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 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[....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 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 2 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: 59
No: Ligand ECFP6 Tc MDL keys Tc
1 PCG 1 1
2 35G 1 1
3 C2E 1 0.986111
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 2BA 0.534091 0.902778
12 CMP 0.534091 0.888889
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 5GP 0.468085 0.945946
20 G 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 GDP BEF 0.445545 0.8625
29 GDP 0.444444 0.933333
30 GP2 0.444444 0.897436
31 GNH 0.44 0.921053
32 P2G 0.4375 0.893333
33 G2P 0.436893 0.897436
34 GDP MG 0.435644 0.884615
35 ALF 5GP 0.431373 0.851852
36 GTP 0.431373 0.933333
37 GMV 0.431373 0.909091
38 G1R 0.427184 0.921053
39 GCP 0.427184 0.909091
40 GNP 0.423077 0.909091
41 GSP 0.423077 0.886076
42 G3D 0.423077 0.945946
43 GDP AF3 0.420561 0.851852
44 BEF GDP 0.419048 0.851852
45 GTP MG 0.419048 0.884615
46 GCP G 0.415094 0.896104
47 G4P 0.415094 0.945946
48 GAV 0.415094 0.897436
49 P1G 0.414141 0.881579
50 Y9Z 0.410714 0.843373
51 G G 0.409091 0.921053
52 GDP ALF 0.407407 0.851852
53 N6R 0.40708 0.818182
54 N6S 0.40708 0.818182
55 G3A 0.403509 0.934211
56 YGP 0.401786 0.8875
57 G5P 0.4 0.934211
58 0O2 0.4 0.945946
59 GPG 0.4 0.922078
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5C8W; Ligand: PCG; Similar sites found: 57
This union binding pocket(no: 1) in the query (biounit: 5c8w.bio5) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5H5O PCG 0.0000274 0.49087 None
2 3M3E GAL A2G NPO 0.01079 0.40927 None
3 3LA3 2FT 0.001616 0.44825 2.0979
4 3MTX PGT 0.01705 0.42066 2.0979
5 4C2W ANP 0.005729 0.40691 2.0979
6 5DA3 58V 0.002776 0.42022 2.7972
7 5H2U 1N1 0.00133 0.41056 2.7972
8 4Q0L V14 0.02116 0.40799 2.7972
9 2XKO AKG 0.001222 0.45449 3.4965
10 2XHK AKG 0.001335 0.45049 3.4965
11 2WEI VGG 0.0002318 0.44981 3.4965
12 2VN9 GVD 0.002067 0.43564 3.4965
13 4XLI 1N1 0.0014 0.40744 3.4965
14 1V0O INR 0.001159 0.40329 3.4965
15 5F6U 5VK 0.002515 0.4414 4.1958
16 4Z1D PEP 0.004996 0.42288 4.1958
17 1EYQ NAR 0.008321 0.40685 4.1958
18 1RYO OXL 0.007833 0.41878 4.8951
19 4NFN 2KC 0.001375 0.40901 4.8951
20 4Y0X ADP 0.002672 0.40639 4.8951
21 3THR C2F 0.001237 0.40894 5.59441
22 1VMK GUN 0.01227 0.4046 5.59441
23 4YEE 4CQ 0.01357 0.40276 6.66667
24 5A6N U7E 0.003921 0.43639 6.99301
25 3ZGJ RMN 0.004794 0.41826 6.99301
26 3SXS PP2 0.0004368 0.40575 6.99301
27 4DC2 ADE 0.004396 0.42932 7.69231
28 5IFK HPA 0.007978 0.41368 7.69231
29 3C0G 3AM 0.003973 0.40536 7.69231
30 1Z0N BCD 0.01671 0.40305 8.33333
31 5MJA 7O3 0.002933 0.40476 8.39161
32 1D8C GLV 0.01115 0.40382 9.09091
33 4X1B MLI 0.015 0.40269 9.09091
34 2V7O DRN 0.001914 0.43722 9.79021
35 4Y8D 49J 0.0002086 0.43063 9.79021
36 3HQP OXL 0.008613 0.42855 9.79021
37 4YMJ 4EJ 0.006053 0.42039 9.79021
38 5HES 032 0.0005153 0.48423 11.1888
39 4Z7X 3CX 0.004308 0.43763 11.1888
40 1Q19 SSC 0.006193 0.42206 11.1888
41 5LXC 7AA 0.003084 0.43506 11.8881
42 1Q8Y ADE 0.004164 0.42118 12.5874
43 5KEW 6SB 0.005718 0.42259 14.5833
44 3HZT J60 0.002685 0.42201 19.5804
45 4AVB CMP 0.000000003346 0.66198 25.8741
46 1ZTH ADP 0.006211 0.40544 28.6713
47 3CF6 SP1 0.000000000588 0.65264 31.4685
48 3KCC CMP 0.000000013 0.57813 31.4685
49 4MUV PCG 0.000000000947 0.64701 37.3239
50 3I54 CMP 0.0000005862 0.54341 39.8601
51 3I59 N6S 0.000000722 0.51977 39.8601
52 3I59 N6R 0.000002347 0.49904 39.8601
53 4CYD CMP 0.000000415 0.55018 41.958
54 5KJZ PCG 0.000000000137 0.67673 43.3566
55 5K8S CMP 0.000000004338 0.6037 44.0559
56 3OF1 CMP 0.0000000001265 0.74885 45.4545
57 1CX4 CMP 0.0000001318 0.55422 48.2517
Pocket No.: 2; Query (leader) PDB : 5C8W; Ligand: PCG; Similar sites found: 7
This union binding pocket(no: 2) in the query (biounit: 5c8w.bio3) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3WV6 GAL GLC 0.006154 0.41585 None
2 4D2S DYK 0.003564 0.40864 None
3 2VZ6 FEF 0.004119 0.40416 3.4965
4 1WD4 AHR 0.01151 0.40013 3.4965
5 4H4D 10E 0.00285 0.40429 4.1958
6 4YEF 4CQ 0.009494 0.4037 6.74157
7 1XVB BBX 0.001376 0.40168 12.5874
Pocket No.: 3; Query (leader) PDB : 5C8W; Ligand: PCG; Similar sites found: 6
This union binding pocket(no: 3) in the query (biounit: 5c8w.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4MKF AP5 0.03694 0.40737 None
2 4TWL ASC 0.01707 0.40199 2.0979
3 1VRP IOM 0.01171 0.41333 4.1958
4 5EOB 5QQ 0.01004 0.44656 4.8951
5 1U6R IOM 0.01505 0.404 5.59441
6 4N9I PCG 0.00000001944 0.41125 9.79021
Pocket No.: 4; Query (leader) PDB : 5C8W; Ligand: PCG; Similar sites found: 1
This union binding pocket(no: 4) in the query (biounit: 5c8w.bio4) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5CDH TLA 0.007352 0.40761 4.1958
Pocket No.: 5; Query (leader) PDB : 5C8W; Ligand: PCG; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 5C8W; Ligand: PCG; Similar sites found: 5
This union binding pocket(no: 6) in the query (biounit: 5c8w.bio6) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1I7A PHE 0.001576 0.42103 None
2 3HMO STU 0.001587 0.40645 None
3 1SLT NDG GAL 0.02264 0.40257 None
4 5DG2 GAL GLC 0.007404 0.40061 None
5 2YMZ LAT 0.01607 0.40269 3.84615
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