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Receptor
PDB id Resolution Class Description Source Keywords
5KHD 1.75 Å NON-ENZYME: BINDING STRUCTURE OF 1.75 A BLDD C-DOMAIN-C-DI-GMP COMPLEX STREPTOMYCES VENEZUELAE BLDD STREPTOMYCES C-DI-GMP DNA BINDING PROTEIN
Ref.: TETRAMERIC C-DI-GMP MEDIATES EFFECTIVE TRANSCRIPTIO DIMERIZATION TO CONTROL STREPTOMYCES DEVELOPMENT. CELL V. 158 1136 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
C2E A:201;
R:201;
A:202;
R:202;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Kd = 2.5 uM
690.411 C20 H24 N10 O14 P2 c1nc2...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5KHD 1.75 Å NON-ENZYME: BINDING STRUCTURE OF 1.75 A BLDD C-DOMAIN-C-DI-GMP COMPLEX STREPTOMYCES VENEZUELAE BLDD STREPTOMYCES C-DI-GMP DNA BINDING PROTEIN
Ref.: TETRAMERIC C-DI-GMP MEDIATES EFFECTIVE TRANSCRIPTIO DIMERIZATION TO CONTROL STREPTOMYCES DEVELOPMENT. CELL V. 158 1136 2014
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 510 families.
1 5TZD - C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
2 5TZG - C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
3 5KHD Kd = 2.5 uM C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
4 5TZF - C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 391 families.
1 5TZD - C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
2 5TZG - C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
3 5KHD Kd = 2.5 uM C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
4 5TZF - 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 298 families.
1 5TZD - C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
2 5TZG - C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
3 5KHD Kd = 2.5 uM C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
4 5TZF - 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 : 5KHD; Ligand: C2E; Similar sites found with APoc: 15
This union binding pocket(no: 1) in the query (biounit: 5khd.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 1SQL GUN None
2 1QXA GLY GLY GLY None
3 6BYF CIT None
4 5T9E NAP 5.49451
5 4G5H UD7 6.59341
6 5CX6 CDP 7.69231
7 1XF1 CIT 7.69231
8 4FLP JQ1 9.89011
9 4UYG 73B 9.89011
10 1UUY PPI 10.989
11 5OJY CIT 12.0879
12 5T9F NAP 13.1868
13 5T9F TYR 13.1868
14 5UAV TFB 23.0769
15 5UAV NDP 23.0769
Pocket No.: 2; Query (leader) PDB : 5KHD; Ligand: C2E; Similar sites found with APoc: 20
This union binding pocket(no: 2) in the query (biounit: 5khd.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 1WLJ U5P None
2 1RZX ACE VAL LYS GLU SER LEU VAL None
3 2GU8 796 None
4 1NXJ GLV None
5 4G0P U5P None
6 5HDA SER MET PRO GLU LEU SER PRO VAL LEU None
7 1RZM E4P 3.2967
8 3SJK LYS PRO VAL LEU ARG THR ALA 3.2967
9 3O5N BR0 3.2967
10 3N75 G4P 5.49451
11 2Z3U CRR 6.59341
12 4XDY NAI 6.59341
13 3W2E NAD 6.59341
14 3W2E FAD 6.59341
15 3RS8 ALA TRP LEU PHE GLU ALA 7.69231
16 1SC6 NAD 7.69231
17 2G5C NAD 7.69231
18 5W3K NDP 9.89011
19 5BSH PRO 31.8681
20 4LO6 SIA GAL 42.8571
Pocket No.: 3; Query (leader) PDB : 5KHD; Ligand: C2E; Similar sites found with APoc: 8
This union binding pocket(no: 3) in the query (biounit: 5khd.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 2XRH NIO None
2 4XTX 590 2.1978
3 3ETG GLU 6.59341
4 3ETG NDP 6.59341
5 1QX4 FAD 6.59341
6 1C1X NAD 6.59341
7 2QX0 PH2 6.59341
8 4N70 2HX 8.79121
Pocket No.: 4; Query (leader) PDB : 5KHD; Ligand: C2E; Similar sites found with APoc: 29
This union binding pocket(no: 4) in the query (biounit: 5khd.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 1M4I KAN None
2 1M4I COA None
3 1M4I PAP None
4 4G6I RS3 None
5 5JWM 6ON None
6 4LAE 1VM 3.2967
7 4LAE NAP 3.2967
8 6B5G CQY 3.2967
9 6B5G NAD 3.2967
10 4X7G 3Y8 3.58566
11 3KCC CMP 4.3956
12 5L2M 6ZY 4.3956
13 4BJX 73B 4.3956
14 5L13 6ZE 5.49451
15 1T90 NAD 5.49451
16 2QE0 NAP 5.49451
17 2GZ3 NAP 5.49451
18 2YDW WSH 6.59341
19 4UYF 73B 6.59341
20 3VZ3 SSN 7.69231
21 1Q19 SSC 7.69231
22 5Z5I XYP 8.79121
23 3I6I NDP 8.79121
24 4PXL NAD 9.89011
25 5AE9 OKO 10.989
26 4I3V NAD 15.3846
27 1KY8 NAP 18.6813
28 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 19.7802
29 2WOX NDP 24.1758
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