Receptor
PDB id Resolution Class Description Source Keywords
5K9B 1.17 Å EC: 1.-.-.- AZOTOBACTER VINELANDII FLAVODOXIN II AZOTOBACTER VINELANDII FLAVODOXIN OXIDIZED ELECTRON TRANSPORT
Ref.: ELECTROCHEMICAL AND STRUCTURAL CHARACTERIZATION OF AZOTOBACTER VINELANDII FLAVODOXIN II. PROTEIN SCI. 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:204;
A:203;
A:202;
Invalid;
Part of Protein;
Invalid;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
FMN A:201;
Valid;
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
5K9B 1.17 Å EC: 1.-.-.- AZOTOBACTER VINELANDII FLAVODOXIN II AZOTOBACTER VINELANDII FLAVODOXIN OXIDIZED ELECTRON TRANSPORT
Ref.: ELECTROCHEMICAL AND STRUCTURAL CHARACTERIZATION OF AZOTOBACTER VINELANDII FLAVODOXIN II. PROTEIN SCI. 2017
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 280 families.
1 1YOB - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 5K9B - 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 1068 families.
1 2WC1 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 1YOB - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 5K9B - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
50% Homology Family (27)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 2WC1 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 3ESY - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 1OBV Kd = 1.04 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
4 1RCF - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
5 2V5V Kd = 4.8 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
6 1OBO Kd = 6.72 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
7 1FLV - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
8 3ESX - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
9 3ESZ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
10 2V5U - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
11 5LJP Ka = 83000000 M^-1 FMN C17 H21 N4 O9 P Cc1cc2c(cc....
12 2FCR - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
13 1YOB - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
14 5K9B - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
15 1D03 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
16 1CZK Kd = 1.5 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
17 1CZN - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
18 1D04 Kd = 0.38 mM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
19 1CZU - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
20 1OFV - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
21 1CZL Kd = 1.4 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
22 1CZH Kd = 3.5 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
23 1CZO Kd = 0.35 mM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
24 1CZR Kd = 1 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
25 2BMV - BEN C7 H8 N2 [H]/N=C(c1....
26 1FUE - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
27 1AG9 Ki = 1 nM 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 : 5K9B; Ligand: FMN; Similar sites found: 62
This union binding pocket(no: 1) in the query (biounit: 5k9b.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1JJ7 ADP 0.01624 0.41592 None
2 3QH2 3NM 0.02253 0.40286 None
3 4QS9 BGC 0.01868 0.40273 2.22222
4 3HQP FDP 0.0003572 0.42019 2.77778
5 4BLW AMP 0.01364 0.40729 2.77778
6 4BLW SAH 0.008529 0.40641 2.77778
7 4LY9 1YY 0.02958 0.40397 2.77778
8 4LY9 S6P 0.02751 0.40397 2.77778
9 2B3D FAD 0.00149 0.43843 3.33333
10 1WKM MET 0.0129 0.41736 3.33333
11 5O4J 9KH 0.01385 0.40697 3.33333
12 5O4J SAH 0.01385 0.40697 3.33333
13 3GXA MET 0.0154 0.40691 3.33333
14 5O4J PJL 0.01387 0.40583 3.33333
15 2VUZ NAG BMA NAG MAN MAN NAG NAG 0.005686 0.4361 3.87597
16 1TLL FMN 0.00000000001088 0.79406 3.88889
17 2POC BG6 0.004354 0.42054 3.88889
18 4G9N NGA 0.02267 0.40057 4.1958
19 4ZOM 4Q3 0.02239 0.42201 4.44444
20 4BWL MN9 0.01262 0.41668 4.44444
21 4XOI GTP 0.008034 0.40451 4.44444
22 1BVY FMN 0.000000000184 0.6902 5
23 3RC3 ANP 0.009647 0.41701 5.55556
24 1RYO OXL 0.02998 0.4106 5.55556
25 3O8M GLC 0.01139 0.40913 5.55556
26 3O8M BGC 0.01139 0.40913 5.55556
27 4B2D FBP 0.0009946 0.44529 6.11111
28 1HGX 5GP 0.01951 0.40179 6.11111
29 4RL4 PPV 0.01616 0.40092 6.11111
30 1T5B FMN 0.0009179 0.43807 6.66667
31 2FJK 13P 0.004716 0.42765 6.66667
32 2QN6 GDP 0.01155 0.41312 6.66667
33 3NTD FAD 0.01864 0.40508 6.66667
34 2OYS FMN 0.00167 0.43089 7.22222
35 2CXS F6P 0.001999 0.41285 7.22222
36 3N39 FMN 0.000000084 0.62332 7.77778
37 1KOJ PAN 0.001744 0.42813 7.77778
38 3GFS FMN 0.00004801 0.46636 8.04598
39 2O2C G6Q 0.00122 0.44131 8.88889
40 1GUZ NAD 0.008659 0.41028 8.88889
41 1WB4 SXX 0.02266 0.40548 8.88889
42 4N65 FMN 0.004469 0.42324 8.96226
43 4N65 AQN 0.004184 0.42017 8.96226
44 4IP7 FBP 0.000869 0.42688 9.44444
45 5GXU FMN 0.0000000000269 0.76135 10
46 3WGT QSC 0.03314 0.40158 10
47 1LFD GNP 0.005813 0.41229 10.3448
48 3F8D FAD 0.03625 0.41146 13.8889
49 4PPF FLC 0.002636 0.4658 16.1111
50 1RLJ FMN 0.000000001012 0.68227 23.0216
51 4OXX FMN 0.00000000008313 0.74033 25.3086
52 4H2D FMN 0.0000000002 0.72396 25.4545
53 4BMO FMN 0.00001672 0.56486 26.8908
54 1B1C FMN 0.00000000005954 0.74655 27.2222
55 5FA6 FAD 0.000000004772 0.75478 30.5556
56 5FA6 FMN 0.000000004772 0.75478 30.5556
57 5FA6 NAP 0.000000005018 0.75478 30.5556
58 2XOD FMN 0.000000001277 0.69308 31.0924
59 5NUL FMN 0.000004094 0.54546 31.8841
60 3FJO FMN 0.0000000001606 0.73197 35
61 5LJI FMN 0.00000001155 0.62929 36.4865
62 1AKV FMN 0.0000000009721 0.70837 44.2177
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