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Receptor
PDB id Resolution Class Description Source Keywords
3F6R 2 Å EC: 1.-.-.- DESULFOVIBRIO DESULFURICANS (ATCC 29577) OXIDIZED FLAVODOXIN DESULFOVIBRIO DESULFURICANS FLAVODOXIN-LIKE FOLD FMN BINDING OXIDIZED ELECTRON TRANSPORT FLAVOPROTEIN FMN TRANSPORT
Ref.: PSEUDOSYMMETRY, HIGH COPY NUMBER AND TWINNING COMPLICATE THE STRUCTURE DETERMINATION OF DESULFOVIBRIO DESULFURICANS (ATCC 29577) FLAVODOXIN. ACTA CRYSTALLOGR.,SECT.D V. 65 523 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FMN A:149;
B:150;
C:151;
D:152;
Valid;
Valid;
Valid;
Valid;
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
3F6R 2 Å EC: 1.-.-.- DESULFOVIBRIO DESULFURICANS (ATCC 29577) OXIDIZED FLAVODOXIN DESULFOVIBRIO DESULFURICANS FLAVODOXIN-LIKE FOLD FMN BINDING OXIDIZED ELECTRON TRANSPORT FLAVOPROTEIN FMN TRANSPORT
Ref.: PSEUDOSYMMETRY, HIGH COPY NUMBER AND TWINNING COMPLICATE THE STRUCTURE DETERMINATION OF DESULFOVIBRIO DESULFURICANS (ATCC 29577) FLAVODOXIN. ACTA CRYSTALLOGR.,SECT.D V. 65 523 2009
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 318 families.
1 3F6R - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 3F6S - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
70% Homology Family (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 280 families.
1 3KAQ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 3KAP Kd = 0.1 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 1WSW - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
4 1AZL Kd = 2.4 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
5 5YOC - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
6 1AKU Kd = 746 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
7 2FX2 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
8 5FX2 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
9 1AKV Kd = 0.0026 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
10 1J8Q - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
11 1XYY - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
12 1FX1 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
13 1J9G - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
14 1AKT Kd = 3.2 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
15 1I1O - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
16 1F4P - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
17 4FX2 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
18 4HEQ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
19 3F6R - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
20 3F6S - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
50% Homology Family (52)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 187 families.
1 3KAQ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 3KAP Kd = 0.1 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 5YOG - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
4 1C7E Kd = 505 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
5 1WSB - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
6 3FX2 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
7 5YOB - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
8 1J9E - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
9 1BU5 - RBF C17 H20 N4 O6 Cc1cc2c(cc....
10 1AKR Kd = 0.82 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
11 1AKW Kd = 2.6 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
12 5YOE - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
13 1C7F Kd = 0.3 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
14 1XT6 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
15 1XYV - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
16 1AKQ Kd = 0.79 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
17 1WSW - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
