Receptor
PDB id Resolution Class Description Source Keywords
5MIR 2 Å EC: 1.8.1.9 CRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS THIOREDOXIN REDUCTAS TO VISIBLE LIGHT (120 MIN) LACTOCOCCUS LACTIS SUBSP. CREMORIS THIOREDOXIN REDUCTASE PHOTOSENSITIVITY REACTIVE OXYGEN SPESI-FACE OPEN SPACE OXYGEN POCKET FAD-NADP+ COMPLEX FO-FRCONFORMATIONS OXIDOREDUCTASE
Ref.: THE STRUCTURE OF LACTOCOCCUS LACTIS THIOREDOXIN RED REVEALS MOLECULAR FEATURES OF PHOTO-OXIDATIVE DAMAG SCI REP V. 7 46282 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PEG A:403;
A:404;
Invalid;
Invalid;
none;
none;
submit data
106.12 C4 H10 O3 C(COC...
SO4 A:405;
A:406;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
FAD A:401;
Valid;
none;
submit data
785.55 C27 H33 N9 O15 P2 Cc1cc...
NAP A:402;
Valid;
none;
submit data
743.405 C21 H28 N7 O17 P3 c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5MIT 1.8 Å EC: 1.8.1.9 CRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS THIOREDOXIN REDUCTAS TO VISIBLE LIGHT (240 MIN) LACTOCOCCUS LACTIS SUBSP. CREMORIS THIOREDOXIN REDUCTASE PHOTOSENSITIVITY REACTIVE OXYGEN SPESI-FACE OPEN SPACE OXYGEN POCKET FAD-NADP+ COMPLEX FO-FRCONFORMATIONS OXIDOREDUCTASE
Ref.: THE STRUCTURE OF LACTOCOCCUS LACTIS THIOREDOXIN RED REVEALS MOLECULAR FEATURES OF PHOTO-OXIDATIVE DAMAG SCI REP V. 7 46282 2017
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 5MIR - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 5MH4 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
3 5MIQ - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
4 5MIP - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
5 5MIT - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
6 5MJK - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
7 5MIS - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 5MIR - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 5MH4 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
3 5MIQ - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
4 5MIP - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
5 5MIT - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
6 5MJK - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
7 5MIS - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
50% Homology Family (23)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5MIR - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 5MH4 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
3 5MIQ - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
4 5MIP - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
5 5MIT - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
6 5MJK - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
7 5MIS - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
8 1FL2 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
9 3CTY - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
10 2Q0K - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
11 2Q0L - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
12 5J60 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
13 2Q7V - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
14 3ITJ - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
15 1VDC - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
16 3F8R - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
17 3F8P - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
18 3F8D - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
19 4UP3 - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
20 1TDF - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
21 1CL0 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
22 1TRB - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
23 1TDE - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
