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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 9 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 8 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 204 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: 57
No: Ligand ECFP6 Tc MDL keys Tc
1 35G 1 0.986111
2 C2E 1 1
3 PCG 1 0.986111
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 CMP 0.534091 0.902778
12 2BA 0.534091 0.916667
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 G 0.468085 0.933333
20 5GP 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 GP2 0.444444 0.886076
29 GDP 0.444444 0.921053
30 GNH 0.44 0.909091
31 P2G 0.4375 0.881579
32 G2P 0.436893 0.886076
33 GMV 0.431373 0.897436
34 GTP 0.431373 0.921053
35 ALF 5GP 0.431373 0.841463
36 G1R 0.427184 0.909091
37 GCP 0.427184 0.897436
38 G3D 0.423077 0.933333
39 9GM 0.423077 0.897436
40 GSP 0.423077 0.875
41 GNP 0.423077 0.897436
42 GDP AF3 0.420561 0.841463
43 G4P 0.415094 0.933333
44 GAV 0.415094 0.886076
45 P1G 0.414141 0.87013
46 Y9Z 0.410714 0.833333
47 GCP G 0.409091 0.894737
48 GDP ALF 0.407407 0.841463
49 ALF GDP 0.407407 0.841463
50 N6R 0.40708 0.831169
51 N6S 0.40708 0.831169
52 G G 0.40708 0.947368
53 G3A 0.403509 0.947368
54 YGP 0.401786 0.876543
55 GPG 0.4 0.935065
56 G5P 0.4 0.947368
57 0O2 0.4 0.933333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4LJ3; Ligand: C2E; Similar sites found with APoc: 51
This union binding pocket(no: 1) in the query (biounit: 4lj3.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 5H20 GLC None
2 4WQQ MAN 1.41844
3 2J5V PCA 1.43369
4 3THR C2F 1.79211
5 4IV9 TSR 2.15054
6 4D5G TPP 2.15054
7 4XH0 ADP 2.15054
8 5A04 BGC 2.50896
9 5ZYN SIN 2.50896
10 2OS2 OGA 2.86738
11 4C2C ALA ALA ALA 2.86738
12 2YBP 2HG 2.86738
13 2Q8E OGA 2.86738
14 2P5B OGA 2.86738
15 2D3Y DU 3.19635
16 1GYM MYG 3.22581
17 6EDK 1YA 3.22581
18 5WS9 OXL 3.22581
19 4Q3S X7A 3.58423
20 5EY0 GTP 3.64964
21 4IU0 ABH 3.93939
22 4RM0 FUC NAG GAL 3.94265
23 2HJ4 PNZ 3.94265
24 6A56 LAT 4.26829
25 3FXU TSU 4.30108
26 1PVC ILE SER GLU VAL 4.42804
27 1VHZ APR 4.54545
28 4AVV CD 4.90196
29 4AVV GHE 4.90196
30 5U75 SIA GAL NDG FUC 5.35714
31 4TVD BGC 5.37634
32 2P4Y C03 5.41516
33 6MJ7 ARG 5.45455
34 4KBA 1QM 5.73477
35 4G9N NGA 6.29371
36 3QX9 ATP 6.52174
37 3E3U NVC 6.59898
38 2W5P CL8 7.38255
39 3QDV NDG 7.69231
40 3QDX CBS 7.69231
41 3HCH RSM 8.21918
42 2Q37 3AL 8.96057
43 4UYW H1S 9.67742
44 5LE1 6UW 9.77444
45 2Z48 NGA 11.1111
46 3GFZ C2E 22.2222
47 4FOJ C2E 33.3333
48 4FOU C2E 33.3333
49 3HV8 C2E 36.9403
50 3PJU C2E 43.7751
51 3N3T C2E 43.8776
Pocket No.: 2; Query (leader) PDB : 4LJ3; Ligand: C2E; Similar sites found with APoc: 9
This union binding pocket(no: 2) in the query (biounit: 4lj3.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 5HZ7 BGC 2.15054
2 3B0P FMN 2.15054
3 5MIT NAP 3.58423
4 5MIT FAD 3.58423
5 3FUR Z12 5.51471
6 3QDU CBS CBS 7.69231
7 3QDW NDG 7.69231
8 1Z44 FMN 7.8853
9 6BND OPE 9.67742
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