Receptor
PDB id Resolution Class Description Source Keywords
3KYG 2.1 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF VCA0042 (L135R) COMPLEXED WITH C-DI-GMP VIBRIO CHOLERAE 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;
B:501;
B:503;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Kd = 55.1 nM
688.4 n/a O=P1(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3KYG 2.1 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF VCA0042 (L135R) COMPLEXED WITH C-DI-GMP VIBRIO CHOLERAE 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 1579 families.
1 3KYG Kd = 55.1 nM 5GP 5GP n/a n/a
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1312 families.
1 3KYG Kd = 55.1 nM 5GP 5GP n/a n/a
2 2RDE Kd = 97.1 nM C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1130 families.
1 3KYG Kd = 55.1 nM 5GP 5GP n/a n/a
2 2RDE Kd = 97.1 nM C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 5GP 5GP; Similar ligands found: 47
No: Ligand ECFP6 Tc MDL keys Tc
1 5GP 5GP 1 1
2 C2E 0.743902 0.958904
3 35G 0.743902 0.945205
4 PCG 0.743902 0.945205
5 1YD 0.632653 0.958904
6 4BW 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 KB7 0.435644 0.768293
24 GNH 0.435644 0.871795
25 6J7 0.434343 0.896104
26 P2G 0.43299 0.868421
27 G3D 0.432692 0.894737
28 G2P 0.432692 0.85
29 GTP 0.427184 0.883117
30 GMV 0.427184 0.860759
31 G4P 0.424528 0.894737
32 GCP 0.423077 0.860759
33 KBD 0.422018 0.8125
34 GPX 0.420561 0.857143
35 GSP 0.419048 0.839506
36 GNP 0.419048 0.860759
37 9GM 0.419048 0.860759
38 GDP AF3 0.416667 0.851852
39 ALF GDP 0.416667 0.851852
40 GDP ALF 0.416667 0.851852
41 GAV 0.411215 0.85
42 P1G 0.41 0.857143
43 Y9Z 0.40708 0.8
44 GCP G 0.405405 0.932432
45 G G 0.403509 0.934211
46 GH3 0.401869 0.883117
47 G3A 0.4 0.909091
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3KYG; 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: 3kyg.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3KYG; 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: 2) in the query (biounit: 3kyg.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3KYG; Ligand: 5GP 5GP; Similar sites found with APoc: 3
This union binding pocket(no: 3) in the query (biounit: 3kyg.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 5XLY C2E 14.2857
2 5Y4R C2E 17.931
3 5Y4R C2E 17.931
Pocket No.: 4; Query (leader) PDB : 3KYG; Ligand: 5GP 5GP; Similar sites found with APoc: 3
This union binding pocket(no: 4) in the query (biounit: 3kyg.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 5XLY C2E 14.2857
2 5Y4R C2E 17.931
3 5Y4R C2E 17.931
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