Receptor
PDB id Resolution Class Description Source Keywords
5vw2 1.45 Å EC: 1.18.1.2 NADPH SOAK OF Y316S MUTANT OF CORN ROOT FERREDOXIN:NADP+ RED ZEA MAYS FLAVOENZYME HYDRIDE TRANSFER PHOTOSYNTHESIS ACTIVE SITE COMPRESSION TRANSFERASE OXIDOREDUCTASE
Ref.: HIGH-RESOLUTION STUDIES OF HYDRIDE TRANSFER IN THE FERREDOXIN:NADP(+) REDUCTASE SUPERFAMILY. FEBS J. V. 284 3302 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:401;
Invalid;
none;
submit data
24.305 Mg [Mg+2...
ACT A:402;
Invalid;
none;
submit data
59.044 C2 H3 O2 CC(=O...
NAP A:404;
Valid;
Atoms found MORE than expected: % Diff = 2;
Kd < 0.02 uM
743.405 C21 H28 N7 O17 P3 c1cc(...
FDA A:403;
Valid;
none;
submit data
787.566 C27 H35 N9 O15 P2 Cc1cc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5VW2 1.45 Å EC: 1.18.1.2 NADPH SOAK OF Y316S MUTANT OF CORN ROOT FERREDOXIN:NADP+ RED ZEA MAYS FLAVOENZYME HYDRIDE TRANSFER PHOTOSYNTHESIS ACTIVE SITE COMPRESSION TRANSFERASE OXIDOREDUCTASE
Ref.: HIGH-RESOLUTION STUDIES OF HYDRIDE TRANSFER IN THE FERREDOXIN:NADP(+) REDUCTASE SUPERFAMILY. FEBS J. V. 284 3302 2017
Members (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 24 families.
1 1JB9 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 5VW9 - NCA C6 H6 N2 O c1cc(cnc1)....
3 5VW8 Kd < 0.02 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
4 5H59 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
5 5VW3 Kd < 0.02 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
6 5VW6 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
7 3LO8 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
8 5VWA - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
9 3LVB - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
10 5VW4 - NCA C6 H6 N2 O c1cc(cnc1)....
11 5VW7 - FDA C27 H35 N9 O15 P2 Cc1cc2c(cc....
12 5VWB - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
13 5VW2 Kd < 0.02 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
14 5VW5 - NCA C6 H6 N2 O c1cc(cnc1)....
70% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 15 families.
1 1JB9 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 5VW9 - NCA C6 H6 N2 O c1cc(cnc1)....
3 5VW8 Kd < 0.02 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
4 5H59 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
5 5VW3 Kd < 0.02 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
6 5VW6 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
7 3LO8 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
8 5VWA - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
9 3LVB - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
10 5VW4 - NCA C6 H6 N2 O c1cc(cnc1)....
11 5VW7 - FDA C27 H35 N9 O15 P2 Cc1cc2c(cc....
12 5VWB - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
13 5VW2 Kd < 0.02 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
14 5VW5 - NCA C6 H6 N2 O c1cc(cnc1)....
50% Homology Family (60)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 1JB9 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 5VW9 - NCA C6 H6 N2 O c1cc(cnc1)....
3 5VW8 Kd < 0.02 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
4 5H59 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
5 5VW3 Kd < 0.02 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
6 5VW6 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
7 3LO8 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
8 5VWA - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
9 3LVB - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
10 5VW4 - NCA C6 H6 N2 O c1cc(cnc1)....
11 5VW7 - FDA C27 H35 N9 O15 P2 Cc1cc2c(cc....
12 5VWB - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
13 5VW2 Kd < 0.02 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
14 5VW5 - NCA C6 H6 N2 O c1cc(cnc1)....
15 2RC5 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
16 1QFZ - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
17 1QFY Kd < 0.2 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
18 1QGA Kd = 5.5 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
19 1QG0 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
20 1E63 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
21 1H42 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
22 1E62 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
23 1H85 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
24 2X3U - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
25 1B2R - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
26 1GO2 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
27 1QUE - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
28 4C43 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
29 1E64 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
30 3ZC3 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
31 1GR1 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
32 1QGY - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
33 1QGZ - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
34 3ZBT - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
35 2BSA Kd < 0.01 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
36 1W34 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
37 2VZL Kd = 550 uM NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
38 1QH0 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
39 1BQE - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
40 1OGJ - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
41 1BJK - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
42 1OGI - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
43 1W35 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
44 4BPR - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
45 1GJR - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
46 2BMW - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
47 2VYQ - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
48 3ZBU - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
49 1QUF - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
50 1GAW - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
51 1FNB - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
52 1BX1 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
53 1FRN - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
54 1FNC - FDA C27 H35 N9 O15 P2 Cc1cc2c(cc....
