Receptor
PDB id Resolution Class Description Source Keywords
5BV6 1.94 Å EC: 2.7.11.12 PKG II'S CARBOXYL TERMINAL CYCLIC NUCLEOTIDE BINDING DOMAIN A COMPLEX WITH CGMP HOMO SAPIENS CYCLIC GMP-DEPENDENT PROTEIN KINASE TYPE II TRANSFERASE
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
35G A:501;
Valid;
none;
Kd = 31 nM
345.205 C10 H12 N5 O7 P c1nc2...
CA A:504;
A:502;
Invalid;
Part of Protein;
none;
none;
submit data
40.078 Ca [Ca+2...
ACT A:503;
Invalid;
none;
submit data
59.044 C2 H3 O2 CC(=O...
NA A:505;
Invalid;
none;
submit data
22.99 Na [Na+]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5BV6 1.94 Å EC: 2.7.11.12 PKG II'S CARBOXYL TERMINAL CYCLIC NUCLEOTIDE BINDING DOMAIN A COMPLEX WITH CGMP HOMO SAPIENS CYCLIC GMP-DEPENDENT PROTEIN KINASE TYPE II TRANSFERASE
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 5BV6 Kd = 31 nM 35G C10 H12 N5 O7 P c1nc2c(n1[....
2 5JIX - 6J7 C10 H11 Br N5 O7 P C1[C@@H]2[....
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 5BV6 Kd = 31 nM 35G C10 H12 N5 O7 P c1nc2c(n1[....
2 5JIX - 6J7 C10 H11 Br N5 O7 P C1[C@@H]2[....
50% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4OFG - PCG C10 H12 N5 O7 P c1nc2c(n1[....
2 5JAX - 6J7 C10 H11 Br N5 O7 P C1[C@@H]2[....
3 5J48 - 6FW C16 H15 Cl N5 O7 P S c1cc(ccc1S....
4 5KJY - CMP C10 H12 N5 O6 P c1nc(c2c(n....
5 5KJX - CMP C10 H12 N5 O6 P c1nc(c2c(n....
6 5KJZ - PCG C10 H12 N5 O7 P c1nc2c(n1[....
7 5T3N Kd = 9.1 nM 75G C10 H11 Cl N5 O5 P S c1nc2c(nc(....
8 5K8S Kd = 6 nM CMP C10 H12 N5 O6 P c1nc(c2c(n....
9 5BV6 Kd = 31 nM 35G C10 H12 N5 O7 P c1nc2c(n1[....
10 5JIX - 6J7 C10 H11 Br N5 O7 P C1[C@@H]2[....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 35G; Similar ligands found: 59
No: Ligand ECFP6 Tc MDL keys Tc
1 PCG 1 1
2 C2E 1 0.986111
3 35G 1 1
4 1YD 0.806818 0.986111
5 4BW 0.806818 0.986111
6 5GP 5GP 0.743902 0.945205
7 4UR 0.731959 0.986111
8 KT2 0.669903 0.986111
9 6SW 0.627907 0.957747
10 1YC 0.616162 0.958333
11 6J7 0.58427 0.946667
12 CMP 0.534091 0.888889
13 2BA 0.534091 0.902778
14 GMP 0.53012 0.84
15 1SY 0.495575 0.986111
16 SGP 0.483871 0.835443
17 6SZ 0.483871 0.902778
18 3GP 0.478261 0.932432
19 1OR 0.474747 0.729412
20 G 0.468085 0.945946
21 5GP 0.468085 0.945946
22 7CH 0.467391 0.875
23 6SX 0.462366 0.847222
24 6JR 0.457944 0.930556
25 G2R 0.457143 0.897436
26 GPX 0.451923 0.906667
27 GP3 0.44898 0.934211
28 2GP 0.446809 0.92
29 GP2 0.444444 0.897436
30 GDP 0.444444 0.933333
31 GNH 0.44 0.921053
32 KB7 0.44 0.790123
33 P2G 0.4375 0.893333
34 G2P 0.436893 0.897436
35 GMV 0.431373 0.909091
36 GTP 0.431373 0.933333
37 ALF 5GP 0.431373 0.851852
