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Receptor
PDB id Resolution Class Description Source Keywords
2XNJ 1.9 Å EC: 1.18.1.2 CRYSTAL STRUCTURE OF AN ENGINEERED FERREDOXIN(FLAVODOXIN) NA REDUCTASE (FPR) FROM ESCHERICHIA COLI ESCHERICHIA COLI OXIDOREDUCTASE
Ref.: SWAPPING FAD BINDING MOTIFS BETWEEN PLASTIDIC AND B FERREDOXIN-NADP(H) REDUCTASES. BIOCHEMISTRY V. 50 2111 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FAD A:1257;
B:1257;
Valid;
Valid;
none;
none;
Kd = 1.1 nM
785.55 C27 H33 N9 O15 P2 Cc1cc...
GOL A:1260;
B:1260;
B:1261;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
NA B:1268;
Invalid;
none;
submit data
22.99 Na [Na+]
NAP A:1258;
B:1258;
Valid;
Valid;
none;
none;
Kd = 7.5 uM
743.405 C21 H28 N7 O17 P3 c1cc(...
TRS A:1259;
B:1259;
Invalid;
Invalid;
none;
none;
submit data
122.143 C4 H12 N O3 C(C(C...
ZN A:1261;
A:1262;
A:1263;
A:1264;
A:1265;
A:1266;
B:1262;
B:1263;
B:1264;
B:1265;
B:1266;
B:1267;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2XNJ 1.9 Å EC: 1.18.1.2 CRYSTAL STRUCTURE OF AN ENGINEERED FERREDOXIN(FLAVODOXIN) NA REDUCTASE (FPR) FROM ESCHERICHIA COLI ESCHERICHIA COLI OXIDOREDUCTASE
Ref.: SWAPPING FAD BINDING MOTIFS BETWEEN PLASTIDIC AND B FERREDOXIN-NADP(H) REDUCTASES. BIOCHEMISTRY V. 50 2111 2011
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 25 families.
1 1FDR - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 2XNJ Kd = 1.1 nM FAD C27 H33 N9 O15 P2 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 17 families.
1 1FDR - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 2XNJ Kd = 1.1 nM FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
50% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 187 families.
1 2QDX - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 3CRZ Kd = 24 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
3 4K1X - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
4 2VNK Kd = 222 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
5 2BGJ - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
6 2VNJ Kd = 222 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
7 2VNH Kd = 222 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
8 2VNI Kd = 204 uM A2P C10 H15 N5 O10 P2 c1nc(c2c(n....
9 2BGI - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
10 1FDR - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
11 2XNJ Kd = 1.1 nM FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
12 4B4D - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
13 1A8P - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: FAD; Similar ligands found: 128
No: Ligand ECFP6 Tc MDL keys Tc
1 FAD 1 1
2 FAS 1 1
3 FAY 0.859259 0.9875
4 RFL 0.852941 0.963855
5 6FA 0.794118 0.987654
6 FAE 0.751773 0.987654
7 SFD 0.651007 0.860215