18 1AZL Kd = 2.4 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
19 5YOC - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
20 1AKU Kd = 746 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
21 2FX2 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
22 5FX2 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
23 1AKV Kd = 0.0026 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
24 1J8Q - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
25 1XYY - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
26 1FX1 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
27 1J9G - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
28 1AKT Kd = 3.2 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
29 1I1O - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
30 1F4P - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
31 4FX2 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
32 6FT1 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
33 6FSG - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
34 6FSI - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
35 3NLL - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
36 2FAX - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
37 5NUL - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
38 2FLV - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
39 4NUL - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
40 1FVX - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
41 2FVX - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
42 1FLN - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
43 6NUL - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
44 2FDX - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
45 5NLL - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
46 2FOX - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
47 1FLD - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
48 1FLA - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
49 6GAQ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
50 4HEQ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
51 3F6R - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
52 3F6S - 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 : 3F6R; Ligand: FMN; Similar sites found with APoc: 150
This union binding pocket(no: 1) in the query (biounit: 3f6r.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 4PTZ FMN None
2 3L6C MLI 0.589971
3 1UKZ ADP 1.35135
4 1C0I FAD 1.35135
5 1C0I BE2 1.35135
6 1TE2 PGA 2.02703
7 5JVB 2PO 2.02703
8 2VDF OCT 2.02703
9 2D2F ADP 3.37838
10 3B5J 12D 3.37838
11 2AWN ADP 3.37838
12 2CBZ ATP 3.37838
13 5BSH PRO 3.37838
14 3QH2 3NM 3.37838
15 2Q9U FMN 4.05405
16 1RRC ADP 4.05405
17 4N65 FMN 4.05405
18 4N65 AQN 4.05405
19 3ITJ CIT 4.05405
20 4UP4 GAL NAG 4.05405
21 3V0H I3P 4.05405
22 1ZDQ MSM 4.05405
23 1G6H ADP 4.72973
24 1KOJ PAN 4.72973
25 3DC4 ADP 4.72973
26 4JLS 3ZE 4.72973
27 4YMU ATP 4.72973
28 1T57 FMN 4.72973
29 4PYA 2X3 4.72973
30 4YJ1 ADP 4.72973
31 1T5B FMN 5.40541
32 1T5C ADP 5.40541
33 1VB3 KPA 5.40541
34 3GFS FMN 5.40541
35 3HQP FDP 5.40541
36 5YV5 ADP 5.40541
37 3RC3 ANP 5.40541
38 5MJI 7O6 5.40541
39 4O48 ASP 5.40541
40 1YQT ADP 5.40541
41 2CXS F6P 5.40541
42 5H68 AGS 5.40541
43 5CGE 51F 5.40541
44 5ZBC FAD 5.40541
45 1RYO OXL 6.08108
46 2KIN ADP 6.08108
47 1M7G ADP 6.08108
48 1M7G ADX 6.08108
49 4JBL MET 6.08108
50 4BMO FMN 6.72269
51 4R2I ANP 6.75676
52 5E5U MLI 6.75676
53 4KFU ACP 6.75676
54 3SVL FMN 6.75676
55 2Y65 ADP 6.75676
56 5ZA2 NXL 6.75676
57 2VVM PRO 6.75676
58 1V8K ANP 6.75676
59 4WOH 4NP 6.75676
60 1RLJ FMN 7.19424
61 1CX9 NHP 7.43243
62 4U00 ADP 7.43243
63 3T5M AMP 7.43243
64 5HV7 RBL 8.10811
65 4C0X AQN 8.10811
66 4C0X FMN 8.10811
67 5WS9 AMP 8.10811
68 4LTN FMN 8.10811
69 5O2J 2PO 8.10811
70 2O2C G6Q 8.10811
