Receptor
PDB id Resolution Class Description Source Keywords
5JFL 2.3 Å EC: 1.-.-.- CRYSTAL STRUCTURE OF RHODOPSEUDOMONAS PALUSTRIS PROPIONALDEH DEHYDROGENASE WITH BOUND NAD+ RHODOPSEUDOMONAS PALUSTRIS (STRAIN BISORGANISM_TAXID: 316056 ACYLATING ALDEHYDE DEHYDROGENASE PROPIONYLCYSTEINE BACTERIMICROCOMPARTMENTS OXIDOREDUCTASE
Ref.: IN VITRO CHARACTERIZATION AND CONCERTED FUNCTION OF CORE ENZYMES OF A GLYCYL RADICAL ENZYME - ASSOCIATE BACTERIAL MICROCOMPARTMENT. SCI REP V. 7 42757 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAD A:600;
G:600;
D:600;
F:600;
B:600;
H:600;
E:600;
C:600;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
663.425 C21 H27 N7 O14 P2 c1cc(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5JFL 2.3 Å EC: 1.-.-.- CRYSTAL STRUCTURE OF RHODOPSEUDOMONAS PALUSTRIS PROPIONALDEH DEHYDROGENASE WITH BOUND NAD+ RHODOPSEUDOMONAS PALUSTRIS (STRAIN BISORGANISM_TAXID: 316056 ACYLATING ALDEHYDE DEHYDROGENASE PROPIONYLCYSTEINE BACTERIMICROCOMPARTMENTS OXIDOREDUCTASE
Ref.: IN VITRO CHARACTERIZATION AND CONCERTED FUNCTION OF CORE ENZYMES OF A GLYCYL RADICAL ENZYME - ASSOCIATE BACTERIAL MICROCOMPARTMENT. SCI REP V. 7 42757 2017
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 280 families.
1 5JFL - 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 247 families.
1 5JFL - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 177 families.
1 5JFL - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
2 5DBV - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
Polypharmacology
Similar Ligands
Ligand no: 1; 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 : 5JFL; Ligand: NAD; 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: 5jfl.bio2) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5JFL; Ligand: NAD; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5jfl.bio2) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5JFL; Ligand: NAD; Similar sites found: 63
This union binding pocket(no: 3) in the query (biounit: 5jfl.bio2) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WG0 CHD 0.006259 0.44467 None
2 4WCX MET 0.001576 0.47353 1.45833
3 3M89 GSP 0.01147 0.41882 1.87354
4 2F5X ASP 0.03213 0.40786 1.92308
5 2Z4T C5P 0.0158 0.41581 1.94553
6 3R4S SIA 0.02457 0.42523 2.0316
7 1KAE NAD 0.009892 0.42198 2.30415
8 2Y5D NAP 0.00001068 0.50077 2.48092
9 4B4Q A2G GAL NAG FUC GAL GLC 0.0214 0.41731 2.64901
10 1GPM CIT 0.01431 0.42831 2.67176
11 4MGA 27L 0.04998 0.40492 2.7451
12 5KF6 NAD 0.000000009129 0.62038 2.8626
13 3JU6 ANP 0.03327 0.40705 2.97297
14 5OFW 9TW 0.03247 0.40744 3.13901
15 4R84 CSF 0.001026 0.46071 3.18091
16 5N53 8NB 0.03909 0.40378 3.58974
17 4JBL MET 0.02615 0.41265 3.62595
18 1HSR BHO 0.009148 0.43865 4.06977
19 3UYW TAU 0.01067 0.43474 4.20561
20 1PVS 7HP 0.03208 0.40509 4.25532
21 4MRP GSH 0.04423 0.41514 4.58015
22 5KY9 GDP 0.01563 0.40853 5
23 4DSU BZI 0.005236 0.45375 5.29101
24 4RDN 6MD 0.02236 0.41629 5.38922