8 FDA 0.641892 0.906977
9 FNK 0.602564 0.876405
10 62F 0.572327 0.939024
11 F2N 0.566265 0.886364
12 FMN 0.543307 0.876543
13 FA9 0.526316 0.939759
14 6YU 0.516304 0.860215
15 P6G FDA 0.511628 0.908046
16 FAD NBT 0.508876 0.83871
17 A2D 0.504065 0.875
18 P5F 0.491329 0.941176
19 FAD CNX 0.488506 0.8125
20 AR6 0.488372 0.851852
21 APR 0.488372 0.851852
22 AGS 0.484615 0.811765
23 SAP 0.484615 0.811765
24 M33 0.484375 0.864198
25 BA3 0.484127 0.875
26 HEJ 0.48062 0.851852
27 ATP 0.48062 0.851852
28 ADP 0.480315 0.851852
29 B4P 0.480315 0.875
30 AP5 0.480315 0.875
31 ANP 0.477273 0.831325
32 AQP 0.476923 0.851852
33 5FA 0.476923 0.851852
34 48N 0.469388 0.902439
35 OAD 0.467626 0.876543
36 9X8 0.467626 0.833333
37 FAD NBA 0.467033 0.793814
38 GTA 0.465753 0.892857
39 AN2 0.465116 0.841463
40 AT4 0.465116 0.821429
41 AD9 0.462121 0.831325
42 3OD 0.460993 0.876543
43 RBF 0.460938 0.790123
44 FB0 0.460606 0.835165
45 139 0.460526 0.858824
46 AP0 0.46 0.835294
47 A22 0.459854 0.864198
48 ACP 0.458015 0.853659
49 8QN 0.456522 0.864198
50 PRX 0.454545 0.831325
51 A3R 0.453237 0.86747
52 A1R 0.453237 0.86747
53 G3A 0.452055 0.902439
54 T5A 0.45098 0.872093
55 G5P 0.44898 0.902439
56 ATF 0.448529 0.821429
57 50T 0.44697 0.819277
58 6YZ 0.445255 0.853659
59 ACQ 0.444444 0.853659
60 CNV FAD 0.443182 0.917647
61 ADQ 0.442857 0.853659
62 PAJ 0.442857 0.847059
63 5AL 0.441176 0.864198
64 ADX 0.439394 0.775281
65 CA0 0.439394 0.853659
66 A4P 0.437909 0.831461
67 25L 0.4375 0.864198
68 P33 FDA 0.436464 0.817204
69 5SV 0.435714 0.793103
70 OMR 0.434211 0.818182
71 TXE 0.434211 0.890244
72 ABM 0.434109 0.829268
73 A 0.433071 0.82716
74 AMP 0.433071 0.82716
75 4AD 0.432624 0.855422
76 ADJ 0.432258 0.818182
77 B5M 0.431507 0.878049
78 B5Y 0.431507 0.878049
79 BIS 0.430556 0.802326
80 SRA 0.429688 0.788235
81 AFH 0.42953 0.825581
82 NXX 0.427632 0.865854
83 DND 0.427632 0.865854
84 UP5 0.427632 0.878049
85 6V0 0.427632 0.857143
86 TXD 0.427632 0.890244
87 DQV 0.426667 0.8875
88 SRP 0.42446 0.843373
89 PR8 0.423611 0.837209
90 T99 0.423358 0.821429
91 TAT 0.423358 0.821429
92 AMO 0.422535 0.865854
93 TXA 0.42069 0.865854
94 FYA 0.42069 0.864198
95 PTJ 0.42069 0.835294
96 CNA 0.420382 0.865854
97 00A 0.41958 0.823529
98 AHX 0.41958 0.835294
99 MAP 0.41844 0.811765
100 NAI 0.418301 0.845238
101 AU1 0.41791 0.831325
102 A12 0.416667 0.843373
103 AP2 0.416667 0.843373
104 25A 0.415493 0.851852
105 9ZA 0.415493 0.845238
106 9ZD 0.415493 0.845238
107 COD 0.415094 0.842697
108 4TC 0.412903 0.879518
109 APC 0.411765 0.843373
110 ME8 0.410959 0.806818
111 1ZZ 0.410959 0.806818
112 NB8 0.410959 0.835294
113 4UW 0.409091 0.825581
114 NAX 0.409091 0.837209
115 F2R 0.408805 0.850575
116 RBY 0.408759 0.843373
117 ADV 0.408759 0.843373
