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Receptor
PDB id Resolution Class Description Source Keywords
3GFS 2.1 Å EC: 1.7.1.6 STRUCTURE OF YHDA, K109D/D137K VARIANT BACILLUS SUBTILIS FLAVOPROTEINS QUINONE REDUCTASE FLAVODOXIN OLIGOMERIZATION FLAVOPROTEIN FMN NADP OXIDOREDUCTASE
Ref.: A SINGLE INTERSUBUNIT SALT BRIDGE AFFECTS OLIGOMERIZATION AND CATALYTIC ACTIVITY IN A BACTERIAL QUINONE REDUCTASE FEBS J. V. 276 5263 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FMN A:200;
B:200;
C:200;
D:200;
E:200;
F:200;
G:200;
H:200;
I:200;
J:200;
K:200;
L:200;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
456.344 C17 H21 N4 O9 P Cc1cc...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3GFS 2.1 Å EC: 1.7.1.6 STRUCTURE OF YHDA, K109D/D137K VARIANT BACILLUS SUBTILIS FLAVOPROTEINS QUINONE REDUCTASE FLAVODOXIN OLIGOMERIZATION FLAVOPROTEIN FMN NADP OXIDOREDUCTASE
Ref.: A SINGLE INTERSUBUNIT SALT BRIDGE AFFECTS OLIGOMERIZATION AND CATALYTIC ACTIVITY IN A BACTERIAL QUINONE REDUCTASE FEBS J. V. 276 5263 2009
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3GFR - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 1NNI - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 3GFS - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3GFR - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 1NNI - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 3GFS - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3GFR - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 1NNI - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 3GFS - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: FMN; Similar ligands found: 15
No: Ligand ECFP6 Tc MDL keys Tc
1 FMN 1 1
2 RBF 0.75641 0.876712
3 RS3 0.571429 0.831169
4 FAD 0.543307 0.876543
5 FAS 0.543307 0.876543
6 FAE 0.539062 0.865854
7 LFN 0.475 0.643836
8 C3F 0.473684 0.74359
9 CF4 0.463918 0.734177
10 FAY 0.446043 0.864198
11 FNR 0.444444 0.909091
12 RFL 0.442857 0.845238
13 4LS 0.411215 0.875
14 1VY 0.406593 0.769231
15 DLZ 0.404494 0.782051
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3GFS; Ligand: FMN; Similar sites found with APoc: 140
This union binding pocket(no: 1) in the query (biounit: 3gfs.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 4OXX FMN None
2 1L5Y BEF None
3 4ITU 1HS None
4 4ITU NAI None
5 3P7G MAN None
6 1ONI BEZ None
7 4LHW GNP None
8 2ED4 FAD None
9 3LF0 ATP None
10 4CO3 ATP None
11 5G6U YJM None
12 4OWK NGA 1.44928
13 1YB5 NAP 1.72414
14 1LVL NAD 2.29885
15 3N39 FMN 2.87356
16 5G3U FDA 2.87356
17 3ZF8 GDP 2.87356
18 1OBV FMN 2.95858
19 5LJI FMN 3.37838
20 3AKI AH8 3.44828
21 4IV9 FAD 3.44828
22 4WCX MET 3.44828
23 1Q0S SAH 3.44828
24 5I60 67W 3.44828
25 1UKG MMA 3.96825
26 1Q8S MAN MMA 3.96825
27 2PHU MAN MAN 3.96825
28 1Q8V MAN MAN 3.96825
29 2PHX MAN MAN 3.96825
30 1Q8Q MAN MMA 3.96825
31 1Q8P MAN MMA 3.96825
32 5ZBC FAD 4.02299