55 1FRQ - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
56 1BX0 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
57 1FND - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
58 1SM4 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
59 3VO2 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
60 3VO1 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: NAP; Similar ligands found: 140
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 NAD IBO 0.716667 0.972222
8 NAD TDB 0.716667 0.972222
9 A3D 0.712 0.972603
10 NBP 0.707692 0.935065
11 NHD 0.68254 0.958904
12 NJP 0.661417 0.972973
13 NFD 0.658915 0.934211
14 DND 0.619048 0.959459
15 AMP NAD 0.606061 0.958904
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 NAJ 0.567164 0.986111
23 A2R 0.563025 0.932432
24 NDC 0.561644 0.922078
25 NA7 0.552846 0.907895
26 ODP 0.551471 0.935065
27 A2P 0.539823 0.930556
28 8ID 0.537313 0.910256
29 NAD BBN 0.525974 0.865854
30 NPW 0.525547 0.8875
31 NZQ 0.521739 0.910256
32 CNA 0.521739 0.959459
33 NAD CJ3 0.519231 0.835294
34 NDP 0.514493 0.922078
35 PO4 PO4 A A A A PO4 0.503937 0.930556
36 1DG 0.503401 0.922078
37 DG1 0.503401 0.922078
38 TXP 0.5 0.922078
39 NMN AMP PO4 0.492958 0.921053
40 XNP 0.492958 0.875
41 25L 0.492308 0.958904
42 25A 0.492063 0.972222
43 NAD NDT 0.490909 0.747368
44 NMN 0.486726 0.888889
45 NGD 0.485714 0.935065
46 9JJ 0.481707 0.8875
47 2AM 0.477876 0.891892
48 NDP DTT 0.461538 0.843373
49 ADP 0.458333 0.945205
50 ADP MG 0.454545 0.944444
51 ADP BEF 0.454545 0.944444
52 A7R 0.452555 0.846154
53 PAP 0.451613 0.931507
54 A2D 0.445378 0.945205
55 AN2 0.442623 0.932432
56 7L1 0.441558 0.777778
57 ADP PO3 0.44 0.944444
58 AGS 0.44 0.896104
59 ATP MG 0.44 0.944444
60 M33 0.439024 0.906667
61 AR6 AR6 0.438849 0.945205
62 BA3 0.438017 0.945205
63 VO4 ADP 0.4375 0.945946
64 BEF ADP 0.436508 0.918919
65 OAD 0.43609 0.92
66 ADP BMA 0.43609 0.92
67 DQV 0.435714 0.958904
68 HEJ 0.435484 0.945205
69 ATP 0.435484 0.945205
70 OOB 0.435115 0.958904
71 AP5 0.434426 0.945205
72 B4P 0.434426 0.945205
73 GAP 0.433071 0.92
74 0WD 0.432432 0.922078
75 5FA 0.432 0.945205
76 2A5 0.432 0.87013
77 AQP 0.432 0.945205
78 AT4 0.430894 0.907895
79 HQG 0.430769 0.932432
80 00A 0.428571 0.909091
81 8LQ 0.427481 0.907895
82 DAL AMP 0.427481 0.932432
83 CA0 0.427419 0.92
84 ANP MG 0.426357 0.932432
85 ALF ADP 0.426357 0.871795
86 9X8 0.425373 0.871795
87 KG4 0.424 0.92
88 ACP 0.424 0.92
89 NAJ PZO 0.423841 0.897436
90 9SN 0.423358 0.897436
91 WAQ 0.422222 0.884615
92 ACQ 0.421875 0.92
93 V3L 0.421875 0.945205
94 ADQ 0.421053 0.92
95 AR6 0.420635 0.918919
96 APR 0.420635 0.918919
97 ATP A 0.42029 0.958333
98 ATP A A A 0.42029 0.958333
99 CO7 0.419753 0.786517
100 3OD 0.419118 0.92
101 1ZZ 0.419118 0.841463
102 DLL 0.41791 0.958904
103 AD9 0.417323 0.92
104 OVE 0.416667 0.857143
105 NAX 0.416667 0.875
106 QA7 0.416667 0.896104
107 MYR AMP 0.416058 0.841463