118 P1H 0.405882 0.818182
119 OOB 0.405594 0.864198
120 LAD 0.40411 0.825581
121 A A 0.40411 0.829268
122 UPA 0.403846 0.86747
123 4UU 0.401316 0.833333
124 GA7 0.401316 0.865854
125 A3D 0.401235 0.876543
126 80F 0.401235 0.808989
127 XAH 0.4 0.806818
128 DLL 0.4 0.864198
Ligand no: 2; Ligand: NAP; Similar ligands found: 123
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 NHD 0.68254 0.958904
10 NJP 0.661417 0.972973
11 NFD 0.658915 0.934211
12 NXX 0.619048 0.959459
13 DND 0.619048 0.959459
14 AMP NAD 0.606061 0.958904
15 ZID 0.605839 0.972603
16 NAQ 0.59854 0.922078
17 ATR 0.59292 0.917808
18 NAE 0.591241 0.946667
19 NDE 0.58042 0.986301
20 A22 0.571429 0.958904
21 NAJ 0.567164 0.986111
22 A2R 0.563025 0.932432
23 NDC 0.561644 0.922078
24 NA7 0.552846 0.907895
25 ODP 0.551471 0.935065
26 A2P 0.539823 0.930556
27 8ID 0.537313 0.910256
28 NPW 0.525547 0.8875
29 NZQ 0.521739 0.910256
30 CNA 0.521739 0.959459
31 NDP 0.514493 0.922078
32 PO4 PO4 A A A A PO4 0.503937 0.930556
33 1DG 0.503401 0.922078
34 DG1 0.503401 0.922078
35 TXP 0.5 0.922078
36 NMN AMP PO4 0.492958 0.921053
37 XNP 0.492958 0.875
38 25L 0.492308 0.958904
39 25A 0.492063 0.972222
40 NMN 0.486726 0.888889
41 NGD 0.485714 0.935065
42 9JJ 0.481707 0.8875
43 2AM 0.477876 0.891892
44 ADP 0.458333 0.945205
45 PAP 0.451613 0.931507
46 A2D 0.445378 0.945205
47 AN2 0.442623 0.932432
48 7L1 0.441558 0.777778
49 ADP PO3 0.44 0.944444
50 SAP 0.44 0.896104
51 AGS 0.44 0.896104
52 M33 0.439024 0.906667
53 AR6 AR6 0.438849 0.945205
54 BA3 0.438017 0.945205
55 OAD 0.43609 0.92
56 ADP BMA 0.43609 0.92
57 DQV 0.435714 0.958904
58 HEJ 0.435484 0.945205
59 ATP 0.435484 0.945205
60 OOB 0.435115 0.958904
61 B4P 0.434426 0.945205
62 AP5 0.434426 0.945205
63 GAP 0.433071 0.92
64 0WD 0.432432 0.922078
65 2A5 0.432 0.87013
66 5FA 0.432 0.945205
67 AQP 0.432 0.945205
68 AT4 0.430894 0.907895
69 00A 0.428571 0.909091
70 DAL AMP 0.427481 0.932432
71 CA0 0.427419 0.92
72 ADP ALF 0.426357 0.871795
73 ALF ADP 0.426357 0.871795
74 9X8 0.425373 0.871795
75 ACP 0.424 0.92
76 NAJ PZO 0.423841 0.897436
77 9SN 0.423358 0.897436
78 ADP VO4 0.423077 0.932432
79 VO4 ADP 0.423077 0.932432
80 WAQ 0.422222 0.884615
81 V3L 0.421875 0.945205
82 ACQ 0.421875 0.92
83 ADQ 0.421053 0.92
84 AR6 0.420635 0.918919
85 APR 0.420635 0.918919
86 ATP A A A 0.42029 0.958333
87 CO7 0.419753 0.786517
88 3OD 0.419118 0.92
89 1ZZ 0.419118 0.841463
90 DLL 0.41791 0.958904
91 AD9 0.417323 0.92
92 NAX 0.416667 0.875
93 OVE 0.416667 0.857143
94 MYR AMP 0.416058 0.841463
95 AV2 0.415385 0.868421
96 A3P 0.414634 0.944444
97 NNR 0.414414 0.72973
98 OMR 0.413793 0.831325
99 6YZ 0.412214 0.92
100 ANP 0.410853 0.92
101 A1R 0.410448 0.860759
102 ABM 0.409836 0.893333
103 A 0.408333 0.944444
