-->
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 6 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: 15
No: Ligand ECFP6 Tc MDL keys Tc
1 FMN 1 1
2 RBF 0.75641 0.876712
3 RS3 0.571429 0.831169
4 FAD 0.543307 0.876543
5 FAS 0.543307 0.876543
6 FAE 0.539062 0.865854
7 LFN 0.475 0.643836
8 C3F 0.473684 0.74359
9 CF4 0.463918 0.734177
10 FAY 0.446043 0.864198
11 FNR 0.444444 0.909091
12 RFL 0.442857 0.845238
13 4LS 0.411215 0.875
14 1VY 0.406593 0.769231
15 DLZ 0.404494 0.782051
Ligand no: 2; Ligand: TXD; Similar ligands found: 250
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 B4P 0.622449 0.933333
8 AP5 0.622449 0.933333
9 ADJ 0.621849 0.91358
10 NAI 0.62069 0.923077
11 AR6 0.613861 0.907895
12 APR 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 HEJ 0.60396 0.907895
18 AT4 0.6 0.873418
19 AN2 0.6 0.896104
20 AQP 0.598039 0.907895
21 5FA 0.598039 0.907895
22 AP0 0.596639 0.8875
23 ACQ 0.596154 0.884615
24 M33 0.594059 0.896104
25 CA0 0.594059 0.909091
26 AD9 0.592233 0.884615
27 SAP 0.592233 0.8625
28 AGS 0.592233 0.8625
29 A3R 0.587156 0.898734
30 A22 0.583333 0.921053
31 3OD 0.580357 0.909091
32 6YZ 0.579439 0.884615
33 OAD 0.576577 0.909091
34 5AL 0.575472 0.896104
35 A1R 0.572727 0.898734
36 80F 0.571429 0.857143
37 ANP 0.566038 0.884615
38 SRP 0.564815 0.873418
39 ADX 0.563107 0.821429
40 9X8 0.5625 0.8625
41 AMP 0.561224 0.881579
42 A 0.561224 0.881579
43 ADQ 0.558559 0.909091
44 4AD 0.558559 0.886076
45 50T 0.557692 0.871795
46 4TC 0.557377 0.911392
47 ATF 0.555556 0.873418
48 UP5 0.553719 0.935065
49 PRX 0.552381 0.860759
50 APC 0.552381 0.873418
51 8QN 0.54955 0.896104
52 48N 0.545455 0.864198
53 PAJ 0.544643 0.853659
54 AMO 0.544643 0.897436
55 ABM 0.544554 0.858974
56 PR8 0.54386 0.865854
57 AHX 0.539823 0.864198
58 00A 0.539823 0.875
59 ME8 0.53913 0.833333
60 EAD 0.537313 0.888889
61 OOB 0.535714 0.921053
62 25L 0.534483 0.921053
63 A12 0.533981 0.873418
64 AP2 0.533981 0.873418
65 AFH 0.533333 0.853659
66 LAD 0.530435 0.853659
67 WAQ 0.530435 0.875
68 9SN 0.529915 0.864198
69 DQV 0.528926 0.946667
70 DND 0.528455 0.922078
71 NXX 0.528455 0.922078
72 CNA 0.527559 0.922078
73 DLL 0.526316 0.921053
74 NB8 0.525862 0.864198
75 BIS 0.525862 0.851852
76 TXA 0.525862 0.897436
77 PTJ 0.525862 0.841463
78 B5M 0.525424 0.886076
79 SRA 0.524752 0.8375
80 TAT 0.522936 0.873418
81 T99 0.522936 0.873418
