Receptor
PDB id Resolution Class Description Source Keywords
3GFZ 2.05 Å NON-ENZYME: OTHER KLEBSIELLA PNEUMONIAE BLRP1 PH 6 MANGANESE/CY-DIGMP COMPLEX KLEBSIELLA PNEUMONIAE SUBSP. PNEUMONIA78578 TIM-BARREL EAL DOMAIN BLUF DOMAIN HYDROLASE SIGNALING PR
Ref.: STRUCTURE AND MECHANISM OF A BACTERIAL LIGHT-REGULA CYCLIC NUCLEOTIDE PHOSPHODIESTERASE. NATURE V. 459 1015 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
C2E A:501;
B:501;
 Valid;
Valid;
 none;
none;
 submit data
690.411 C20 H24 N10 O14 P2 c1nc2...
FMN A:504;
B:504;
 Valid;
Valid;
 none;
none;
 submit data
456.344 C17 H21 N4 O9 P Cc1cc...
MN A:502;
A:503;
B:502;
B:503;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
 submit data
54.938 Mn [Mn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3GFZ 2.05 Å NON-ENZYME: OTHER KLEBSIELLA PNEUMONIAE BLRP1 PH 6 MANGANESE/CY-DIGMP COMPLEX KLEBSIELLA PNEUMONIAE SUBSP. PNEUMONIA78578 TIM-BARREL EAL DOMAIN BLUF DOMAIN HYDROLASE SIGNALING PR
Ref.: STRUCTURE AND MECHANISM OF A BACTERIAL LIGHT-REGULA CYCLIC NUCLEOTIDE PHOSPHODIESTERASE. NATURE V. 459 1015 2009
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 3GG1 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 3GFZ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 3GFX - 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 1331 families.
1 3GG1 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 3GFZ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 3GFX - 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 1144 families.
1 3GG1 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 3GFZ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 3GFX - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: C2E; Similar ligands found: 59
No: Ligand ECFP6 Tc MDL keys Tc
1 PCG 1 0.986111
2 C2E 1 1
3 35G 1 0.986111
4 1YD 0.806818 1
5 4BW 0.806818 1
6 5GP 5GP 0.743902 0.958904
7 4UR 0.731959 1
8 KT2 0.669903 1
9 6SW 0.627907 0.944444
10 1YC 0.616162 0.972222
11 6J7 0.58427 0.934211
12 CMP 0.534091 0.902778
13 2BA 0.534091 0.916667
14 GMP 0.53012 0.828947
15 1SY 0.495575 1
16 SGP 0.483871 0.825
17 6SZ 0.483871 0.916667
18 3GP 0.478261 0.92
19 1OR 0.474747 0.741176
20 G 0.468085 0.933333
21 5GP 0.468085 0.933333
22 7CH 0.467391 0.888889
23 6SX 0.462366 0.861111
24 6JR 0.457944 0.944444
25 G2R 0.457143 0.886076
26 GPX 0.451923 0.894737
27 GP3 0.44898 0.947368
28 2GP 0.446809 0.907895
29 GP2 0.444444 0.886076
30 GDP 0.444444 0.921053
31 GNH 0.44 0.909091
32 KB7 0.44 0.780488
33 P2G 0.4375 0.881579
34 G2P 0.436893 0.886076
35 GMV 0.431373 0.897436
36 GTP 0.431373 0.921053
37 ALF 5GP 0.431373 0.841463
38 GDP BEF 0.427184 0.884615
39 G1R 0.427184 0.909091
40 GCP 0.427184 0.897436
41 GTP MG 0.423077 0.907895
42 G3D 0.423077 0.933333
43 GNP 0.423077 0.897436
44 9GM 0.423077 0.897436
45 GSP 0.423077 0.875
46 GDP AF3 0.420561 0.841463
47 G4P 0.415094 0.933333
48 GAV 0.415094 0.886076
49 P1G 0.414141 0.87013
50 KBD 0.412844 0.825
51 Y9Z 0.410714 0.833333
52 GDP ALF 0.407407 0.841463
53 N6R 0.40708 0.831169
54 N6S 0.40708 0.831169
55 G3A 0.403509 0.947368
56 YGP 0.401786 0.876543
57 GPG 0.4 0.935065
58 0O2 0.4 0.933333
59 G5P 0.4 0.947368
Ligand no: 2; Ligand: FMN; Similar ligands found: 18