33 4DP3 NDP 4.02299
34 2Q9U FMN 4.5977
35 4HA6 FAD 4.5977
36 2GCE SFC 4.5977
37 5BRE 4UZ 4.5977
38 1CZR FMN 4.73373
39 1AKV FMN 4.7619
40 4ITH RCM 5.17241
41 3QJ4 FAD 5.17241
42 6CI9 NAP 5.17241
43 5LKC FUC GLA A2G 5.17241
44 6GAQ FMN 5.19481
45 3F6R FMN 5.40541
46 3KAP FMN 5.44218
47 5LMC FMN 5.74713
48 2WC1 FMN 5.74713
49 3WDM ADN 5.74713
50 2GMH FAD 5.74713
51 2R4J FAD 5.74713
52 2R4J 13P 5.74713
53 5BRT CH9 5.74713
54 5BRT FAD 5.74713
55 2NS1 ADP 5.74713
56 4C4P GNP 5.78035
57 3B4Y F42 6.32184
58 6FSG FMN 6.80272
59 4N82 FMN 6.89655
60 2F6U CIT 6.89655
61 4EIP FAD 6.89655
62 5EJ2 NAD 6.89655
63 3AXB FAD 6.89655
64 3AXB PRO 6.89655
65 1E5D FMN 7.47126
66 6F97 FAD 7.47126
67 2BD0 NAP 7.47126
68 4JCA CIT 7.78443
69 3N5B ADP 8.03571
70 5K9B FMN 8.04598
71 1GPE FAD 8.04598
72 3Q9T FAY 8.62069
73 1TLL FMN 8.62069
74 2FCR FMN 8.67052
75 4HEQ FMN 8.90411
76 3GXZ NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 8.91089
77 3L9W FMN 9.1954
78 4O48 ASP 9.1954
79 5ECP MET 9.1954
80 2FKA BEF 9.30233
81 2ZJ1 ARJ 9.77011
82 2ZJ1 NAD 9.77011
83 3NRR D16 9.77011
84 1OIX GDP 9.77011
85 1NU4 MLA 10.3093
86 5GXU FMN 10.3448
87 1B1C FMN 10.3448
88 1WD4 AHR 10.3448
89 1G0N NDP 10.3448
90 1G0N PHH 10.3448
91 5FJN FAD 10.3448
92 5ZYN FAD 10.9195
93 6FRN FMN 11.2195
94 5VEG FMN 11.4943
95 1RLJ FMN 11.5108
96 6EBQ FMN 11.875
97 5MJI 7O6 12.069
98 4BMO FMN 12.069
99 5FA6 FMN 12.6437
100 5FA6 FAD 12.6437
101 5FA6 NAP 12.6437
102 3FJO FMN 12.6437
103 16PK BIS 12.6437
104 1QO8 FAD 12.6437
105 4H2D FMN 12.7273
106 1RHC F42 ACN 13.2184
107 5EY9 5SV 13.7931
108 4X9M FAD 13.7931
109 2DPM SAM 13.7931
110 1COY FAD 14.3678
111 5NUL FMN 14.4928
112 1FDJ 2FP 14.9425
113 4YQE PLQ 16.092
114 4YQE FMN 16.092
115 4QED NAP 16.6667
116 1RYI GOA 17.2414
117 1RYI FAD 17.2414
118 1ZBQ NAD 17.2414
119 4C0X AQN 17.8161
120 4C0X FMN 17.8161
121 1T5B FMN 18.3908
122 3UXH FAD 20.6897
123 3UXH UXH 20.6897
124 2B3D FAD 22.4138
125 3DLG GWE 22.4138
126 3JSX FAD 23.5632
127 3JSX CC2 23.5632
128 3S2Y FMN 24.7126
129 4R81 FMN 25.8621
130 1BVY FMN 25.8621
131 4PTZ FMN 27.2251
132 2OHH FMN 27.5862
133 1AG9 FMN 28.1609
134 4LTN NAI 29.3103
135 4LTN FMN 29.3103
136 1QRD FAD 29.3103
137 2OYS FMN 29.8851
138 3SVL FMN 29.8851
139 1SQS TLA 29.8851
140 1T0I FMN 33.3333
Pocket No.: 2; Query (leader) PDB : 3GFS; Ligand: FMN; Similar sites found with APoc: 26
This union binding pocket(no: 2) in the query (biounit: 3gfs.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 5FFF NAP None
2 5B4T NAD 1.72414
3 5B4T 3HR 1.72414
4 2RI1 GLP 2.29885
5 3HP8 SUC 2.72727
6 5XWV NDP 3.44828
7 2Q2V NAD 3.44828
8 2H1H AFH 3.59281
9 5BSH PRO 4.5977
10 1AOE NDP 5.17241
11 1AOE GW3 5.17241
12 1U29 I3P 5.42636
13 2Z3Y F2N 5.74713
14 3RS8 APR 6.89655
15 1J3I NDP 6.89655
16 1J3I WRA 6.89655
17 5M67 3D1 7.47126
18 5M67 NAD 7.47126
19 2D7C GTP 10.1796
20 1JA9 NDP 11.4943
21 4O33 3PG 13.2184
22 4O33 TZN 13.2184