108 AV2 0.415385 0.868421
109 A3P 0.414634 0.944444
110 NNR 0.414414 0.72973
111 ALF ADP 3PG 0.413793 0.8625
112 OMR 0.413793 0.831325
113 6YZ 0.412214 0.92
114 ANP 0.410853 0.92
115 A1R 0.410448 0.860759
116 45A 0.409836 0.893333
117 ABM 0.409836 0.893333
118 AMP 0.408333 0.944444
119 A 0.408333 0.944444
120 SON 0.408 0.933333
121 PPS 0.407692 0.829268
122 8LE 0.407692 0.896104
123 5AL 0.407692 0.932432
124 NAI 0.406897 0.909091
125 7D3 0.406504 0.857143
126 AMP MG 0.404959 0.930556
127 ADX 0.404762 0.829268
128 ATF 0.40458 0.907895
129 3UK 0.404412 0.945946
130 AMP DBH 0.404255 0.894737
131 139 0.402685 0.875
132 50T 0.401575 0.906667
133 8LH 0.401515 0.907895
134 SRP 0.401515 0.907895
135 B5V 0.40146 0.933333
136 3AM 0.4 0.90411
137 B5M 0.4 0.921053
138 A3R 0.4 0.860759
139 KMQ 0.4 0.883117
140 FA5 0.4 0.933333
Ligand no: 2; Ligand: FDA; Similar ligands found: 162
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 JNT 0.6 0.835294
9 6YU 0.586207 0.903226
10 RFL 0.585987 0.876405
11 FAD NBT 0.584906 0.902174
12 FAY 0.579618 0.895349
13 CNV FAD 0.578616 0.954023
14 FAJ 0.575758 0.886364
15 62F 0.573248 0.895349
16 DAL FAD PER 0.573171 0.922222
17 FA9 0.554217 0.918605
18 FAD CNX 0.551515 0.873684
19 FAD T2C 0.547619 0.902174
20 P5F 0.545455 0.920455
21 UBG 0.540373 0.918605
22 FNR 0.532258 0.892857
23 FAD NBA 0.526012 0.873684
24 A2D 0.516667 0.833333
25 AR6 0.5 0.811765
26 APR 0.5 0.811765
27 M33 0.496 0.823529
28 BA3 0.495935 0.833333
29 P6G FDA 0.494186 0.827957
30 B4P 0.491935 0.833333
31 AP5 0.491935 0.833333
32 DJC FAD 0.489474 0.912088
33 ANP 0.488372 0.813953
34 AGS 0.484375 0.795455
35 ATP 0.480315 0.833333
36 HEJ 0.480315 0.833333
37 ADP 0.48 0.833333
38 48N 0.479167 0.818182
39 FB0 0.478261 0.819149
40 5FA 0.476562 0.833333
41 AQP 0.476562 0.833333
42 AT4 0.47619 0.804598
43 AN2 0.47619 0.823529
44 GTA 0.475524 0.831461
45 HQG 0.473684 0.823529
46 AD9 0.472868 0.813953
47 3OD 0.471014 0.835294
48 FAE 0.46988 0.896552
49 ATF 0.469697 0.804598
50 AP0 0.469388 0.860465
51 ACP 0.46875 0.835294
52 OAD 0.467153 0.835294
53 9X8 0.467153 0.795455
54 A3R 0.463235 0.827586
55 A1R 0.463235 0.827586
56 PAJ 0.463235 0.808989
57 G3A 0.461538 0.83908
58 T5A 0.46 0.896552
59 A22 0.459259 0.845238
60 8LQ 0.459259 0.825581
61 G5P 0.458333 0.83908
62 6YZ 0.455224 0.835294
63 DQV 0.455172 0.845238
64 ACQ 0.454545 0.835294
65 PRX 0.453846 0.793103
66 5AL 0.451128 0.823529
67 ADX 0.449612 0.741935
68 CA0 0.449612 0.813953
69 QA7 0.448529 0.816092
70 KG4 0.446154 0.813953
71 50T 0.446154 0.802326
72 8QN 0.445255 0.823529
73 45A 0.444444 0.790698
74 8LH 0.444444 0.804598
75 ABM 0.444444 0.790698
76 A 0.443548 0.809524
77 AMP 0.443548 0.809524
78 OMR 0.442953 0.782609
79 TXE 0.442953 0.892857
80 AMO 0.442029 0.825581
81 ADQ 0.442029 0.813953
82 139 0.440789 0.862069
83 ADJ 0.440789 0.822222
84 KMQ 0.440559 0.825581
85 B5M 0.440559 0.837209
86 8LE 0.440298 0.816092