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: NAP; Similar ligands found: 127
No: Ligand ECFP6 Tc MDL keys Tc
1 NAP 1 1
2 NA0 0.881356 0.986301
3 TAP 0.872881 0.934211
4 NDO 0.840336 0.972603
5 NAD 0.811966 0.986111
6 N01 0.733871 0.958904
7 A3D 0.712 0.972603
8 NBP 0.707692 0.935065
9 NAD IBO 0.688 0.921053
10 NHD 0.68254 0.958904
11 NJP 0.661417 0.972973
12 NAJ PYZ 0.659091 0.898734
13 NFD 0.658915 0.934211
14 DND 0.619048 0.959459
15 NXX 0.619048 0.959459
16 ZID 0.605839 0.972603
17 NAQ 0.59854 0.922078
18 ATR 0.59292 0.917808
19 NAE 0.591241 0.946667
20 NDE 0.58042 0.986301
21 A22 0.571429 0.958904
22 AMP NAD 0.571429 0.933333
23 NAJ 0.567164 0.986111
24 A2R 0.563025 0.932432
25 NDC 0.561644 0.922078
26 NA7 0.552846 0.907895
27 ODP 0.551471 0.935065
28 A2P 0.539823 0.930556
29 8ID 0.537313 0.910256
30 NAD BBN 0.525974 0.865854
31 NPW 0.525547 0.8875
32 CNA 0.521739 0.959459
33 NZQ 0.521739 0.910256
34 NAD CJ3 0.519231 0.835294
35 NDP 0.514493 0.922078
36 PO4 PO4 A A A A PO4 0.503937 0.930556
37 DG1 0.503401 0.922078
38 1DG 0.503401 0.922078
39 NAD TDB 0.5 0.696078
40 TXP 0.5 0.922078
41 NMN AMP PO4 0.492958 0.921053
42 XNP 0.492958 0.875
43 25L 0.492308 0.958904
44 25A 0.492063 0.972222
45 NAD NDT 0.490909 0.747368
46 NMN 0.486726 0.888889
47 NGD 0.485714 0.935065
48 2AM 0.477876 0.891892
49 ADP 0.458333 0.945205
50 PAP 0.451613 0.931507
51 ADP MG 0.45082 0.906667
52 BEF ADP 0.447154 0.883117
53 ADP BEF 0.447154 0.883117
54 A2D 0.445378 0.945205
55 AN2 0.442623 0.932432
56 ADP PO3 0.44 0.944444
57 SAP 0.44 0.896104
58 AGS 0.44 0.896104
59 M33 0.439024 0.906667
60 AR6 AR6 0.438849 0.945205
61 BA3 0.438017 0.945205
62 ATP MG 0.436508 0.906667
63 ADP BMA 0.43609 0.92
64 OAD 0.43609 0.92
65 ATP 0.435484 0.945205
66 OOB 0.435115 0.958904
67 B4P 0.434426 0.945205
68 AP5 0.434426 0.945205
69 GAP 0.433071 0.92
70 0WD 0.432432 0.922078
71 5FA 0.432 0.945205
72 2A5 0.432 0.87013
73 AQP 0.432 0.945205
74 00A 0.428571 0.909091
75 CA0 0.427419 0.92
76 ALF ADP 0.426357 0.871795
77 ADP ALF 0.426357 0.871795
78 ACP 0.424 0.92
79 NAJ PZO 0.423841 0.897436
80 9SN 0.423358 0.897436
81 VO4 ADP 0.423077 0.932432
82 ANP MG 0.423077 0.896104
83 ADP VO4 0.423077 0.932432
84 WAQ 0.422222 0.884615
85 ACQ 0.421875 0.92
86 V3L 0.421875 0.945205
87 ADQ 0.421053 0.92
88 AR6 0.420635 0.918919
89 APR 0.420635 0.918919
90 ATP A A A 0.42029 0.958333
91 CO7 0.419753 0.786517
92 1ZZ 0.419118 0.841463
93 3OD 0.419118 0.92
94 DLL 0.41791 0.958904
95 AD9 0.417323 0.92
96 NAX 0.416667 0.875
97 OVE 0.416667 0.857143
98 MYR AMP 0.416058 0.841463
99 AV2 0.415385 0.868421
100 A3P 0.414634 0.944444
101 NNR 0.414414 0.72973
102 ALF ADP 3PG 0.413793 0.8625
103 OMR 0.413793 0.831325
104 LA8 ALF 3PG 0.413793 0.8625
105 ANP 0.410853 0.92
106 A1R 0.410448 0.860759
107 ABM 0.409836 0.893333
108 AMP 0.408333 0.944444
109 A 0.408333 0.944444
110 SON 0.408 0.933333
111 PPS 0.407692 0.829268
112 5AL 0.407692 0.932432
113 TYR AMP 0.407143 0.933333
114 NAI 0.406897 0.909091
115 7D3 0.406504 0.857143
116 DAL AMP 0.406015 0.932432
117 ADX 0.404762 0.829268
118 ATF 0.40458 0.907895
119 3UK 0.404412 0.945946
120 AMP DBH 0.404255 0.894737
121 139 0.402685 0.875
122 AMP MG 0.401639 0.893333
123 50T 0.401575 0.906667
124 SRP 0.401515 0.907895
125 A A 0.40146 0.972222
126 FA5 0.4 0.933333
127 3AM 0.4 0.90411
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5MIT; Ligand: NAP; 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: 5mit.bio1) has 110 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5MIT; Ligand: FAD; 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: 5mit.bio1) has 110 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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