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 280 families.
1 3F6R - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 3F6S - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 247 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 4HEQ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
4 3F6R - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
5 3F6S - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
50% Homology Family (46)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 177 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 5ULL - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
4 4NLL - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
5 3NLL - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
6 2FAX - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
7 5NUL - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
8 2FLV - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
9 4NUL - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
10 1FVX - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
11 2FVX - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
12 1FLN - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
13 6NUL - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
14 2FDX - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
15 5NLL - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
16 2FOX - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
17 1FLD - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
18 1FLA - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
19 1C7E Kd = 505 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
20 1WSB - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
21 3FX2 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
22 1J9E - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
23 1BU5 - RBF C17 H20 N4 O6 Cc1cc2c(cc....
24 1AKR Kd = 0.82 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
25 1AKW Kd = 2.6 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
26 1C7F Kd = 0.3 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
27 1XT6 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
28 1XYV - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
29 1AKQ Kd = 0.79 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
30 1WSW - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
31 1AZL Kd = 2.4 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
32 1AKU Kd = 746 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
33 2FX2 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
34 5FX2 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
35 1AKV Kd = 0.0026 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
36 1J8Q - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
37 1XYY - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
38 1FX1 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
39 1J9G - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
40 1AKT Kd = 3.2 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
41 1I1O - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
42 1F4P - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
43 4FX2 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
44 4HEQ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
45 3F6R - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
46 3F6S - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: FMN; Similar ligands found: 16
No: Ligand ECFP6 Tc MDL keys Tc
1 FMN 1 1
2 RBF 0.75641 0.876712
3 RS3 0.571429 0.831169
4 FAS 0.543307 0.876543
5 FAD 0.543307 0.876543
6 FAE 0.539062 0.865854
7 DAL FAD PER 0.5 0.833333
8 LFN 0.475 0.643836
9 C3F 0.473684 0.74359
10 CF4 0.463918 0.734177
11 FAY 0.446043 0.864198
12 FNR 0.444444 0.909091
13 RFL 0.442857 0.845238
14 4LS 0.411215 0.875
15 1VY 0.406593 0.769231
16 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: 95
This union binding pocket(no: 1) in the query (biounit: 3f6r.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4PTZ FMN 0.0006647 0.44626 None
2 3L6C MLI 0.02048 0.40143 0.589971
3 1TE2 PGA 0.006464 0.43042 2.02703
4 2VDF OCT 0.02033 0.40493 2.02703
5 2D2F ADP 0.0007945 0.49362 3.37838
6 3B5J 12D 0.009528 0.42005 3.37838
7 3QH2 3NM 0.01363 0.41217 3.37838
8 2AWN ADP 0.01381 0.41037 3.37838
9 2CBZ ATP 0.02295 0.40897 3.37838
10 2Q9U FMN 0.00007962 0.4772 4.05405
11 1RRC ADP 0.006552 0.43022 4.05405
12 3V0H I3P 0.02187 0.4017 4.05405
13 1G6H ADP 0.002516 0.45739 4.72973
14 1KOJ PAN 0.0009212 0.428 4.72973
15 3DC4 ADP 0.006919 0.4271 4.72973
16 4YMU ATP 0.007752 0.41978 4.72973
17 1T5B FMN 0.0006366 0.43979 5.40541