71 4LTN NAI 8.10811
72 1D1Q 4NP 8.10811
73 2W58 ADP 8.10811
74 6DNT NAD 8.10811
75 2NCD ADP 8.10811
76 6BYF CIT 8.10811
77 1JJ7 ADP 8.78378
78 4CP8 MLI 8.78378
79 1D6Z HY1 8.78378
80 6EBQ FMN 9.45946
81 1LCF OXL 9.45946
82 4KCT FDP 9.45946
83 2PZE ATP 9.45946
84 2XT3 ADP 9.45946
85 3SBZ MLI 9.45946
86 3FJO FMN 10.1351
87 4PPF FLC 10.1351
88 1BG2 ADP 10.1351
89 3LRE ADP 10.1351
90 1WQ1 AF3 10.1351
91 2WPB ZZI 10.1351
92 3WYF GTP 10.1351
93 3N39 FMN 10.8108
94 2OFW ADX 10.8108
95 1GOJ ADP 10.8108
96 4IP7 FBP 11.4865
97 5X7Q GLC GLC GLC GLC 11.4865
98 1XX6 ADP 11.4865
99 3COB ADP 11.4865
100 4D9C PMP 11.4865
101 2VVG ADP 12.1622
102 2F5X ASP 12.1622
103 1LVK MNT BEF 12.1622
104 3H4S ADP 12.1622
105 4FRZ ADP 12.1622
106 4X1B MLI 12.8378
107 4WZ6 ATP 12.8378
108 2J5V PCA 12.8378
109 1J0D 5PA 12.8378
110 1QF9 ALF 12.8378
111 1QF9 C5P 12.8378
112 1QF9 ADP 12.8378
113 2GDJ ANP 12.8378
114 3NHB ADP 13.5135
115 3LN9 FLC 13.6691
116 6A20 ADP 14.1892
117 4HE2 AMP 14.8649
118 3VPB GLU 14.8649
119 2Z9C FMN 15.5405
120 2Z9C DTC 15.5405
121 4B2D FBP 15.5405
122 5LU5 M7P 15.5405
123 1G8S MET 16.8919
124 1DCP HBI 17.3077
125 2OG2 MLI 22.2973
126 6AM8 PLT 22.2973
127 6AMI TRP 22.2973
128 6AM8 TRP 22.2973
129 3B9Q MLI 22.2973
130 6CUZ FEV 22.973
131 4R5M 4NO 23.6486
132 4R5M NAP 23.6486
133 1PIG BGC 24.3243
134 4YQE PLQ 25
135 4YQE FMN 25
136 1TLL FMN 25.6757
137 4H2D FMN 31.5152
138 5GXU FMN 35.1351
139 2FCR FMN 36.4865
140 2WC1 FMN 40.5405
141 1B1C FMN 40.5405
142 1AG9 FMN 42.5676
143 5LJI FMN 43.2432
144 4OXX FMN 43.2432
145 1BVY FMN 44.5946
146 5FA6 NAP 45.9459
147 5FA6 FAD 45.9459
148 5FA6 FMN 45.9459
149 5VEG FMN 47.973
150 1OBV FMN 48.6486
Pocket No.: 2; Query (leader) PDB : 3F6R; Ligand: FMN; Similar sites found with APoc: 36
This union binding pocket(no: 2) in the query (biounit: 3f6r.bio3) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 3F81 STT None
2 3L6R MLI 0.578035
3 5GVR LMR 1.35135
4 2I3G NAP 3.37838
5 1VJ7 GPX 3.37838
6 4LY9 1YY 4.05405
7 4LY9 S6P 4.05405
8 3ITJ FAD 4.05405
9 4UP4 NDG 4.05405
10 4WQM FAD 4.05405
11 1YQD NAP 4.72973
12 4AVB ACO 4.72973
13 4LO6 SIA GAL 5.40541
14 3FC4 EDO 5.40541
15 2PWY SAH 6.08108
16 6HKE MLT 6.08108
17 1T3D CYS 6.08108
18 6HKE LMR 6.08108
19 3KO8 NAD 6.75676
20 1X9I G6Q 6.75676
21 3FJG 3PG 6.75676
22 5LV1 78T 8.10811
23 2POC BG6 8.10811
24 2ZJ3 G6P 8.10811
25 4P83 U5P 9.45946
26 4DPL NAP 10.8108
27 1BGQ RDC 10.8108
28 3MB5 SAM 12.1622
29 5X2N ALA 12.8378
30 2J4D MHF 14.8649
31 1G4U AF3 15.5405
32 3ENV ABF 16.2162
33 1I9G SAM 16.2162
34 3NJ4 NAD 18.9189
35 2C5A NAD 20.9459
36 2C5A GDC 20.9459
Pocket No.: 3; Query (leader) PDB : 3F6R; Ligand: FMN; Similar sites found with APoc: 21
This union binding pocket(no: 3) in the query (biounit: 3f6r.bio4) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 1U72 NDP None
2 1U72 MTX None
3 5C9P FUC 1.35135
4 1U70 MTX 1.35135
5 1U70 NDP 1.35135
6 1PCA CIT 2.02703
7 2WQ4 SFU 2.5641
8 3AKI AH8 4.05405
9 4DDY DN6 4.72973
10 3WXL ADP 4.72973
11 5EJL C2E 6.08108
12 1L7N ALF 6.75676
13 5LQ8 GB 8.78378
14 1U0J ADP 11.4865
15 1RYI FAD 11.4865
16 1RYI GOA 11.4865
17 1LYX PGA 13.5135
18 4TR9 38D 16.2162
19 1XP8 AGS 25
20 1PMO PLR 26.3514
21 3WGT FAD 27.7027
Pocket No.: 4; Query (leader) PDB : 3F6R; Ligand: FMN; Similar sites found with APoc: 18
This union binding pocket(no: 4) in the query (biounit: 3f6r.bio2) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 3RGQ 5P5 None
2 1LNX URI 3.7037
3 1MXG ACR 4.72973
4 4AF0 MOA 4.72973
5 5ECP ATP 6.75676
6 5A96 GTP 6.75676
7 1JI0 ATP 7.43243
8 4L2I FAD 8.78378
9 3EWA ANP 9.45946
10 5BYK A3P 10.1351
11 5BYK OAQ 10.1351
12 5OFW 9TW 10.8108
13 1F9V ADP 10.8108
14 2JK0 ASP 11.4865
15 1YNS HPO 11.4865
16 1GXU 2HP 12.0879
17 2ZFZ ARG 13.9241
18 1BO4 COA 14.8649
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