Receptor
PDB id Resolution Class Description Source Keywords
4LJ3 1.7 Å EC: 3.1.4.- CRYSTAL STRUCTURE OF THE EAL DOMAIN OF C-DI-GMP SPECIFIC PHOSPHODIESTERASE YAHA IN COMPLEX WITH SUBSTRATE C-DI-GMP A ESCHERICHIA COLI PGPG PHOSPHODIESTERASE TIM-BARREL HYDROLASE
Ref.: INHERENT REGULATION OF EAL DOMAIN-CATALYZED HYDROLY SECOND MESSENGER CYCLIC DI-GMP. J.BIOL.CHEM. V. 289 6978 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA B:402;
B:403;
A:402;
A:403;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
40.078 Ca [Ca+2...
IMD B:404;
A:404;
Invalid;
Invalid;
none;
none;
submit data
69.085 C3 H5 N2 c1c[n...
C2E B:401;
A:401;
Valid;
Valid;
none;
none;
Kd < 1 nM
690.411 C20 H24 N10 O14 P2 c1nc2...
HB0 A:405;
B:405;
Invalid;
Invalid;
none;
none;
submit data
130.185 C7 H14 O2 C1CC(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4LJ3 1.7 Å EC: 3.1.4.- CRYSTAL STRUCTURE OF THE EAL DOMAIN OF C-DI-GMP SPECIFIC PHOSPHODIESTERASE YAHA IN COMPLEX WITH SUBSTRATE C-DI-GMP A ESCHERICHIA COLI PGPG PHOSPHODIESTERASE TIM-BARREL HYDROLASE
Ref.: INHERENT REGULATION OF EAL DOMAIN-CATALYZED HYDROLY SECOND MESSENGER CYCLIC DI-GMP. J.BIOL.CHEM. V. 289 6978 2014
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4LJ3 Kd < 1 nM C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4LJ3 Kd < 1 nM C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 181 families.
1 5M1T - C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
2 5MF5 - C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
3 5MFU - G G n/a n/a
4 4LJ3 Kd < 1 nM C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: C2E; Similar ligands found: 59
No: Ligand ECFP6 Tc MDL keys Tc
1 PCG 1 0.986111
2 35G 1 0.986111
3 C2E 1 1
4 4BW 0.806818 1
5 1YD 0.806818 1
6 5GP 5GP 0.743902 0.958904
7 4UR 0.731959 1
8 6SW 0.627907 0.944444
9 1YC 0.616162 0.972222
10 6J7 0.58427 0.934211
11 2BA 0.534091 0.916667
12 CMP 0.534091 0.902778
13 GMP 0.53012 0.828947
14 1SY 0.495575 1
15 SGP 0.483871 0.825
16 6SZ 0.483871 0.916667
17 3GP 0.478261 0.92
18 1OR 0.474747 0.741176
19 5GP 0.468085 0.933333
20 G 0.468085 0.933333
21 7CH 0.467391 0.888889
22 6SX 0.462366 0.861111
23 6JR 0.457944 0.944444
24 G2R 0.457143 0.886076
25 GPX 0.451923 0.894737
26 GP3 0.44898 0.947368
27 2GP 0.446809 0.907895
28 GDP BEF 0.445545 0.851852
29 GDP 0.444444 0.921053
30 GP2 0.444444 0.886076
31 GNH 0.44 0.909091
32 P2G 0.4375 0.881579
33 G2P 0.436893 0.886076
34 GDP MG 0.435644 0.873418
35 ALF 5GP 0.431373 0.841463
36 GTP 0.431373 0.921053
37 GMV 0.431373 0.897436
38 G1R 0.427184 0.909091
39 GCP 0.427184 0.897436
40 GNP 0.423077 0.897436
41 GSP 0.423077 0.875
42 G3D 0.423077 0.933333
43 GDP AF3 0.420561 0.841463
44 BEF GDP 0.419048 0.841463
45 GTP MG 0.419048 0.873418
46 GCP G 0.415094 0.884615
47 G4P 0.415094 0.933333
48 GAV 0.415094 0.886076
49 P1G 0.414141 0.87013
50 Y9Z 0.410714 0.833333
51 G G 0.409091 0.934211
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 G5P 0.4 0.947368
58 0O2 0.4 0.933333
59 GPG 0.4 0.935065
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4LJ3; Ligand: C2E; Similar sites found: 29
This union binding pocket(no: 1) in the query (biounit: 4lj3.bio1) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WQQ MAN 0.04949 0.40349 1.41844
2 2J5V PCA 0.01721 0.41071 1.43369
3 4IV9 TSR 0.02586 0.40474 2.15054
4 4XH0 ADP 0.03478 0.40112 2.15054
5 2OS2 OGA 0.0263 0.40793 2.86738
6 4C2C ALA ALA ALA 0.02463 0.40747 2.86738
7 2YBP 2HG 0.02705 0.40712 2.86738
8 2Q8E OGA 0.02726 0.40698 2.86738
9 2P5B OGA 0.01945 0.40064 2.86738
10 4Q3S X7A 0.01881 0.40134 3.58423
11 5EY0 GTP 0.01785 0.40624 3.64964
12 4RM0 FUC NAG GAL 0.01341 0.42189 3.94265
13 1VHZ APR 0.01202 0.43016 4.54545
14 5U75 SIA GAL NDG FUC 0.01066 0.42215 5.35714
15 4KBA 1QM 0.02784 0.40045 5.73477
16 3QX9 ATP 0.006705 0.43886 6.52174
17 2W5P CL8 0.02415 0.40954 7.38255
18 3QDW NDG 0.01145 0.42718 7.69231
19 3QDV NDG 0.02362 0.40941 7.69231
20 3HCH RSM 0.03032 0.40339 8.21918
21 2Q37 3AL 0.03335 0.40263 8.96057
22 4UYW H1S 0.005584 0.42199 9.67742
23 5LE1 6UW 0.01831 0.41236 9.77444
24 3GFZ C2E 0.0000000004755 0.6887 22.2222
25 4FOJ C2E 0.0000002468 0.61846 33.3333
26 4FOU C2E 0.000001948 0.56335 33.3333
27 3HV8 C2E 0.0000000009785 0.69879 36.9403
28 3PJU C2E 0.000000002505 0.62046 43.7751
29 3N3T C2E 0.00000000000334 0.77283 43.8776
Pocket No.: 2; Query (leader) PDB : 4LJ3; Ligand: C2E; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4lj3.bio1) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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