87 PTJ 0.439716 0.818182
88 ME8 0.439716 0.771739
89 BIS 0.439716 0.786517
90 TXA 0.439716 0.825581
91 AFH 0.438356 0.788889
92 A4P 0.437086 0.876405
93 UP5 0.436242 0.880952
94 DND 0.436242 0.825581
95 TXD 0.436242 0.870588
96 6V0 0.436242 0.882353
97 5SV 0.434783 0.758242
98 SRP 0.433824 0.804598
99 4AD 0.431655 0.816092
100 DJ0 FAD 0.430769 0.847826
101 B5Y 0.430556 0.837209
102 P1H 0.430303 0.842697
103 FYA 0.429577 0.823529
104 SRA 0.428571 0.772727
105 AHX 0.428571 0.797753
106 AMP MG 0.428571 0.776471
107 P33 FDA 0.427778 0.821053
108 MAP 0.427536 0.795455
109 AU1 0.427481 0.813953
110 NAI 0.426667 0.870588
111 25L 0.426573 0.845238
112 AP2 0.426357 0.825581
113 A12 0.426357 0.825581
114 OZV 0.42446 0.811765
115 EAD 0.423313 0.862069
116 COD 0.423077 0.806452
117 PR8 0.422535 0.8
118 T99 0.422222 0.804598
119 TAT 0.422222 0.804598
120 APC 0.421053 0.825581
121 4TC 0.421053 0.882353
122 ADP MG 0.419847 0.788235
123 ADP BEF 0.419847 0.788235
124 1ZZ 0.41958 0.771739
125 NB8 0.41958 0.797753
126 GA7 0.418919 0.825581
127 4UU 0.418919 0.837209
128 00A 0.41844 0.786517
129 ADV 0.41791 0.804598
130 RBY 0.41791 0.804598
131 A3D 0.417722 0.835294
132 NAX 0.417219 0.862069
133 ANP MG 0.416058 0.781609
134 VO4 ADP 0.416058 0.793103
135 OOB 0.414286 0.823529
136 25A 0.414286 0.833333
137 LAD 0.412587 0.788889
138 UPA 0.411765 0.870588
139 CNA 0.410256 0.825581
140 80F 0.408805 0.833333
141 V2G 0.408759 0.83908
142 DLL 0.408451 0.823529
143 XAH 0.408163 0.771739
144 4UW 0.407895 0.829545
145 F2R 0.407643 0.793478
146 ATP MG 0.407407 0.788235
147 APC MG 0.407407 0.770115
148 ADP PO3 0.407407 0.788235
149 DAL AMP 0.407143 0.802326
150 3UK 0.405594 0.835294
151 4UV 0.405405 0.837209
152 TYM 0.405229 0.825581
153 NAD 0.405063 0.823529
154 BEF ADP 0.404412 0.770115
155 9ZD 0.404255 0.827586
156 9ZA 0.404255 0.827586
157 9SN 0.40411 0.797753
158 WAQ 0.402778 0.806818
159 B5V 0.402778 0.825581
160 L3W 0.402597 0.869048
161 FA5 0.401361 0.825581
162 YLP 0.401316 0.793478
Similar Ligands (3D)
Ligand no: 1; Ligand: NAP; Similar ligands found: 4
No: Ligand Similarity coefficient
1 TXD 0.9146
2 6V0 0.9079
3 AP0 0.8967
4 TXE 0.8646
Ligand no: 2; Ligand: FDA; Similar ligands found: 1
No: Ligand Similarity coefficient
1 FDA T2C 0.8779
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5VW2; Ligand: NAP; Similar sites found with APoc: 5
This union binding pocket(no: 1) in the query (biounit: 5vw2.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
1 4DQL NAP 27.2152
2 4DQL NAP 27.2152
3 1TLL FAD 28.481
4 1TLL FAD 28.481
5 4U9U FAD 30.9609
Pocket No.: 2; Query (leader) PDB : 5VW2; Ligand: FDA; Similar sites found with APoc: 5
This union binding pocket(no: 2) in the query (biounit: 5vw2.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
1 4DQL NAP 27.2152
2 4DQL NAP 27.2152
3 1TLL FAD 28.481
4 1TLL FAD 28.481
5 4U9U FAD 30.9609
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