23 5HM3 649 13.2184
24 4CQM NAP 14.3678
25 3CTY FAD 16.092
26 5X2N ALA 16.092
Pocket No.: 3; Query (leader) PDB : 3GFS; Ligand: FMN; Similar sites found with APoc: 12
This union binding pocket(no: 3) in the query (biounit: 3gfs.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 1TLG GAL None
2 2QGI UDP 2.29885
3 2PHW MAN MAN 3.96825
4 4RFM 3P6 4.02299
5 4DP3 MMV 4.02299
6 4XFR CIT 4.5977
7 1L7N ALF 4.5977
8 3ABI NAD 6.89655
9 5M67 ADE 7.47126
10 3OZ2 FAD 8.62069
11 1VBO MAN MAN MAN 9.39597
12 2TPI ILE VAL 9.77011
Pocket No.: 4; Query (leader) PDB : 3GFS; Ligand: FMN; Similar sites found with APoc: 49
This union binding pocket(no: 4) in the query (biounit: 3gfs.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 1PTR PRB None
2 1LVL FAD 2.29885
3 3OND NAD 3.44828
4 3OND ADN 3.44828
5 3GD4 FAD 3.44828
6 1L2T ATP 3.44828
7 2C6Q NDP 3.44828
8 3CGB FAD 3.54167
9 1Q8O MAN MMA 3.96825
10 1UDY FAD 4.02299
11 4JNA FAD 4.02299
12 1RP0 AHZ 4.02299
13 5XDT MB3 4.22078
14 3HVJ 705 4.5977
15 4GKV NAD 4.5977
16 2V2V V12 4.5977
17 1NAA 6FA 5.17241
18 1NAA ABL 5.17241
19 6H3O FAD 5.17241
20 1T7Q COA 5.17241
21 1T7Q 152 5.17241
22 1EBF NAD 5.17241
23 1ZUI SKM 5.17241
24 6F3N NAD 5.74713
25 6F3N ADN 5.74713
26 5ODQ FAD 5.74713
27 3B0P FMN 6.32184
28 5N0J FAD 6.32184
29 4GPS CIT 6.32184
30 5LYH 7B8 6.89655
31 2UVO NAG 7.01754
32 2Q7V FAD 7.47126
33 1H6C NDP 7.47126
34 1Q9I FAD 8.04598
35 1Q9I TEO 8.04598
36 3FPZ AHZ 9.77011
37 2HQM FAD 10.3448
38 3AD8 NAD 10.8911
39 4NTD FAD 11.4943
40 5J60 FAD 11.4943
41 3ZLB ANP 12.6437
42 5DEY 59T 12.6437
43 1D4D FAD 13.7931
44 3ICT FAD 16.6667
45 3ICS FAD 16.6667
46 3ICR FAD 16.6667
47 3QWI NAP 18.9655
48 3QWI CUE 18.9655
49 2GAG NAD 26.4368
Pocket No.: 5; Query (leader) PDB : 3GFS; Ligand: FMN; Similar sites found with APoc: 5
This union binding pocket(no: 5) in the query (biounit: 3gfs.bio3) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 5XWV 8H6 3.44828
2 4HXY NDP 4.02299
3 4RSL FAD 5.17241
4 3FC4 EDO 6.32184
5 2D24 XYS XYS 8.62069
Pocket No.: 6; Query (leader) PDB : 3GFS; Ligand: FMN; Similar sites found with APoc: 41
This union binding pocket(no: 6) in the query (biounit: 3gfs.bio3) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 5ZWP GSH None
2 3REF GDP 2.29885
3 3IA4 NDP 2.46914
4 3DC4 ADP 3.44828
5 1M5B BN1 3.44828
6 4U8P UDP 3.44828
7 4U8P FDA 3.44828
8 1AXD GGL CYW GLY 3.44828
9 5UY8 AMZ 4.02299
10 4WOH 4NP 4.21687
11 5E5U MLI 4.5977
12 2X7J TPP 4.5977
13 1M7G ADP 4.5977
14 3FSY SCA 4.5977
15 1M7G ADX 4.5977
16 5A96 GTP 4.5977
17 3HQP OXL 5.17241
18 1JLV GSH 5.74713
19 3ITJ CIT 6.32184
20 1JG3 ADN 6.89655
21 4D0G GTP 7.24638
22 4PPF FLC 7.47126
23 3WYW GSH 7.47126
24 5NM7 GLY 8.04598
25 6BSX E7S 8.04598
26 6BSX GDP 8.04598
27 3B8I OXL 8.62069
28 4R29 SAM 9.1954
29 2G50 PYR 9.77011
30 3JUC PCA 9.80392
31 2HV8 GTP 9.88372
32 4WOP CTP 10.2222
33 2QQ0 ANP 12.069
34 2QQ0 THM 12.069
35 2QQ0 ADP 12.069
