Receptor
PDB id Resolution Class Description Source Keywords
5VWA 1.8 Å EC: 1.18.1.2 Y316F MUTANT OF CORN ROOT FERREDOXIN:NADP+ REDUCTASE 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. 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...
FAD A:402;
Valid;
none;
submit data
785.55 C27 H33 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. 2017
Members (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 22 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 8 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
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
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5VW2; Ligand: NAP; Similar sites found: 56
This union binding pocket(no: 1) in the query (biounit: 5vw2.bio1) has 42 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4BWL MN9 0.02167 0.43117 1.97368
2 5UDS ATP 0.009969 0.43911 2.7972
3 1T9M FMN 0.02706 0.40308 2.80374
4 3VSV XYS 0.01431 0.43604 3.16456
5 5DCH 1YO 0.04771 0.41095 3.64583
6 1M0S CIT 0.02883 0.41863 3.65297
7 3MQ2 SAH 0.0267 0.40336 4.12844
8 3SJK LYS PRO VAL LEU ARG THR ALA 0.03597 0.41897 4.21053
9 2CBZ ATP 0.04626 0.40572 4.21941
10 4F07 FAD 0.01921 0.40436 4.73684
11 4NS0 PIO 0.01731 0.44631 5.26316
12 1QKQ MAN 0.04235 0.4039 5.6338
13 3BY9 SIN 0.01997 0.43516 5.76923
14 2BVE PH5 0.006791 0.4658 6.72269
15 2BOS GLA GAL GLC NBU 0.04755 0.40947 7.35294
16 2BOS GLA GAL GLC 0.04981 0.40808 7.35294
17 4RHS SIA SIA GAL 0.0344 0.42235 7.37705
18 4DS0 A2G GAL NAG FUC 0.01282 0.44327 7.97546
19 5LNE A2G GAL 0.03196 0.41157 8.53659
20 3P13 RIP 0.02079 0.42769 9.02778
21 5JSQ 6MS 0.04254 0.40251 9.25926
22 4YRY NAD 0.00000001502 0.57709 9.42029
23 4AG5 ADP 0.04869 0.41114 10.1266
24 5IL1 SAM 0.01124 0.41825 11.3208
25 3CRZ NAP 0.0000000002445 0.60635 13.2296
26 3CRZ FAD 0.000001993 0.424 13.2296
27 1N13 AG2 0.04967 0.41056 14.1593
28 3OZV FAD 0.00007502 0.4474 14.2405
29 3OZV ECN 0.0002296 0.43523 14.2405
30 3W2E NAD 0.000000008839 0.57308 16.2362
31 3W2E FAD 0.000000008839 0.57308 16.2362
32 4WQM FAD 0.0000004869 0.44531 19.3038
33 1KRH FAD 0.00000005834 0.45108 20.5696
34 1A8P FAD 0.000007441 0.40867 22.093
35 2CND FAD 0.00001021 0.55519 22.963
36 1QX4 FAD 0.00000009092 0.51718 24.0876
37 2QTZ NAP 0.0000000000801 0.61772 25.3165
38 2QTZ FAD 0.00000001716 0.45253 25.3165
39 2EIX FAD 0.000131 0.47546 27.1605
40 4DQL NAP 0.000000000005819 0.66759 27.2152
41 4DQL FAD 0.00000004794 0.47384 27.2152
42 1TLL NAP 0.000000111 0.47334 28.481
43 1F20 FAD 0.000000005776 0.47261 28.481
44 1TLL FAD 0.000000005259 0.47137 28.481
45 1F20 NAP 0.0000002656 0.41723 28.481
46 4G1V FAD 0.000001334 0.45212 28.7975
47 4U9U FAD 0.000000001365 0.7245 30.9609
48 4KJU 1RH 0.04984 0.41219 31.3953
49 5FA6 NAP 0.00000000009333 0.68646 31.962