38 GDP BEF 0.427184 0.896104
39 G1R 0.427184 0.921053
40 GCP 0.427184 0.909091
41 GTP MG 0.423077 0.92
42 G3D 0.423077 0.945946
43 GNP 0.423077 0.909091
44 9GM 0.423077 0.909091
45 GSP 0.423077 0.886076
46 GDP AF3 0.420561 0.851852
47 G4P 0.415094 0.945946
48 GAV 0.415094 0.897436
49 P1G 0.414141 0.881579
50 KBD 0.412844 0.8125
51 Y9Z 0.410714 0.843373
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 GPG 0.4 0.922078
58 0O2 0.4 0.945946
59 G5P 0.4 0.934211
Similar Ligands (3D)
Ligand no: 1; Ligand: 35G; Similar ligands found: 110
No: Ligand Similarity coefficient
1 75G 0.9840
2 SP1 0.9760
3 RP1 0.9756
4 CC7 0.9151
5 AMP 0.9100
6 8MF 0.9053
7 6SY 0.9033
8 0NH 0.9032
9 9PP 0.9019
10 CJN 0.8998
11 7FZ 0.8977
12 DGP 0.8960
13 MG7 0.8947
14 NYM 0.8929
15 TMP 0.8923
16 UFP 0.8917
17 AGI 0.8907
18 DG 0.8903
19 IMH 0.8901
20 5HM 0.8887
21 94M 0.8882
22 3AM 0.8871
23 71V 0.8859
24 3WK 0.8851
25 LU2 0.8827
26 NXB 0.8827
27 IMK 0.8826
28 5HU 0.8808
29 ADN 0.8806
30 8OG 0.8804
31 1Q4 0.8804
32 MQ1 0.8799
33 D5M 0.8798
34 LRT 0.8798
35 3AD 0.8786
36 IXG 0.8774
37 0QX 0.8773
38 NOJ BGC 0.8760
39 2DT 0.8758
40 INI 0.8758
41 47X 0.8757
42 9W8 0.8755
43 HFS 0.8752
44 C4F 0.8747
45 6QX 0.8740
46 KS5 0.8739
47 9RK 0.8736
48 TOP 0.8734
49 GEN 0.8733
50 4UO 0.8732
51 KMP 0.8713
52 147 0.8712
53 TCW 0.8708
54 IMP 0.8704
55 6EL 0.8703
56 AX6 0.8699
57 8CS 0.8699
58 FZB 0.8697
59 CWE 0.8693
60 M77 0.8691
61 J5Z 0.8691
62 JZ8 0.8691
63 NAR 0.8690
64 E2N 0.8687
65 F1T 0.8686
66 LVY 0.8685
67 W72 0.8681
68 QUE 0.8680
69 697 0.8679
70 H52 0.8671
71 205 0.8667
72 6OG 0.8665
73 IXE 0.8661
74 D59 0.8659
75 AJ8 0.8658
76 XYS XYS 0.8657
77 DH2 0.8656
78 6WU 0.8650
79 AJ6 0.8650
80 XYP XYP 0.8647
81 FY8 0.8647
82 3WN 0.8640
83 3WO 0.8640
84 PRH 0.8640
85 Y70 0.8639
86 SIJ 0.8638
87 5YA 0.8638
88 2H4 0.8636
89 TVZ 0.8635
90 EF2 0.8633
91 MTA 0.8631
92 OAK 0.8625
93 5FD 0.8622
94 BK4 0.8607
95 UMP 0.8606
96 CHJ 0.8602
97 5P7 0.8588
98 5AD 0.8576
99 DQH 0.8576
100 FDM 0.8573
101 C 0.8573
102 OJ7 0.8565
103 XYP XYS 0.8560
104 LOX XYP 0.8558
105 C5Q 0.8556
106 NQE 0.8555
107 3JC 0.8554
108 NQK 0.8546
109 1FL 0.8544
110 BK2 0.8534
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5BV6; Ligand: 35G; Similar sites found with APoc: 10
This union binding pocket(no: 1) in the query (biounit: 5bv6.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 4MUV PCG 32.3944
2 4MUV PCG 32.3944
3 4MUV PCG 32.3944
4 4MUV PCG 32.3944
5 3PNA CMP 38.1579
6 3PNA CMP 38.1579
7 2PTM CMP 38.8158
8 1CX4 CMP 47.3684
9 1NE6 SP1 47.3684
10 1NE6 SP1 47.3684
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