104 AMP 0.408333 0.944444
105 SON 0.408 0.933333
106 PPS 0.407692 0.829268
107 5AL 0.407692 0.932432
108 NAI 0.406897 0.909091
109 7D3 0.406504 0.857143
110 ADX 0.404762 0.829268
111 ATF 0.40458 0.907895
112 3UK 0.404412 0.945946
113 TYR AMP 0.404255 0.921053
114 AMP DBH 0.404255 0.894737
115 139 0.402685 0.875
116 50T 0.401575 0.906667
117 SRP 0.401515 0.907895
118 A A 0.40146 0.972222
119 B5V 0.40146 0.933333
120 A3R 0.4 0.860759
121 3AM 0.4 0.90411
122 B5M 0.4 0.921053
123 FA5 0.4 0.933333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2XNJ; Ligand: NAP; Similar sites found with APoc: 34
This union binding pocket(no: 1) in the query (biounit: 2xnj.bio2) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 2Z9I GLY ALA THR VAL 1.50376
2 1PCA CIT 1.8797
3 1RJW ETF 3.00752
4 5YS9 FAD 3.00752
5 5ZMY TAR 3.38346
6 5OLK DTP 3.38346
7 5OFW 9TW 4.4843
8 3QFS NAP 4.51128
9 3QFS FAD 4.51128
10 1L5Y BEF 4.51613
11 5N53 8NB 5.12821
12 2WQ4 SFU 5.12821
13 2P39 SCR 5.80645
14 2PEL LBT 5.9322
15 2PEL LAT 5.9322
16 3HY2 ATP 6.36364
17 4LO2 GAL BGC 6.76692
18 2Z4T C5P 7.5188
19 4YRY NAD 8.27068
20 5XHA FRU 8.64662
21 4NMC 2OP 10.9023
22 4NMC FAD 10.9023
23 1LOJ U 13.7931
24 1LOJ URI 13.7931
25 4DQL NAP 16.1654
26 2QTZ NAP 23.3083
27 5FA6 FAD 26.3158
28 5FA6 FMN 26.3158
29 5FA6 NAP 26.3158
30 1TLL NAP 32.3308
31 1F20 NAP 32.3308
32 1QX4 FAD 34.9624
33 3W2E FAD 36.0902
34 3W2E NAD 36.0902
Pocket No.: 2; Query (leader) PDB : 2XNJ; Ligand: FAD; Similar sites found with APoc: 55
This union binding pocket(no: 2) in the query (biounit: 2xnj.bio2) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 3QDV NDG 2.0979
2 3QDX CBS 2.0979
3 3QDY CBS 2.0979
4 3QDW NDG 2.0979
5 2WBV SIA 2.1164
6 1KZL CRM 2.40385
7 4G6I RS3 3.33333
8 1NE7 16G 3.38346
9 3QFS FAD 4.51128
10 3QFS NAP 4.51128
11 5GXU FAD 4.88722
12 4UZI IMD 5.26316
13 1T9M FMN 6.54206
14 5JCA FAD 6.76692
15 3UEC ALA ARG TPO LYS 7.53425
16 1N13 AG2 7.9646
17 4YRY NAD 8.27068
18 4YRY FAD 8.27068
19 4QVB F42 8.84354
20 3I7V B4P 8.95522
21 5O0X FAD 9.02256
22 3FJO FAD 10.989
23 3A3B FMN 11.0526
24 3A3B RBF 11.0526
25 1PVC ILE SER GLU VAL 11.6541
26 4YHB FAD 11.6541
27 6GEH FAD 11.7188
28 4CQK PIO 14.8936
29 4DQL FAD 16.1654
30 4DQL NAP 16.1654
31 5VKM GAL SIA 16.5414
32 1VHZ APR 16.6667
33 4G1V FAD 18.0451
34 2PIA FMN 18.797
35 1EP2 FAD 20.6897
36 2QTZ FAD 23.3083
37 2QTZ NAP 23.3083
38 5YLY FAD 25.5639
39 4U9U FAD 26.3158
40 5FA6 FAD 26.3158
41 5FA6 FMN 26.3158
42 5FA6 NAP 26.3158
43 1DDG FAD 29.3233
44 1TLL FAD 32.3308
45 1F20 FAD 32.3308
46 2CND FAD 32.3308
47 5OGX FAD 33.4586
48 4WQM FAD 34.5865
49 1QX4 FAD 34.9624
50 3W2E FAD 36.0902
51 3W2E NAD 36.0902
52 1KRH FAD 36.8421
53 3OZV ECN 39.8496
54 3OZV FAD 39.8496
55 2EIX FAD 39.9177
