Receptor
PDB id Resolution Class Description Source Keywords
5C6C 2.05 Å EC: 2.7.11.12 PKG II'S AMINO TERMINAL CYCLIC NUCLEOTIDE BINDING DOMAIN (CN COMPLEX WITH CAMP HOMO SAPIENS BINDING SITES CYCLIC AMP CYCLIC GMP CYCLIC GMP-DEPENDENT KINASE TYPE II MUTAGENESIS SITE-DIRECTED PROTEIN BINDING
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
CO A:307;
B:305;
A:306;
A:305;
Invalid;
Invalid;
Invalid;
Part of Protein;
none;
none;
none;
none;
submit data
58.933 Co [Co+2...
CA B:306;
A:308;
Part of Protein;
Part of Protein;
none;
none;
submit data
40.078 Ca [Ca+2...
CMP B:304;
A:304;
Valid;
Valid;
none;
none;
Kd = 418 nM
329.206 C10 H12 N5 O6 P c1nc(...
CD B:301;
A:303;
B:302;
B:303;
A:302;
A:301;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
112.411 Cd [Cd+2...
NA B:307;
Part of Protein;
none;
submit data
22.99 Na [Na+]
EDO A:309;
Invalid;
none;
submit data
62.068 C2 H6 O2 C(CO)...
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: CMP; Similar ligands found: 94
No: Ligand ECFP6 Tc MDL keys Tc
1 CMP 1 1
2 2BA 1 0.984848
3 SP1 0.757143 0.928571
4 RP1 0.757143 0.928571
5 1YD 0.727273 0.902778
6 4BW 0.727273 0.902778
7 1SY 0.653061 0.902778
8 1OR 0.635294 0.807692
9 4UR 0.626263 0.902778
10 7CH 0.580247 0.984615
11 6SX 0.573171 0.953846
12 6SZ 0.559524 0.984848
13 N6S 0.535354 0.914286
14 N6R 0.535354 0.914286
15 C2E 0.534091 0.902778
16 35G 0.534091 0.888889
17 PCG 0.534091 0.888889
18 1YC 0.53 0.875
19 Y3J 0.506667 0.753623
20 5CD 0.5 0.811594
21 XYA 0.5 0.826087
22 ACK 0.5 0.897059
23 ADN 0.5 0.826087
24 RAB 0.5 0.826087
25 6SW 0.494382 0.9
26 5AD 0.493151 0.776119
27 5N5 0.486842 0.8
28 75G 0.483146 0.890411
29 A4D 0.480519 0.8
30 M2T 0.475 0.736842
31 MTA 0.469136 0.777778
32 CC5 0.466667 0.850746
33 EP4 0.4625 0.756757
34 DTA 0.45679 0.816901
35 QQX 0.452381 0.835616
36 AMP 0.447059 0.927536
37 A 0.447059 0.927536
38 QQY 0.447059 0.847222
39 3DH 0.440476 0.777778
40 AMP MG 0.436782 0.875
41 3AM 0.435294 0.913043
42 ABM 0.431818 0.901408
43 J7C 0.431818 0.75
44 A2D 0.431818 0.928571
45 ZAS 0.430233 0.77027
46 7D7 0.428571 0.771429
47 S4M 0.426966 0.666667
48 6RE 0.425287 0.74026
49 SRA 0.425287 0.876712
50 3AD 0.425 0.838235
51 2AM 0.423529 0.9
52 AP2 0.422222 0.864865
53 A12 0.422222 0.864865
54 BA3 0.422222 0.928571
55 MAO 0.422222 0.740741
56 NEC 0.420455 0.726027
57 A3G 0.420455 0.780822
58 DSH 0.420455 0.727273
59 AOC 0.420455 0.802817
60 BEF ADP 0.419355 0.84
61 SFG 0.419355 0.753425
62 ADP BEF 0.419355 0.84
63 6JR 0.419048 0.927536
64 B4P 0.417582 0.928571
65 5AS 0.417582 0.741176
66 AP5 0.417582 0.928571
67 ADP 0.417582 0.901408
68 A3N 0.41573 0.767123
69 APC 0.414894 0.864865
70 SON 0.413043 0.864865
71 AN2 0.413043 0.888889
72 EEM 0.412371 0.691358
73 GJV 0.411111 0.730769
74 GGZ 0.41 0.78481
75 OVE 0.409091 0.863014
76 ADP MG 0.408602 0.863014
77 AU1 0.408602 0.876712
78 M33 0.408602 0.888889
79 CA0 0.408602 0.876712
80 ADX 0.408602 0.810127
81 A3P 0.406593 0.927536
82 5X8 0.404255 0.767123
83 50T 0.404255 0.888889
84 ATP 0.404255 0.901408
85 ACP 0.404255 0.876712
86 VO4 ADP 0.40404 0.888889
87 ADP VO4 0.40404 0.888889
88 SAM 0.402062 0.691358
89 0UM 0.401961 0.7
90 AQP 0.4 0.901408
91 APR 0.4 0.901408
92 PRX 0.4 0.876712
93 AR6 0.4 0.901408
94 5FA 0.4 0.901408
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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