82 25A 0.522124 0.907895
83 3UK 0.521739 0.909091
84 AU1 0.518868 0.884615
85 RBY 0.518519 0.873418
86 ADV 0.518519 0.873418
87 B5V 0.517241 0.897436
88 DAL AMP 0.513274 0.871795
89 1ZZ 0.512821 0.833333
90 FA5 0.512605 0.897436
91 YAP 0.512605 0.886076
92 G3A 0.512397 0.8875
93 OMR 0.512 0.845238
94 F2R 0.511628 0.835294
95 P1H 0.510791 0.86747
96 SON 0.509434 0.873418
97 GAP 0.509091 0.884615
98 9ZD 0.508772 0.851852
99 5SV 0.508772 0.819277
100 9ZA 0.508772 0.851852
101 XAH 0.508333 0.833333
102 G5P 0.508197 0.8875
103 T5A 0.507812 0.879518
104 0WD 0.507692 0.911392
105 ADP PO3 0.504587 0.881579
106 GTA 0.504065 0.855422
107 LAQ 0.5 0.833333
108 B5Y 0.5 0.886076
109 FYA 0.5 0.896104
110 NAJ PZO 0.496241 0.864198
111 COD 0.496183 0.827586
112 NDP 0.496124 0.911392
113 4UU 0.495935 0.910256
114 VO4 ADP 0.495575 0.871795
115 ADP VO4 0.495575 0.871795
116 A4P 0.492188 0.858824
117 4UV 0.491803 0.910256
118 TYM 0.488189 0.897436
119 MAP 0.486957 0.8625
120 ADP ALF 0.486726 0.817073
121 ALF ADP 0.486726 0.817073
122 LMS 0.485437 0.77907
123 NPW 0.484615 0.878049
124 139 0.484615 0.9125
125 UPA 0.484375 0.923077
126 YLP 0.484127 0.835294
127 GA7 0.483871 0.873418
128 NAJ PYZ 0.481752 0.823529
129 DZD 0.481203 0.948718
130 NZQ 0.480916 0.9
131 4UW 0.480315 0.876543
132 A2R 0.478261 0.896104
133 A3D 0.477612 0.909091
134 IOT 0.476923 0.825581
135 NAD 0.473684 0.921053
136 XNP 0.473684 0.865854
137 YLA 0.473282 0.857143
138 YLC 0.472868 0.855422
139 YLB 0.472868 0.835294
140 ADP BMA 0.470588 0.884615
141 AYB 0.469697 0.825581
142 2A5 0.468468 0.860759
143 TYR AMP 0.467742 0.8625
144 AF3 ADP 3PG 0.465116 0.809524
145 ATR 0.464286 0.881579
146 ITT 0.463636 0.857143
147 FB0 0.462069 0.820225
148 A5A 0.46087 0.781609
149 ARG AMP 0.460317 0.802326
150 7MD 0.460317 0.878049
151 HFD 0.460177 0.8625
152 BT5 0.459259 0.804598
153 MYR AMP 0.459016 0.811765
154 5AS 0.458716 0.775281
155 NA7 0.458333 0.897436
156 AVV 0.457627 0.864198
157 TAD 0.456693 0.853659
158 NJP 0.455224 0.910256
159 A A 0.454545 0.883117
160 AHZ 0.453125 0.790698
161 54H 0.452991 0.764045
162 VMS 0.452991 0.764045
163 PAP 0.451327 0.894737
164 JB6 0.45082 0.875
165 7D4 0.45045 0.825
166 NAQ 0.45 0.864198
167 LPA AMP 0.449612 0.811765
168 TSB 0.449153 0.793103
169 AOC 0.448598 0.815789
170 G5A 0.447368 0.775281
171 N0B 0.446809 0.879518
172 M24 0.446043 0.843373
