Receptor
PDB id Resolution Class Description Source Keywords
3PFD 2.1 Å EC: 1.3.99.3 CRYSTAL STRUCTURE OF AN ACYL-COA DEHYDROGENASE FROM MYCOBACT THERMORESISTIBILE BOUND TO REDUCED FLAVIN ADENINE DINUCLEOTB Y COMBINED IODIDE ION SAD MR MYCOBACTERIUM THERMORESISTIBILE STRUCTURAL GENOMICS SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE SSGCID DEHYDROGENASE DE NOVO PHASE DETERMINATION IODIDE ION SAD ACYL COA DEHYDROGENASE REDUFLAVIN ADENINE DINUCLEOTIDE FAD FATTY ACID METABOLISM OXIDOREDUCTASE
Ref.: SAD PHASING USING IODIDE IONS IN A HIGH-THROUGHPUT STRUCTURAL GENOMICS ENVIRONMENT. J.STRUCT.FUNCT.GENOM. V. 12 83 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FDA A:390;
B:390;
C:390;
D:390;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
787.566 C27 H35 N9 O15 P2 Cc1cc...
IOD A:391;
A:392;
A:393;
A:394;
A:395;
A:396;
A:397;
A:398;
A:399;
A:400;
A:401;
A:402;
A:403;
A:404;
A:405;
A:406;
A:407;
A:408;
A:409;
A:410;
A:411;
A:412;
A:413;
A:414;
A:415;
A:416;
A:417;
A:418;
A:419;
A:420;
A:421;
B:391;
B:392;
B:393;
B:394;
B:395;
B:396;
B:397;
B:398;
B:399;
B:400;
B:401;
B:402;
B:403;
B:404;
B:405;
B:406;
B:407;
B:408;
B:409;
B:410;
B:411;
B:412;
B:413;
B:414;
B:415;
B:416;
B:417;
B:418;
C:391;
C:392;
C:393;
C:394;
C:395;
C:396;
C:397;
C:398;
C:399;
C:400;
C:401;
C:402;
C:403;
C:404;
C:405;
C:406;
C:407;
C:408;
C:409;
C:410;
C:411;
C:412;
D:391;
D:392;
D:393;
D:394;
D:395;
D:396;
D:397;
D:398;
D:399;
D:400;
D:401;
D:402;
D:403;
D:404;
D:405;
D:406;
D:407;
D:408;
D:409;
D:410;
D:411;
D:412;
D:413;
D:414;
D:415;
D:416;
D:417;
D:418;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
126.904 I [I-]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3PFD 2.1 Å EC: 1.3.99.3 CRYSTAL STRUCTURE OF AN ACYL-COA DEHYDROGENASE FROM MYCOBACT THERMORESISTIBILE BOUND TO REDUCED FLAVIN ADENINE DINUCLEOTB Y COMBINED IODIDE ION SAD MR MYCOBACTERIUM THERMORESISTIBILE STRUCTURAL GENOMICS SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE SSGCID DEHYDROGENASE DE NOVO PHASE DETERMINATION IODIDE ION SAD ACYL COA DEHYDROGENASE REDUFLAVIN ADENINE DINUCLEOTIDE FAD FATTY ACID METABOLISM OXIDOREDUCTASE
Ref.: SAD PHASING USING IODIDE IONS IN A HIGH-THROUGHPUT STRUCTURAL GENOMICS ENVIRONMENT. J.STRUCT.FUNCT.GENOM. V. 12 83 2011
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3PFD - FDA C27 H35 N9 O15 P2 Cc1cc2c(cc....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3PFD - FDA C27 H35 N9 O15 P2 Cc1cc2c(cc....
50% Homology Family (18)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1UDY - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 3MDE - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
3 3MDD - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
4 4L1F - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
5 2R0N - TGC C25 H40 N7 O19 P3 S2 CC(C)(CO[P....
6 1SIQ - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
7 5AHS - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
8 5AF7 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
9 1EGD - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
10 3PFD - FDA C27 H35 N9 O15 P2 Cc1cc2c(cc....
11 3GQT - UFO C11 H17 N3 CN1CCN(c2c....
12 3GNC - QQQ C10 H12 N2 O3 S CC(C)n1c2c....
13 1JQI - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
14 1BUC - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
15 1UKW - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
16 3MPJ - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
17 3MPI - GRA C26 H42 N7 O19 P3 S CC(C)(CO[P....
