 0.001005 0.445 3.207
26 5EYW PGA 0.001713 0.47391 3.21285
27 4UTU LRY 0.0003162 0.49447 3.49345
28 4UTW RFW 0.0004449 0.48221 3.49345
29 4XP7 FNR 0.00000006017 0.64891 3.49854
30 2RDT FMN 0.00003518 0.49404 3.49854
31 2RDT 2RD 0.00007496 0.4622 3.49854
32 4H0I MMA 0.01831 0.41848 3.58566
33 1SW0 PGA 0.001081 0.4735 3.62903
34 1M5W DXP 0.04916 0.40125 3.7037
35 1OFD AKG 0.00008228 0.45236 3.79009
36 1OFD FMN 0.00008342 0.44284 3.79009
37 4Q4K FMN 0.00005711 0.43928 3.79009
38 4CCK OGA 0.01524 0.4267 3.79009
39 3GLC R5P 0.01867 0.41194 3.79009
40 4NKT 2KH 0.0109 0.41979 3.81232
41 2F6U CIT 0.002264 0.47313 3.84615
42 2Z6I FMN 0.0001806 0.4771 3.91566
43 3OVR 5SP 0.001523 0.43734 3.94737
44 4EWN 0VR 0.00295 0.44319 3.95257
45 1I1E DM2 0.0311 0.41208 4.08163
46 4HKP 16B 0.004662 0.42633 4.16667
47 4HKP TKW 0.005849 0.4122 4.16667
48 3B0P FMN 0.000000000573 0.76171 4.37318
49 2GPT SKM 0.03427 0.4098 4.37318
50 2WZ5 MET 0.0141 0.41328 4.57516
51 4IXH IMP 0.006597 0.40705 4.66472
52 4BXF AKG 0.04752 0.40191 4.66472
53 2QCD U5P 0.002043 0.4389 5
54 2Z6J FMN 0.000271 0.44767 5.12048
55 4I9A NCN 0.003511 0.43568 5.20833
56 1L6O SER LEU LYS LEU MET THR THR VAL 0.02255 0.40108 5.26316
57 4DSU BZI 0.02128 0.4249 5.29101
58 3QMN A3P 0.005484 0.4543 5.42636
59 3EXS 5RP 0.00005342 0.54508 5.42986
60 1DBT U5P 0.007193 0.41774 5.43933
61 2FLI DX5 0.0009455 0.44995 5.45455
62 1P4C FMN 0.0001402 0.45203 5.53936
63 1QDS PGA 0.0006996 0.48835 5.57769
64 3VKC FPQ 0.003783 0.42358 5.59441
65 4C1K PEP 0.02168 0.42055 5.72519
66 3VKX T3 0.02371 0.41429 5.74713
67 2GJN FMN 0.0005645 0.44503 5.79268
68 2GJN NIS 0.0007864 0.43281 5.79268
69 3BW2 FMN 0.00007731 0.46514 5.8309
70 1AL8 FMN 0.00001057 0.5249 5.84958
71 1AL8 DHP 0.0001135 0.45882 5.84958
72 2BVE PH5 0.04427 0.41034 5.88235
73 3W9Z FMN 0.0000003311 0.61521 5.90062
74 1Q6O LG6 0.000876 0.46824 6.01852
75 5LUB 3Y7 0.04914 0.40101 6.10687
76 3AQT RCO 0.02961 0.41429 6.12245
77 4JEJ 1GP 0.001111 0.47292 6.14754
78 3QH2 3NM 0.001362 0.48492 6.33484
79 4QEK GLC 0.002979 0.43954 6.64452
80 3B9O FMN 0.017 0.40372 6.99708
81 4N02 FNR 0.00006739 0.43194 7.0028
82 1QPR PPC 0.003679 0.4241 7.04225
83 2NLI FMN 0.00002454 0.50949 7.28863
84 2NLI LAC 0.0000789 0.47204 7.28863
85 1OX5 1PR 0.002218 0.41511 7.28863
86 1RZM PEP 0.02192 0.42029 7.39645
87 1GTE FMN 0.00008587 0.44681 7.58017
88 1GTE IUR 0.00008587 0.44681 7.58017
89 2DKD NG1 0.009017 0.4363 7.87172
90 1MZV AMP 0.02036 0.4138 8.08511
91 1OVD ORO 0.0001248 0.43381 8.36013
92 1OVD FMN 0.0001248 0.43381 8.36013
93 3C3N FMN 0.0003323 0.42082 8.65385
94 1EP2 FMN 0.00002955 0.48878 8.68167
95 1EP2 ORO 0.00005312 0.45399 8.68167
96 3MJY FMN 0.0001189 0.45148 9.0379
97 3MJY IJZ 0.0001189 0.45148 9.0379
98 2B4G FMN 0.0001462 0.46513 9.46372
99 5EXK MET 0.04219 0.40588 9.91254
100 1VHN FMN 0.00000872 0.57735 10.6918
101 1FTH A3P 0.02085 0.42147 12.2951
102 3AXK NDP 0.008456 0.42144 12.4031
103 1YFS ALA 0.033 0.40455 12.828
104 1VKF CIT 0.007103 0.4427 13.2979
105 1U29 I3P 0.04373 0.40403 13.9535
106 3CTL S6P 0.002854 0.43241 17.316
107 1TRD PGH 0.001177 0.47167 17.6
108 4NAE 1GP 0.0005937 0.51115 30.837
109 4M5P FMN 0.000000004733 0.68189 33.5277
110 4TMC FMN 0.00000001307 0.65487 33.5277
111 4TMC HBA 0.000000008019 0.64912 33.5277
112 4M5P 23W 0.0009061 0.51179 33.5277
113 4JIQ FMN 0.000000004922 0.65073 35.277
114 4JIQ 1L5 0.000000004922 0.65073 35.277
115 4QNW FMN 0.000000000483 0.72526 38.1924
116 1PS9 FMN 0.0000002841 0.4945 44.0233
117 1DJN FMN 0.0000004744 0.58172 45.1895
118 2GOU FMN 0.00000001566 0.58514 45.7726
119 4A3U FMN 0.000000003408 0.54365 46.6472
120 1ICP FMN 0.0000000002661 0.67967 47.8134
121 2Q3O FMN 0.000000007929 0.66418 47.8134
122 2Q3R FMN 0.000000001513 0.54934 47.8134
123 2HSA FMN 0.00000001199 0.61581 48.105
124 2R14 FMN 0.000000006494 0.63902 48.9796
125 2R14 TXD 0.0000000328 0.58772 48.9796
Pocket No.: 3; Query (leader) PDB : 3KRU; Ligand: FMN; 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: 3kru.bio1) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3KRU; Ligand: FMN; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 3kru.bio1) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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