18 1T5C ADP 0.005453 0.43516 5.40541
19 1VB3 KPA 0.006856 0.4273 5.40541
20 3GFS FMN 0.004225 0.4234 5.40541
21 3HQP FDP 0.005561 0.42221 5.40541
22 3RC3 ANP 0.008944 0.41672 5.40541
23 4O48 ASP 0.0137 0.41536 5.40541
24 1YQT ADP 0.01644 0.41095 5.40541
25 5CGE 51F 0.01872 0.40515 5.40541
26 2CXS F6P 0.003308 0.40109 5.40541
27 1RYO OXL 0.00591 0.44394 6.08108
28 2KIN ADP 0.005451 0.43359 6.08108
29 2CJZ PTR 0.01163 0.41189 6.08108
30 4JBL MET 0.0218 0.40178 6.08108
31 2XOD FMN 0.000000006138 0.63321 6.72269
32 4BMO FMN 0.000000006474 0.56985 6.72269
33 4R2I ANP 0.004551 0.43631 6.75676
34 5E5U MLI 0.001334 0.43542 6.75676
35 4KFU ACP 0.009731 0.42286 6.75676
36 3SVL FMN 0.004575 0.40972 6.75676
37 2VVM PRO 0.03725 0.40287 6.75676
38 1V8K ANP 0.01459 0.40205 6.75676
39 4WOH 4NP 0.008788 0.40183 6.75676
40 1RLJ FMN 0.00000002666 0.63786 7.19424
41 4U00 ADP 0.006118 0.43275 7.43243
42 3T5M AMP 0.01522 0.41288 7.43243
43 5HV7 RBL 0.001483 0.4776 8.10811
44 4LTN FMN 0.0007839 0.43107 8.10811
45 2O2C G6Q 0.002212 0.42761 8.10811
46 4LTN NAI 0.0009101 0.41831 8.10811
47 1D1Q 4NP 0.01586 0.40953 8.10811
48 2W58 ADP 0.0242 0.40659 8.10811
49 2NCD ADP 0.02258 0.40294 8.10811
50 1JJ7 ADP 0.004058 0.44404 8.78378
51 4CP8 MLI 0.006781 0.43017 8.78378
52 1D6Z HY1 0.01833 0.40645 8.78378
53 4KCT FDP 0.0009242 0.45427 9.45946
54 1LCF OXL 0.005918 0.42036 9.45946
55 2PZE ATP 0.01333 0.416 9.45946
56 2XT3 ADP 0.02001 0.40576 9.45946
57 3SBZ MLI 0.01202 0.40247 9.45946
58 3FJO FMN 0.0000003442 0.56577 10.1351
59 4PPF FLC 0.001261 0.47042 10.1351
60 1BG2 ADP 0.00386 0.44283 10.1351
61 3LRE ADP 0.01247 0.41859 10.1351
62 1WQ1 AF3 0.01124 0.41708 10.1351
63 3N39 FMN 0.0000001658 0.54528 10.8108
64 1GOJ ADP 0.01595 0.40888 10.8108
65 4IP7 FBP 0.001541 0.43461 11.4865
66 1XX6 ADP 0.009345 0.42186 11.4865
67 5X7Q GLC GLC GLC GLC 0.01453 0.42146 11.4865
68 3COB ADP 0.02214 0.40163 11.4865
69 2VVG ADP 0.009525 0.42306 12.1622
70 2F5X ASP 0.01031 0.41831 12.1622
71 4FRZ ADP 0.02033 0.40546 12.1622
72 4X1B MLI 0.009799 0.43224 12.8378
73 4WZ6 ATP 0.01411 0.41436 12.8378
74 2J5V PCA 0.0243 0.40918 12.8378
75 2GDJ ANP 0.01369 0.40339 12.8378
76 3NHB ADP 0.01697 0.41014 13.5135
77 3LN9 FLC 0.0002968 0.50668 13.6691
78 3VPB GLU 0.0185 0.40883 14.8649
79 2Z9C FMN 0.0003036 0.44637 15.5405
80 4B2D FBP 0.002541 0.42493 15.5405
81 1G8S MET 0.001865 0.45991 16.8919
82 2OG2 MLI 0.01033 0.43129 22.2973
83 3B9Q MLI 0.0206 0.41496 22.2973
84 1PIG BGC 0.001269 0.46726 24.3243
85 1TLL FMN 0.0000005229 0.53073 25.6757
86 4H2D FMN 0.000001817 0.54782 31.5152
87 5GXU FMN 0.00000263 0.54089 35.1351
88 2FCR FMN 0.000000007282 0.67199 36.4865
89 2WC1 FMN 0.000000005458 0.65236 40.5405
90 1B1C FMN 0.000002411 0.54282 40.5405
91 1AG9 FMN 0.000000001292 0.67806 42.5676
92 5LJI FMN 0.000000000007902 0.80411 43.2432
93 4OXX FMN 0.0000003177 0.57927 43.2432
94 1BVY FMN 0.0000002709 0.55887 44.5946
95 1OBV FMN 0.0000000001978 0.69434 48.6486
Pocket No.: 2; Query (leader) PDB : 3F6R; Ligand: FMN; Similar sites found: 12
This union binding pocket(no: 2) in the query (biounit: 3f6r.bio3) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3F81 STT 0.01248 0.40265 None
2 3L6R MLI 0.01434 0.41449 0.578035
3 5GVR LMR 0.01861 0.40202 1.35135
4 1VJ7 GPX 0.01768 0.40123 3.37838
5 4UP4 NDG 0.009754 0.40818 4.05405
6 4UP4 GAL NAG 0.02362 0.40337 4.05405
7 4LO6 SIA GAL 0.0177 0.43146 5.40541
8 1X9I G6Q 0.008991 0.406 6.75676
9 3FJG 3PG 0.02046 0.40254 6.75676
10 2POC BG6 0.004824 0.41438 8.10811
11 2J4D MHF 0.02327 0.40066 14.8649
12 1G4U AF3 0.008335 0.42773 15.5405
Pocket No.: 3; Query (leader) PDB : 3F6R; Ligand: FMN; Similar sites found: 9
This union binding pocket(no: 3) in the query (biounit: 3f6r.bio4) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1PCA CIT 0.01051 0.40327 2.02703
2 2WQ4 SFU 0.02311 0.4058 2.5641
3 3WXL ADP 0.02078 0.41443 4.72973
4 1U0J ADP 0.004852 0.43372 11.4865
5 1LYX PGA 0.01065 0.40446 13.5135
6 1SW0 PGA 0.01371 0.40308 15.5405
7 5CEO 50D 0.008458 0.40182 15.5405
8 2XBL M7P 0.008673 0.40487 16.2162
9 1XP8 AGS 0.01752 0.40588 25
Pocket No.: 4; Query (leader) PDB : 3F6R; Ligand: FMN; Similar sites found: 8
This union binding pocket(no: 4) in the query (biounit: 3f6r.bio2) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5EEL MLA 0.041 0.40549 None
2 3RGQ 5P5 0.02216 0.40383 None
3 1MXG ACR 0.01858 0.40284 4.72973
4 4AF0 MOA 0.02639 0.4002 4.72973
5 1JI0 ATP 0.0239 0.40154 7.43243
6 1F9V ADP 0.02497 0.40284 10.8108
7 1YNS HPO 0.02233 0.40548 11.4865
8 1GXU 2HP 0.0297 0.40382 12.0879
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