18 1RX0 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: FDA; Similar ligands found: 132
No: Ligand ECFP6 Tc MDL keys Tc
1 FDA 1 1
2 FNK 0.691781 0.965517
3 F2N 0.647436 0.976744
4 FAD 0.641892 0.906977
5 FAS 0.641892 0.906977
6 SFD 0.630872 0.787879
7 6FA 0.61745 0.896552
8 6YU 0.586207 0.903226
9 RFL 0.585987 0.876405
10 FAD NBT 0.584906 0.902174
11 FAY 0.579618 0.895349
12 CNV FAD 0.578616 0.954023
13 62F 0.573248 0.895349
14 FA9 0.554217 0.918605
15 FAD CNX 0.551515 0.873684
16 FAD NBA 0.549708 0.882979
17 P5F 0.545455 0.920455
18 FNR 0.532258 0.892857
19 A2D 0.516667 0.833333
20 APR 0.5 0.811765
21 AR6 0.5 0.811765
22 M33 0.496 0.823529
23 BA3 0.495935 0.833333
24 P6G FDA 0.494186 0.827957
25 DAL FAD PER 0.494118 0.865169
26 B4P 0.491935 0.833333
27 AP5 0.491935 0.833333
28 ANP 0.488372 0.813953
29 SAP 0.484375 0.795455
30 AGS 0.484375 0.795455
31 ATP 0.480315 0.833333
32 ADP 0.48 0.833333
33 48N 0.479167 0.818182
34 FB0 0.478261 0.819149
35 5FA 0.476562 0.833333
36 AQP 0.476562 0.833333
37 AN2 0.47619 0.823529
38 GTA 0.475524 0.831461
39 AD9 0.472868 0.813953
40 3OD 0.471014 0.835294
41 FAE 0.46988 0.896552
42 ATF 0.469697 0.804598
43 AP0 0.469388 0.860465
44 ACP 0.46875 0.835294
45 OAD 0.467153 0.835294
46 A1R 0.463235 0.827586
47 PAJ 0.463235 0.808989
48 G3A 0.461538 0.83908
49 T5A 0.46 0.896552
50 A22 0.459259 0.845238
51 G5P 0.458333 0.83908
52 ACQ 0.454545 0.835294
53 PRX 0.453846 0.793103
54 5AL 0.451128 0.823529
55 CA0 0.449612 0.813953
56 ADX 0.449612 0.741935
57 50T 0.446154 0.802326
58 8QN 0.445255 0.823529
59 ABM 0.444444 0.790698
60 A 0.443548 0.809524
61 AMP 0.443548 0.809524
62 OMR 0.442953 0.782609
63 TXE 0.442953 0.892857
64 ADQ 0.442029 0.813953
65 AMO 0.442029 0.825581
66 139 0.440789 0.862069
67 ADJ 0.440789 0.822222
68 ME8 0.439716 0.771739
69 BIS 0.439716 0.786517
70 TXA 0.439716 0.825581
71 PTJ 0.439716 0.818182
72 AFH 0.438356 0.788889
73 A4P 0.437086 0.876405
74 TXD 0.436242 0.870588
75 UP5 0.436242 0.880952
76 NXX 0.436242 0.825581
77 6V0 0.436242 0.882353
78 DND 0.436242 0.825581
79 5SV 0.434783 0.758242
80 SRP 0.433824 0.804598
81 4AD 0.431655 0.816092
82 P1H 0.430303 0.842697
83 FYA 0.429577 0.823529
84 AHX 0.428571 0.797753
85 SRA 0.428571 0.772727
86 P33 FDA 0.427778 0.821053
87 MAP 0.427536 0.795455
88 AU1 0.427481 0.813953
89 NAI 0.426667 0.870588
90 25L 0.426573 0.845238
91 A12 0.426357 0.825581
92 AP2 0.426357 0.825581
93 AMP MG 0.425197 0.75
94 EAD 0.423313 0.862069
95 COD 0.423077 0.806452
96 PR8 0.422535 0.8
97 TAT 0.422222 0.804598
98 4TC 0.421053 0.882353
99 APC 0.421053 0.825581
100 NB8 0.41958 0.797753
101 1ZZ 0.41958 0.771739
102 4UU 0.418919 0.837209
103 00A 0.41844 0.786517
104 RBY 0.41791 0.804598
105 ADV 0.41791 0.804598
106 A3D 0.417722 0.835294
107 NAX 0.417219 0.862069
108 ADP MG 0.416667 0.761364
109 25A 0.414286 0.833333
110 OOB 0.414286 0.823529
111 ADP BEF 0.413534 0.744444
112 BEF ADP 0.413534 0.744444
113 ANP MG 0.413043 0.755556
114 LAD 0.412587 0.788889
115 UPA 0.411765 0.870588
116 CNA 0.410256 0.825581
117 DLL 0.408451 0.823529
118 XAH 0.408163 0.771739
119 4UW 0.407895 0.829545
120 ADP PO3 0.407407 0.788235
121 3UK 0.405594 0.835294
122 4UV 0.405405 0.837209
123 TYM 0.405229 0.825581
124 NAD 0.405063 0.823529
125 ATP MG 0.404412 0.761364
126 9SN 0.40411 0.797753
127 ADP VO4 0.402878 0.781609
128 VO4 ADP 0.402878 0.781609
