Receptor
PDB id Resolution Class Description Source Keywords
3kyf 2.1 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF P4397 COMPLEXED WITH C-DI-GMP PSEUDOMONAS PUTIDA C-DI-GMP PILZ DOMAIN PP4397 VCA0042 UNKNOWN FUNCTION
Ref.: STRUCTURE OF PP4397 REVEALS THE MOLECULAR BASIS FOR DIFFERENT C-DI-GMP BINDING MODES BY PILZ DOMAIN PROTEINS. J.MOL.BIOL. V. 398 97 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
5GP 5GP A:501;
A:503;
 Valid;
Valid;
 none;
none;
 Kd = 165 nM
688.4 n/a O=P1(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3KYF 2.1 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF P4397 COMPLEXED WITH C-DI-GMP PSEUDOMONAS PUTIDA C-DI-GMP PILZ DOMAIN PP4397 VCA0042 UNKNOWN FUNCTION
Ref.: STRUCTURE OF PP4397 REVEALS THE MOLECULAR BASIS FOR DIFFERENT C-DI-GMP BINDING MODES BY PILZ DOMAIN PROTEINS. J.MOL.BIOL. V. 398 97 2010
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 3KYF Kd = 165 nM 5GP 5GP n/a n/a
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 3KYF Kd = 165 nM 5GP 5GP n/a n/a
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 3KYF Kd = 165 nM 5GP 5GP n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 5GP 5GP; Similar ligands found: 46
No: Ligand ECFP6 Tc MDL keys Tc
1 5GP 5GP 1 1
2 35G 0.743902 0.945205
3 PCG 0.743902 0.945205
4 C2E 0.743902 0.958904
5 4BW 0.632653 0.958904
6 1YD 0.632653 0.958904
7 4UR 0.579439 0.958904
8 KT2 0.530973 0.958904
9 GMP 0.52381 0.815789
10 1YC 0.518868 0.931507
11 3GP 0.473118 0.906667
12 G 0.463158 0.894737
13 5GP 0.463158 0.894737
14 SGP 0.463158 0.8125
15 GDP 0.454545 0.883117
16 6SW 0.453608 0.90411
17 G1R 0.45098 0.871795
18 GP3 0.444444 0.909091
19 2GP 0.442105 0.87013
20 ALF 5GP 0.441176 0.851852
21 GP2 0.44 0.85
22 G2R 0.439252 0.85
23 GDP BEF 0.436893 0.896104
24 KB7 0.435644 0.768293
25 GNH 0.435644 0.871795
26 6J7 0.434343 0.896104
27 P2G 0.43299 0.868421
28 G2P 0.432692 0.85
29 G3D 0.432692 0.894737
30 GTP MG 0.432692 0.92
31 GTP 0.427184 0.883117
32 GMV 0.427184 0.860759
33 G4P 0.424528 0.894737
34 GCP 0.423077 0.860759
35 KBD 0.422018 0.8125
36 GPX 0.420561 0.857143
37 9GM 0.419048 0.860759
38 GSP 0.419048 0.839506
39 GNP 0.419048 0.860759
40 GDP ALF 0.416667 0.851852
41 GDP AF3 0.416667 0.851852
42 GAV 0.411215 0.85
43 P1G 0.41 0.857143
44 Y9Z 0.40708 0.8
45 GH3 0.401869 0.883117
46 G3A 0.4 0.909091
Similar Ligands (3D)
Ligand no: 1; Ligand: 5GP 5GP; Similar ligands found: 1
No: Ligand Similarity coefficient
1 2BA 0.9723
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3KYF; Ligand: 5GP 5GP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3kyf.bio2) has 10 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3KYF; Ligand: 5GP 5GP; Similar sites found with APoc: 2
This union binding pocket(no: 2) in the query (biounit: 3kyf.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 5Y4R C2E 10.3448
2 5Y4R C2E 10.3448
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