No: Ligand ECFP6 Tc MDL keys Tc
1 FMN 1 1
2 RBF 0.75641 0.876712
3 9O9 0.574468 0.934211
4 RS3 0.571429 0.831169
5 FAD 0.543307 0.876543
6 FAS 0.543307 0.876543
7 FAE 0.539062 0.865854
8 UBG 0.534351 0.888889
9 5DD 0.475248 0.972603
10 LFN 0.475 0.643836
11 C3F 0.473684 0.74359
12 CF4 0.463918 0.734177
13 FAY 0.446043 0.864198
14 FNR 0.444444 0.909091
15 RFL 0.442857 0.845238
16 4LS 0.411215 0.875
17 1VY 0.406593 0.769231
18 DLZ 0.404494 0.782051
Similar Ligands (3D)
Ligand no: 1; Ligand: C2E; Similar ligands found: 1
No: Ligand Similarity coefficient
1 G G 0.9210
Ligand no: 2; Ligand: FMN; Similar ligands found: 10
No: Ligand Similarity coefficient
1 7O6 0.9670
2 4X4 0.8996
3 4LU 0.8884
4 E2U 0.8865
5 HDF 0.8834
6 AFQ 0.8817
7 E2X 0.8805
8 E89 0.8698
9 1WJ 0.8673
10 FZZ 0.8606
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3GFZ; Ligand: FMN; Similar sites found with APoc: 32
This union binding pocket(no: 1) in the query (biounit: 3gfz.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 4YUS FMN 13.8743
2 5MBC FMN 14.4476
3 5MBC FMN 14.4476
4 2HFN FMN 35.9477
5 2HFN FMN 35.9477
6 2HFN FMN 35.9477
7 2HFN FMN 35.9477
8 2HFN FMN 35.9477
9 2HFN FMN 35.9477
10 2HFN FMN 35.9477
11 2HFN FMN 35.9477
12 2HFN FMN 35.9477
13 2HFN FMN 35.9477
14 2IYG FMN 37.9032
15 2IYG FMN 37.9032
16 1YRX FMN 38.843
17 1YRX FMN 38.843
18 1YRX FMN 38.843
19 1YRX FMN 38.843
20 1YRX FMN 38.843
21 1YRX FMN 38.843
22 1YRX FMN 38.843
23 1X0P FAD 39.1608
24 1X0P FAD 39.1608
25 1X0P FAD 39.1608
26 1X0P FAD 39.1608
27 1X0P FAD 39.1608
28 1X0P FAD 39.1608
29 1X0P FAD 39.1608
30 1X0P FAD 39.1608
31 1X0P FAD 39.1608
32 1X0P FAD 39.1608
Pocket No.: 2; Query (leader) PDB : 3GFZ; Ligand: C2E; Similar sites found with APoc: 7
This union binding pocket(no: 2) in the query (biounit: 3gfz.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 3HV8 C2E 25
2 3N3T C2E 26.3923
3 3N3T C2E 26.3923
4 5MF5 C2E 26.9531
5 5MKG C2E 27.1654
6 5M1T C2E 28.4698
7 5M1T C2E 28.4698
Pocket No.: 3; Query (leader) PDB : 3GFZ; Ligand: C2E; Similar sites found with APoc: 9
This union binding pocket(no: 3) in the query (biounit: 3gfz.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 4LJ3 C2E 22.2222
2 3HV8 C2E 25
3 3N3T C2E 26.3923
4 3N3T C2E 26.3923
5 5MF5 C2E 26.9531
6 5MKG C2E 27.1654
7 5MKG C2E 27.1654
8 5M1T C2E 28.4698
9 5M1T C2E 28.4698
Pocket No.: 4; Query (leader) PDB : 3GFZ; Ligand: FMN; Similar sites found with APoc: 32
This union binding pocket(no: 4) in the query (biounit: 3gfz.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 4YUS FMN 13.8743
2 5MBC FMN 14.4476
3 5MBC FMN 14.4476
4 2HFN FMN 35.9477
5 2HFN FMN 35.9477
6 2HFN FMN 35.9477
7 2HFN FMN 35.9477
8 2HFN FMN 35.9477
9 2HFN FMN 35.9477
10 2HFN FMN 35.9477
11 2HFN FMN 35.9477
12 2HFN FMN 35.9477
13 2HFN FMN 35.9477
14 2IYG FMN 37.9032
15 2IYG FMN 37.9032
16 1YRX FMN 38.843
17 1YRX FMN 38.843
18 1YRX FMN 38.843
19 1YRX FMN 38.843
20 1YRX FMN 38.843
21 1YRX FMN 38.843
22 1YRX FMN 38.843
23 1X0P FAD 39.1608
24 1X0P FAD 39.1608
25 1X0P FAD 39.1608
26 1X0P FAD 39.1608
27 1X0P FAD 39.1608
28 1X0P FAD 39.1608
29 1X0P FAD 39.1608
30 1X0P FAD 39.1608
31 1X0P FAD 39.1608
32 1X0P FAD 39.1608
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