173 YLY 0.446043 0.825581
174 SSA 0.444444 0.775281
175 AMP DBH 0.444444 0.860759
176 62F 0.444444 0.878049
177 1DG 0.443662 0.911392
178 DG1 0.443662 0.911392
179 NAE 0.442857 0.886076
180 NSS 0.441667 0.775281
181 DSZ 0.441667 0.775281
182 BTX 0.441176 0.813953
183 4TA 0.441176 0.845238
184 52H 0.440678 0.755556
185 7D3 0.440367 0.825
186 5CD 0.44 0.753247
187 ATP A A A 0.44 0.894737
188 6AD 0.439655 0.831325
189 7MC 0.439394 0.857143
190 9K8 0.439024 0.712766
191 RAB 0.438776 0.789474
192 ADN 0.438776 0.789474
193 XYA 0.438776 0.789474
194 NVA LMS 0.438017 0.731183
195 53H 0.436975 0.755556
196 8X1 0.436975 0.75
197 5CA 0.436975 0.775281
198 ZID 0.43662 0.909091
199 FDA 0.436242 0.870588
200 FNK 0.435065 0.840909
201 LEU LMS 0.434426 0.731183
202 ODP 0.433824 0.9
203 6FA 0.433333 0.879518
204 MTA 0.432692 0.746835
205 P5A 0.430894 0.76087
206 AMP NAD 0.430657 0.896104
207 NMN AMP PO4 0.430657 0.886076
208 5N5 0.43 0.789474
209 LSS 0.429752 0.73913
210 NDE 0.428571 0.897436
211 FAS 0.427632 0.890244
212 FAD 0.427632 0.890244
213 SFD 0.427632 0.768421
214 EP4 0.427184 0.75
215 AR6 AR6 0.426357 0.883117
216 A4D 0.425743 0.766234
217 A2P 0.423423 0.868421
218 A3P 0.423423 0.881579
219 DTA 0.423077 0.759494
220 NDC 0.422819 0.8875
221 U A 0.421429 0.898734
222 5X8 0.421053 0.759494
223 GSU 0.419355 0.755556
224 KAA 0.419355 0.75
225 3AT 0.418803 0.883117
226 DTP 0.418803 0.848101
227 PPS 0.415254 0.8
228 7D5 0.415094 0.8
229 ARU 0.414634 0.831325
230 YSA 0.414062 0.775281
231 FAY 0.414013 0.901235
232 6RE 0.412844 0.714286
233 AV2 0.411765 0.835443
234 RFL 0.411392 0.880952
235 3DH 0.411215 0.746835
236 SAI 0.410256 0.731707
237 M2T 0.409524 0.710843
238 SFG 0.408696 0.725
239 DAT 0.408696 0.848101
240 F2N 0.408537 0.850575
241 3AM 0.407407 0.844156
242 8PZ 0.40625 0.795455
243 J7C 0.405405 0.722892
244 IMO 0.405405 0.844156
245 P5F 0.404908 0.860465
246 A U 0.404412 0.886076
247 Z5A 0.40411 0.816092
248 SA8 0.401709 0.72619
249 9JJ 0.401235 0.855422
250 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 with APoc: 164
This union binding pocket(no: 1) in the query (biounit: 3kru.bio1) has 33 residues
No: Leader PDB Ligand Sequence Similarity
1 2ZFZ ARG None
2 1TB3 FMN 1.74927
3 2Z9V PXM 1.74927
4 3TTN SPD 1.76471
5 3K8D CTP 1.89394
6 1W8S FBP 1.90114
7 1TV5 FMN 2.04082
8 4WZH FMN 2.04082
9 1EIX BMQ 2.04082
10 2JE7 XMM 2.09205