129 WAQ 0.402778 0.806818
130 FA5 0.401361 0.825581
131 YAP 0.401361 0.816092
132 YLP 0.401316 0.793478
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3PFD; Ligand: FDA; Similar sites found: 33
This union binding pocket(no: 1) in the query (biounit: 3pfd.bio1) has 39 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3TW1 AHN 0.03747 0.41489 2.1097
2 3VV5 SLZ 0.02198 0.41831 2.30769
3 5EYW PGA 0.03951 0.40854 2.81124
4 2UVO NAG 0.04181 0.41975 2.92398
5 2UVO NDG 0.04311 0.41819 2.92398
6 2YJP CYS 0.04512 0.40909 3.09278
7 1PA9 CSN 0.03112 0.40355 3.16901
8 5IDB BMA 0.01965 0.42817 3.52113
9 5IDB MAN 0.01965 0.42817 3.52113
10 1B74 DGN 0.02638 0.41532 3.93701
11 4MG8 27J 0.006571 0.43723 4.31373
12 1NSA BEN 0.02142 0.41538 4.83461
13 1GPM AMP 0.04628 0.41072 4.83461
14 1QH5 GSH 0.04847 0.40477 5
15 3UUA 0CZ 0.01286 0.42274 5.17928
16 3UU7 2OH 0.03362 0.41628 5.17928
17 3IP8 B85 0.0316 0.41004 5.24194
18 1GQ2 OXL 0.03103 0.41935 5.85242
19 3ALG NAG NAG NAG NAG 0.03592 0.40042 7.36544
20 4IBF 1D5 0.03543 0.40072 9.30233
21 1U8V FAD 0.00000004354 0.58444 10.687
22 1UO5 PIH 0.02678 0.41232 14.7059
23 2DDH HXD 0.000008504 0.42202 31.2977
24 3DJL FAD 0.0000008426 0.50928 35.369
25 1W07 FAD 0.0000000002808 0.64776 37.1501
26 4XVX P6G FDA 0.0000005191 0.50389 39.3316
27 4XVX P33 FDA 0.000003176 0.48124 39.3316
28 4X28 FDA 0.00000000002138 0.63567 41.4758
29 2C0U FAD NBT 0.0000003621 0.52617 43.5115
30 3MKH FAD 0.0000002243 0.54898 44.7837
31 1R2J FAD 0.000000000291 0.78946 45.6284
32 3D9F N6C 0.0000002285 0.48222 46.3104
33 3D9F FAD 0.0000002285 0.48222 46.3104
Pocket No.: 2; Query (leader) PDB : 3PFD; Ligand: FDA; 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: 3pfd.bio1) has 39 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3PFD; Ligand: FDA; 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: 3pfd.bio1) has 38 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3PFD; Ligand: FDA; 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: 3pfd.bio1) has 38 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 3PFD; Ligand: FDA; Similar sites found: 11
This union binding pocket(no: 5) in the query (biounit: 3pfd.bio5) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1YXM ADE 0.02181 0.40603 1.9802
2 2F5X ASP 0.03044 0.40096 3.52564
3 4CFT H4B 0.02182 0.4106 3.56234
4 1ICV NIO 0.0253 0.41064 4.60829
5 3HQ9 OXL 0.02181 0.4108 4.63768
6 5O4F 8VE 0.02184 0.40273 6.20155
7 5MR6 FAD 0.0008238 0.43809 6.36132
8 3UDG TMP 0.03271 0.40763 7.97342
9 2ZFZ ARG 0.04882 0.41099 8.86076
10 2DDH FAD 0.00006647 0.50196 31.2977
11 4KCF FMN 0.00007151 0.45947 37.659
Pocket No.: 6; Query (leader) PDB : 3PFD; Ligand: FDA; Similar sites found: 2
This union binding pocket(no: 6) in the query (biounit: 3pfd.bio3) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4CU1 H4B 0.02621 0.40277 3.56234
2 5HCY 60D 0.006209 0.42706 3.92749
Pocket No.: 7; Query (leader) PDB : 3PFD; Ligand: FDA; Similar sites found: 2
This union binding pocket(no: 7) in the query (biounit: 3pfd.bio4) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2WQ4 SFU 0.007539 0.41707 3.84615
2 3WMX THR 0.03083 0.40279 5.58659
Pocket No.: 8; Query (leader) PDB : 3PFD; Ligand: FDA; 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: 3pfd.bio2) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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