25 2P0D I3P 0.01761 0.41903 5.42636
26 1WLJ U5P 0.03988 0.40269 5.82011
27 4USI AKG 0.0342 0.40713 5.84416
28 2D3Y DU 0.01681 0.4242 5.93607
29 1EZ0 NAP 0.00005526 0.45917 6.07843
30 4F97 GDP 0.01276 0.42051 6.23742
31 2CJU PHX 0.03288 0.40512 7.07965
32 3NZ1 3NY 0.03752 0.4101 7.66284
33 2XG5 EC2 0.001212 0.48398 8.67052
34 2XG5 EC5 0.001212 0.48398 8.67052
35 1N13 AG2 0.04422 0.40341 8.84956
36 4XFR CIT 0.01565 0.4294 8.8993
37 1I7M CG 0.001098 0.47971 8.95522
38 4NS3 NAD 0.000009421 0.54362 9.73282
39 5TVF CGQ 0.002467 0.45165 11.7647
40 4ZO3 C6L 0.01279 0.41649 12.2449
41 4P8O 883 0.03712 0.40059 12.2995
42 2WME NAP 0.00001146 0.45076 12.6531
43 2WOX NDP 0.00000001563 0.61564 12.6789
44 5F7Y GLC GAL NAG GAL FUC A2G 0.02506 0.40202 13.3333
45 4G05 JZ3 0.01384 0.4239 13.5647
46 4LH0 GLV 0.0000009077 0.4915 14.5038
47 3EFV NAD 0.0000001731 0.56469 15.1515
48 4ZUL UN1 0.000004273 0.50415 15.3996
49 5KY4 GDP 0.03195 0.40027 20
50 5L13 6ZE 0.0000005534 0.43987 21.6634
51 3RHJ NAP 0.00000001448 0.54222 21.7557
52 1O9J NAD 0.0000001074 0.5748 21.9561
53 4I8P NAD 0.00000002692 0.60438 25
54 5UCD NAP 0.0000009481 0.54661 25.7634
55 4A0M NAD 0.00000001721 0.5849 26.2097
56 3IWJ NAD 0.000003295 0.45702 27.833
57 4I3V NAD 0.000000004827 0.60467 29.3033
58 4PZ2 NAD 0.00000003437 0.57345 29.3893
59 2QE0 NAP 0.0000000411 0.50842 30.1527
60 1T90 NAD 0.00000003537 0.59549 31.1069
61 3JZ4 NAP 0.000001379 0.5402 31.1069
62 3IWK NAD 0.000004872 0.54452 33.7786
63 2IMP NAI 0.04078 0.41673 34.1603
Pocket No.: 4; Query (leader) PDB : 5JFL; Ligand: NAD; 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: 5jfl.bio2) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5JFL; Ligand: NAD; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 5jfl.bio1) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 5JFL; Ligand: NAD; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 5jfl.bio1) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 5JFL; Ligand: NAD; Similar sites found: 16
This union binding pocket(no: 7) in the query (biounit: 5jfl.bio1) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1RJW ETF 0.01761 0.42756 2.35988
2 5KOD IAC 0.03227 0.42253 2.48092
3 5KXQ GDP 0.02461 0.40241 2.82486
4 4WOE ADP 0.04143 0.40331 3.43511
5 5FUI APY 0.004387 0.43582 3.78788
6 1I9Z 2IP 0.03797 0.40229 3.81679
7 2X1L ADN 0.01729 0.40641 4.00763
8 2G30 ALA ALA PHE 0.004271 0.42849 4.26357
9 3KP6 SAL 0.04355 0.4142 4.63576
10 3LRE ADP 0.04003 0.40328 4.77099
11 1BW9 PPY 0.00974 0.41844 6.17978
12 1C1X HFA 0.01227 0.41737 6.19718
13 1UPR 4IP 0.03554 0.40712 8.13008
14 1P0Z FLC 0.02192 0.41836 9.92366
15 4HZ0 1AV 0.02139 0.41932 10.7981
16 4O4Z N2O 0.02515 0.40935 22.0779
Pocket No.: 8; Query (leader) PDB : 5JFL; Ligand: NAD; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 5jfl.bio1) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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