11 3NZ1 3NY 2.29885
12 1KBI FMN 2.33236
13 1KBI PYR 2.33236
14 1KBJ FMN 2.33236
15 2ZRU FMN 2.33236
16 3OIX FMN 2.33236
17 2BTM PGA 2.38095
18 6BKA FMN 2.62391
19 1FDJ 13P 2.62391
20 1FDJ 2FP 2.62391
21 3KP6 SAL 2.64901
22 1F76 FMN 2.67857
23 2YPI PGA 2.83401
24 2B1Q TRE 2.86885
25 5TCI MLI 2.91545
26 1DQX BMP 2.99625
27 5CSS G3P 3.09735
28 4BI7 PGA 3.11284
29 2GNM MAN 3.1746
30 4YMZ 13P 3.18725
31 4CW5 FMN 3.207
32 4ORM ORO 3.207
33 4ORM 2V6 3.207
34 4ORM FMN 3.207
35 5EYW PGA 3.21285
36 6FK6 DOK 3.36391
37 3TAO PGH 3.37079
38 4UTU LRY 3.49345
39 4UTW RFW 3.49345
40 2RDT FMN 3.49854
41 4XP7 FNR 3.49854
42 2RDT 2RD 3.49854
43 4IGH 1EA 3.49854
44 4IGH FMN 3.49854
45 4IGH ORO 3.49854
46 4H0I MMA 3.58566
47 1SW0 PGA 3.62903
48 1LYX PGA 3.62903
49 1M5W DXP 3.7037
50 1OFD AKG 3.79009
51 1OFD FMN 3.79009
52 4Q4K FMN 3.79009
53 4CCK OGA 3.79009
54 3GLC R5P 3.79009
55 4NKT 2KH 3.81232
56 2F6U CIT 3.84615
57 2Z6I FMN 3.91566
58 3OVR 5SP 3.94737
59 4EWN 0VR 3.95257
60 1I1E DM2 4.08163
61 4HKP 16B 4.16667
62 4HKP TKW 4.16667
63 3B0P FMN 4.37318
64 2GPT SKM 4.37318
65 4IXH IMP 4.66472
66 4BXF AKG 4.66472
67 5M0T AKG 4.7619
68 6DVH FMN 4.95627
69 2QCD U5P 5
70 2Z6J FMN 5.12048
71 4I9A NCN 5.20833
72 1L6O SER LEU LYS LEU MET THR THR VAL 5.26316
73 5OCG 9R5 5.29101
74 3QMN A3P 5.42636
75 3EXS 5RP 5.42986
76 1DBT U5P 5.43933
77 2FLI DX5 5.45455
78 1P4C FMN 5.53936
79 6BFG FMN 5.53936
80 2WQ4 SFU 5.53936
81 2YKX AKG 5.53936
82 5AHM IMP 5.53936
83 1QDS PGA 5.57769
84 3VKC FPQ 5.59441
85 4C1K PEP 5.72519
86 3VKX T3 5.74713
87 2GJN NIS 5.79268
88 2GJN FMN 5.79268
89 3BW2 FMN 5.8309
90 1AL8 FMN 5.84958
91 1AL8 DHP 5.84958
92 2BVE PH5 5.88235
93 3W9Z FMN 5.90062
94 1Q6O LG6 6.01852
95 5LUB 3Y7 6.10687
96 3AQT RCO 6.12245
97 4JEJ 1GP 6.14754
98 3QH2 3NM 6.33484
99 6FA4 D1W 6.35838
100 3UWV 2PG 6.51341
101 4QEK GLC 6.64452
102 5YJS SAL 6.99708
103 3B9O FMN 6.99708
104 4N02 FNR 7.0028
105 1QPR PPC 7.04225
106 2NLI LAC 7.28863
107 2NLI FMN 7.28863
108 1OX5 1PR 7.28863
109 1RZM PEP 7.39645
110 1GTE FMN 7.58017
111 1GTE IUR 7.58017
112 5N9Z CAP 7.58017
113 2HK1 FUD 7.76699
114 2DKD NG1 7.87172
115 1MZV AMP 8.08511
116 1OVD ORO 8.36013
117 1OVD FMN 8.36013
118 3C3N FMN 8.65385
119 1EP2 ORO 8.68167
120 1EP2 FMN 8.68167
121 3GD8 GOL 8.96861
122 6BVE PGA 8.97959
123 5XFV FMN 8.98204
124 3MJY IJZ 9.0379
125 3MJY FMN 9.0379
126 5EXK MET 9.91254
