Receptor
PDB id Resolution Class Description Source Keywords
5C8W 1.8 Å EC: 2.7.11.12 PKG II'S AMINO TERMINAL CYCLIC NUCLEOTIDE BINDING DOMAIN (CN COMPLEX WITH CGMP HOMO SAPIENS BINDING SITES CYCLIC AMP CYCLIC GMP CYCLIC GMP-DEPENDENT KINASE TYPE II MUTAGENESIS SITE-DIRECTED PROTEIN BINDINGTRANSFERASE
Ref.: STRUCTURAL BASIS OF CYCLIC NUCLEOTIDE SELECTIVITY I CGMP-DEPENDENT PROTEIN KINASE II. J.BIOL.CHEM. V. 291 5623 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PCG C:302;
A:302;
E:302;
D:302;
F:302;
B:303;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
Kd = 43.8 nM
345.205 C10 H12 N5 O7 P c1nc2...
NA F:303;
C:303;
A:303;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
22.99 Na [Na+]
MLA D:301;
A:301;
B:302;
E:301;
F:301;
B:301;
C:301;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
submit data
104.061 C3 H4 O4 C(C(=...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5C8W 1.8 Å EC: 2.7.11.12 PKG II'S AMINO TERMINAL CYCLIC NUCLEOTIDE BINDING DOMAIN (CN COMPLEX WITH CGMP HOMO SAPIENS BINDING SITES CYCLIC AMP CYCLIC GMP CYCLIC GMP-DEPENDENT KINASE TYPE II MUTAGENESIS SITE-DIRECTED PROTEIN BINDINGTRANSFERASE
Ref.: STRUCTURAL BASIS OF CYCLIC NUCLEOTIDE SELECTIVITY I CGMP-DEPENDENT PROTEIN KINASE II. J.BIOL.CHEM. V. 291 5623 2016
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 5C6C Kd = 418 nM CMP C10 H12 N5 O6 P c1nc(c2c(n....
2 5C8W Kd = 43.8 nM PCG C10 H12 N5 O7 P c1nc2c(n1[....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 5C6C Kd = 418 nM CMP C10 H12 N5 O6 P c1nc(c2c(n....
2 5C8W Kd = 43.8 nM PCG C10 H12 N5 O7 P c1nc2c(n1[....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3OCP Kd = 27 nM CMP C10 H12 N5 O6 P c1nc(c2c(n....
2 5C6C Kd = 418 nM CMP C10 H12 N5 O6 P c1nc(c2c(n....
3 5C8W Kd = 43.8 nM PCG C10 H12 N5 O7 P c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PCG; Similar ligands found: 57
No: Ligand ECFP6 Tc MDL keys Tc
1 35G 1 1
2 C2E 1 0.986111
3 PCG 1 1
4 4BW 0.806818 0.986111
5 1YD 0.806818 0.986111
6 5GP 5GP 0.743902 0.945205
7 4UR 0.731959 0.986111
8 6SW 0.627907 0.957747
9 1YC 0.616162 0.958333
10 6J7 0.58427 0.946667
11 CMP 0.534091 0.888889
12 2BA 0.534091 0.902778
13 GMP 0.53012 0.84
14 1SY 0.495575 0.986111
15 SGP 0.483871 0.835443
16 6SZ 0.483871 0.902778
17 3GP 0.478261 0.932432
18 1OR 0.474747 0.729412
19 G 0.468085 0.945946
20 5GP 0.468085 0.945946
21 7CH 0.467391 0.875
22 6SX 0.462366 0.847222
23 6JR 0.457944 0.930556
24 G2R 0.457143 0.897436
25 GPX 0.451923 0.906667
26 GP3 0.44898 0.934211
27 2GP 0.446809 0.92
28 GP2 0.444444 0.897436
29 GDP 0.444444 0.933333
30 GNH 0.44 0.921053
31 P2G 0.4375 0.893333
32 G2P 0.436893 0.897436
33 GMV 0.431373 0.909091
34 GTP 0.431373 0.933333
35 ALF 5GP 0.431373 0.851852
36 G1R 0.427184 0.921053
37 GCP 0.427184 0.909091
38 G3D 0.423077 0.945946
39 9GM 0.423077 0.909091
40 GSP 0.423077 0.886076
41 GNP 0.423077 0.909091
42 GDP AF3 0.420561 0.851852
43 G4P 0.415094 0.945946
44 GAV 0.415094 0.897436
45 P1G 0.414141 0.881579
46 Y9Z 0.410714 0.843373
47 GCP G 0.409091 0.906667
48 GDP ALF 0.407407 0.851852
49 ALF GDP 0.407407 0.851852
50 N6R 0.40708 0.818182
51 N6S 0.40708 0.818182
52 G G 0.40708 0.934211
53 G3A 0.403509 0.934211
54 YGP 0.401786 0.8875
55 GPG 0.4 0.922078
56 G5P 0.4 0.934211
57 0O2 0.4 0.945946
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5C8W; Ligand: PCG; Similar sites found with APoc: 11
This union binding pocket(no: 1) in the query (biounit: 5c8w.bio5) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 4N9I PCG 9.79021
2 4AVB CMP 25.8741
3 2PTM CMP 30.7692
4 3CF6 SP1 31.4685
5 3KCC CMP 31.4685
6 4NVP 7CH 33.5664
7 4MUV PCG 37.3239
8 5KJZ PCG 43.3566
9 5K8S CMP 44.0559
10 3OF1 CMP 45.4545
11 1CX4 CMP 48.2517
Pocket No.: 2; Query (leader) PDB : 5C8W; Ligand: PCG; 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: 5c8w.bio3) has 15 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5C8W; Ligand: PCG; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5c8w.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5C8W; Ligand: PCG; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5c8w.bio4) has 15 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5C8W; Ligand: PCG; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 5c8w.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 5C8W; Ligand: PCG; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 5c8w.bio6) has 15 residues
No: Leader PDB Ligand Sequence Similarity
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