Pocket No.: 3; Query (leader) PDB : 2XNJ; Ligand: NAP; Similar sites found with APoc: 78
This union binding pocket(no: 3) in the query (biounit: 2xnj.bio1) has 37 residues
No: Leader PDB Ligand Sequence Similarity
1 1ZEI CRS None
2 4HMX FMN 1.86047
3 4MOB ADP 1.8797
4 3BP1 GUN 1.8797
5 5OKT 9XK 1.8797
6 2WBV SIA 2.1164
7 1KZL CRM 2.40385
8 4NZF ARB 2.63158
9 5WHT SIA 2.89855
10 5WBF LAC 3.00752
11 4KSY 1SY 3.30579
12 4G6I RS3 3.33333
13 1NE7 16G 3.38346
14 1ONI BEZ 3.62319
15 6EBQ FMN 3.75
16 1FQK ALF 3.7594
17 3QPB URA 3.7594
18 3IX1 NFM 3.7594
19 4Z7X 3CX 3.78151
20 4WNP 3RJ 4.51128
21 1O5O U5P 4.52489
22 5BSH PRO 4.88722
23 5GXU FAD 4.88722
24 6EOM ALA LYS 4.88722
25 2Q37 3AL 4.97238
26 3MYZ TFX 5
27 3RK0 AMP 5.06329
28 6MJ7 ARG 5.45455
29 4EZW ASN ARG LEU LEU LEU THR GLY 5.93607
30 4PO2 ASN ARG LEU LEU LEU THR GLY 6.38298
31 1US2 XYP XYP XYP XYP 6.39098
32 1MEX RAC 6.51163
33 1T9M FMN 6.54206
34 5JCA FAD 6.76692
35 2UYP PPI 6.97674
36 2UYN 2KT 6.97674
37 3UEC ALA ARG TPO LYS 7.53425
38 1N13 AG2 7.9646
39 2PS1 ORO 7.9646
40 2QQC AG2 8.03571
41 2QQD AG2 8.03571
42 4YRY FAD 8.27068
43 4QVB F42 8.84354
44 4LO6 SIA GAL 8.94737
45 3I7V B4P 8.95522
46 5O0X FAD 9.02256
47 1KGZ PRP 9.02256
48 5H4S RAM 9.3985
49 2H6T IVA VAL VAL STA ALA STA 9.77444
50 4ONT SIA GAL BGC 10.1504
51 3FJO FAD 10.989
52 3A3B FMN 11.0526
53 3A3B RBF 11.0526
54 1PVC ILE SER GLU VAL 11.6541
55 4YHB FAD 11.6541
56 6GEH FAD 11.7188
57 5Z20 OXM 13.1579
58 5HP8 PYR 14.5161
59 6BJO DUY 15.2
60 4DQL FAD 16.1654
61 5VKM GAL SIA 16.5414
62 4G1V FAD 18.0451
63 2PIA FMN 18.797
64 2NGR AF3 20.4188
65 1EP2 FAD 20.6897
66 2QTZ FAD 23.3083
67 5YLY FAD 25.5639
68 4U9U FAD 26.3158
69 1DDG FAD 29.3233
70 1TLL FAD 32.3308
71 2CND FAD 32.3308
72 1F20 FAD 32.3308
73 5OGX FAD 33.4586
74 4WQM FAD 34.5865
75 1KRH FAD 36.8421
76 3OZV ECN 39.8496
77 3OZV FAD 39.8496
78 2EIX FAD 39.9177
Pocket No.: 4; Query (leader) PDB : 2XNJ; Ligand: FAD; Similar sites found with APoc: 33
This union binding pocket(no: 4) in the query (biounit: 2xnj.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 1ZEI CRS None
2 1G79 FMN 1.37615
3 1G79 PLP 1.37615
4 2OFE NAG 1.40845
5 4HMX FMN 1.86047
6 5WS9 ATP 3.38346
7 2WD7 VGD 3.38346
8 1FEC FAD 3.38346
9 6EBQ FMN 3.75
10 3IX1 NFM 3.7594
11 1BZL FAD 3.7594
12 4Z7X 3CX 3.78151
13 4HMT NNV 4
14 4HMT FMN 4
15 2BVE PH5 4.20168
16 1RL4 BL5 4.25532
17 3ITA AIC 4.51128
18 4XPQ FUL 4.51128
19 3MYZ TFX 5
20 2AJH MET 6.12245
21 4PO2 ASN ARG LEU LEU LEU THR GLY 6.38298
22 3RNM FAD 6.89655
23 4KOT CE3 7.40741
24 4F07 FAD 7.89474
25 2QQC AG2 8.03571
26 2QQD AG2 8.03571
27 4LO6 SIA GAL 8.94737
28 2F5Z FAD 9.375
29 3ZOD HQE 9.94764
30 3ZOD FMN 9.94764
31 4ONT SIA GAL BGC 10.1504
32 6CZ7 MGD 12.0301
33 2HQM FAD 25.5639
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