127 4TVD BGC 10.2041
128 1VHN FMN 10.6918
129 5GVH FMN 10.828
130 4G6I RS3 11.9048
131 5AHN IMP 11.9534
132 1FTH A3P 12.2951
133 3AXK NDP 12.4031
134 1YFS ALA 12.828
135 1VKF CIT 13.2979
136 1U29 I3P 13.9535
137 4AF0 IMP 14.8688
138 2GBB CIT 15.3846
139 1UUO BRF 16.035
140 1UUO ORO 16.035
141 1UUO FMN 16.035
142 3CTL S6P 17.316
143 1TRD PGH 17.6
144 3FYP PEP 27.5
145 4NAE 1GP 30.837
146 4TMC HBA 33.5277
147 4M5P FMN 33.5277
148 4TMC FMN 33.5277
149 4M5P 23W 33.5277
150 4M5P MLA 33.5277
151 4JIQ FMN 35.277
152 4JIQ 1L5 35.277
153 4QNW FMN 38.1924
154 1PS9 FMN 44.0233
155 1DJN FMN 45.1895
156 2GOU FMN 45.7726
157 4A3U FMN 46.6472
158 4A3U NCA 46.6472
159 1ICP FMN 47.8134
160 2Q3R FMN 47.8134
161 2Q3O FMN 47.8134
162 2HSA FMN 48.105
163 2R14 FMN 48.9796
164 2R14 TXD 48.9796
Pocket No.: 2; Query (leader) PDB : 3KRU; Ligand: FMN; Similar sites found with APoc: 14
This union binding pocket(no: 2) in the query (biounit: 3kru.bio1) has 30 residues
No: Leader PDB Ligand Sequence Similarity
1 1WUW TSU None
2 1R6W 164 1.86335
3 3BMO AX4 2.08333
4 5A5W GUO 3.16206
5 1OFZ FUL 3.20513
6 2JLD ALA GLY GLY ALA ALA ALA ALA ALA 3.79009
7 5J5R 6G1 3.85604
8 5J5R IMP 3.85604
9 4OKD GLC GLC GLC 4.95627
10 3HCH RSM 5.47945
11 3S6X SIA GAL BGC 5.84615
12 3HP8 SUC 6.36364
13 2OEM 1AE 8.45481
14 3GE7 AFQ 11.3703
Pocket No.: 3; Query (leader) PDB : 3KRU; Ligand: FMN; Similar sites found with APoc: 23
This union binding pocket(no: 3) in the query (biounit: 3kru.bio1) has 30 residues
No: Leader PDB Ligand Sequence Similarity
1 1O68 KIV 1.09091
2 4XMF HSM 2.17391
3 2VL1 GLY GLY 2.33236
4 4UBS DIF 2.33236
5 5U75 SIA GAL NDG FUC 2.38095
6 5JIB OIA 2.67062
7 5A1S FLC 2.91545
8 1TD2 PXL 3.13589
9 1DRJ RIP 3.69004
10 4CCO OGA 3.79009
11 2FVK DUC 3.79009
12 1Y0Y L2O VAL VAL ASP 4.95627
13 3U6W KIV 5.24781
14 1BTN I3P 6.60377
15 2JIG PD2 6.69643
16 1F6D UDP 6.70554
17 5GZZ GSH 7.28863
18 2IOY RIP 8.12721
19 2Y6P CTP 9.82906
20 6FIV 3TL 11.5044
21 1M3U KPL 11.7424
22 2Y88 2ER 11.8852
23 4YGM URA 25
Pocket No.: 4; Query (leader) PDB : 3KRU; Ligand: FMN; Similar sites found with APoc: 7
This union binding pocket(no: 4) in the query (biounit: 3kru.bio1) has 30 residues
No: Leader PDB Ligand Sequence Similarity
1 5GQX GLC GLC GLC GLC 2.04082
2 4F9U PBD 4.16667
3 2AWN ADP 5.51181
4 1TZJ A3B 5.91716
5 3BPX SAL 6.08108
6 2W5P CL8 6.71141
7 3TFC PEP 7.28863
APoc FAQ
Feedback