36 2QQ0 TMP 12.069
37 2B8W ALF 5GP 12.069
38 3KJS DQ1 12.6437
39 2BL9 CP6 20.6897
40 2BL9 NDP 20.6897
41 3IID APR 21.2644
Pocket No.: 7; Query (leader) PDB : 3GFS; Ligand: FMN; Similar sites found with APoc: 26
This union binding pocket(no: 7) in the query (biounit: 3gfs.bio3) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 2BOS GLA GAL GLC None
2 2BOS GLA GAL GLC NBU None
3 1SL6 GAL NDG FUC 2.87356
4 3LAD FAD 2.87356
5 2V1O COA 3.31126
6 2VVL FAD 3.44828
7 1LLU NAD 4.02299
8 5EXW 7DT 4.02299
9 4NTC FAD 4.02299
10 5TUK FAD 4.5977
11 1YZN GNP 4.5977
12 1L7N AF3 4.5977
13 2ZFZ ARG 5.06329
14 2BUP ADP 5.17241
15 2BUP ATP 5.17241
16 3TN7 NJP 6.32184
17 1Q1R FAD 7.47126
18 5WS9 AMP 9.1954
19 1DR1 HBI 9.52381
20 1DR1 NAP 9.52381
21 1ZK7 FAD 9.77011
22 4XQC NAD 10.3448
23 4XQC 13D 10.3448
24 1XHL NDP 10.9195
25 1QH9 LAC 12.069
26 4PIV NDP 16.092
Pocket No.: 8; Query (leader) PDB : 3GFS; Ligand: FMN; Similar sites found with APoc: 26
This union binding pocket(no: 8) in the query (biounit: 3gfs.bio3) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 5G3L SIA None
2 4CUB GAL NAG None
3 4GNC ASO 1.72414
4 1NMK SFM 1.81818
5 5FEU NAP 2.29885
6 3UOY NAP 2.87356
7 3UOY FAD 2.87356
8 1VPE ANP 3.44828
9 2PHT MAN MAN MAN 3.96825
10 2E5V FAD 4.02299
11 4Z87 5GP 4.02299
12 5K0A FAD 5.17241
13 5EZ7 FAD 5.74713
14 6F3M NAD 5.74713
15 3KO8 NAD 5.74713
16 2ZXI FAD 6.32184
17 2YG3 FAD 6.89655
18 1H5Q NAP 6.89655
19 1RYD NDP 7.47126
20 1H6C SIN 7.47126
21 3AJM 4IP 7.47126
22 3AB1 FAD 8.04598
23 4OOE NDP 8.62069
24 2E7Z MGD 16.6667
25 4MO2 FAD 22.4138
26 4MO2 FDA 22.4138
Pocket No.: 9; Query (leader) PDB : 3GFS; Ligand: FMN; Similar sites found with APoc: 4
This union binding pocket(no: 9) in the query (biounit: 3gfs.bio2) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 4RF2 NAP None
2 1UDY CS8 4.02299
3 5L2Z 70C 5.17241
4 1REO FAD 10.3448
Pocket No.: 10; Query (leader) PDB : 3GFS; Ligand: FMN; Similar sites found with APoc: 4
This union binding pocket(no: 10) in the query (biounit: 3gfs.bio2) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 3FXU TSU None
2 3A4V NAD 3.44828
3 3A4V PYR 3.44828
4 4IEN GDP 7.36196
Pocket No.: 11; Query (leader) PDB : 3GFS; Ligand: FMN; Similar sites found with APoc: 11
This union binding pocket(no: 11) in the query (biounit: 3gfs.bio2) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 4LAE 1VM None
2 4LAE NAP None
3 6BE0 COA 2.29885
4 5FJJ MAN 2.87356
5 1IZC PYR 4.02299
6 2J0W ASP 4.5977
7 5OCQ CIT 6.32184
8 2JFQ DGL 7.47126
9 3AJ6 NGA 10.3448
10 1Q19 SSC 14.9425
11 1OFS SUC 18.75
Pocket No.: 12; Query (leader) PDB : 3GFS; Ligand: FMN; Similar sites found with APoc: 3
This union binding pocket(no: 12) in the query (biounit: 3gfs.bio2) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 4K49 HFQ 4.41176
2 5BVA FAD 6.89655
3 1RSG FAD 12.6437
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