50 5FA6 FAD 0.00000000008634 0.68646 31.962
51 5FA6 FMN 0.00000000008634 0.68646 31.962
52 3QFS FAD 0.00000000005301 0.63729 31.962
53 3QFS NAP 0.00000000005301 0.63729 31.962
54 5GXU FAD 0.0000001349 0.47875 31.962
55 3FJO FAD 0.00000006602 0.43341 31.962
56 1DDG FAD 0.000000161 0.63098 38.2911
Pocket No.: 2; Query (leader) PDB : 5VW2; Ligand: FDA; Similar sites found: 56
This union binding pocket(no: 2) in the query (biounit: 5vw2.bio1) has 42 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4BWL MN9 0.02167 0.43117 1.97368
2 5UDS ATP 0.009969 0.43911 2.7972
3 1T9M FMN 0.02706 0.40308 2.80374
4 3VSV XYS 0.01431 0.43604 3.16456
5 5DCH 1YO 0.04771 0.41095 3.64583
6 1M0S CIT 0.02883 0.41863 3.65297
7 3MQ2 SAH 0.0267 0.40336 4.12844
8 3SJK LYS PRO VAL LEU ARG THR ALA 0.03597 0.41897 4.21053
9 2CBZ ATP 0.04626 0.40572 4.21941
10 4F07 FAD 0.01921 0.40436 4.73684
11 4NS0 PIO 0.01731 0.44631 5.26316
12 1QKQ MAN 0.04235 0.4039 5.6338
13 3BY9 SIN 0.01997 0.43516 5.76923
14 2BVE PH5 0.006791 0.4658 6.72269
15 2BOS GLA GAL GLC NBU 0.04755 0.40947 7.35294
16 2BOS GLA GAL GLC 0.04981 0.40808 7.35294
17 4RHS SIA SIA GAL 0.0344 0.42235 7.37705
18 4DS0 A2G GAL NAG FUC 0.01282 0.44327 7.97546
19 5LNE A2G GAL 0.03196 0.41157 8.53659
20 3P13 RIP 0.02079 0.42769 9.02778
21 5JSQ 6MS 0.04254 0.40251 9.25926
22 4YRY NAD 0.00000001502 0.57709 9.42029
23 4AG5 ADP 0.04869 0.41114 10.1266
24 5IL1 SAM 0.01124 0.41825 11.3208
25 3CRZ NAP 0.0000000002445 0.60635 13.2296
26 3CRZ FAD 0.000001993 0.424 13.2296
27 1N13 AG2 0.04967 0.41056 14.1593
28 3OZV FAD 0.00007502 0.4474 14.2405
29 3OZV ECN 0.0002296 0.43523 14.2405
30 3W2E NAD 0.000000008839 0.57308 16.2362
31 3W2E FAD 0.000000008839 0.57308 16.2362
32 4WQM FAD 0.0000004869 0.44531 19.3038
33 1KRH FAD 0.00000005834 0.45108 20.5696
34 1A8P FAD 0.000007441 0.40867 22.093
35 2CND FAD 0.00001021 0.55519 22.963
36 1QX4 FAD 0.00000009092 0.51718 24.0876
37 2QTZ NAP 0.0000000000801 0.61772 25.3165
38 2QTZ FAD 0.00000001716 0.45253 25.3165
39 2EIX FAD 0.000131 0.47546 27.1605
40 4DQL NAP 0.000000000005819 0.66759 27.2152
41 4DQL FAD 0.00000004794 0.47384 27.2152
42 1TLL NAP 0.000000111 0.47334 28.481
43 1F20 FAD 0.000000005776 0.47261 28.481
44 1TLL FAD 0.000000005259 0.47137 28.481
45 1F20 NAP 0.0000002656 0.41723 28.481
46 4G1V FAD 0.000001334 0.45212 28.7975
47 4U9U FAD 0.000000001365 0.7245 30.9609
48 4KJU 1RH 0.04984 0.41219 31.3953
49 5FA6 NAP 0.00000000009333 0.68646 31.962
50 5FA6 FAD 0.00000000008634 0.68646 31.962
51 5FA6 FMN 0.00000000008634 0.68646 31.962
52 3QFS FAD 0.00000000005301 0.63729 31.962
53 3QFS NAP 0.00000000005301 0.63729 31.962
54 5GXU FAD 0.0000001349 0.47875 31.962
55 3FJO FAD 0.00000006602 0.43341 31.962
56 1DDG FAD 0.000000161 0.63098 38.2911
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