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 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[....
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 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 (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5JAX - 6J7 C10 H11 Br N5 O7 P C1[C@@H]2[....
2 4QX5 - CMP C10 H12 N5 O6 P c1nc(c2c(n....
3 5BV6 Kd = 31 nM 35G C10 H12 N5 O7 P c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 35G; 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 : 5BV6; Ligand: 35G; Similar sites found: 91
This union binding pocket(no: 1) in the query (biounit: 5bv6.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3FIU POP 0.02941 0.40196 None
2 5HES 032 0.009227 0.40025 None
3 5N1X 8HH 0.00259 0.44108 1.69492
4 5IFK HPA 0.005232 0.44004 1.97368
5 3M3E GAL A2G NPO 0.00944 0.41847 1.97368
6 1QVJ RP5 0.01998 0.40735 1.97368
7 1A78 TDG 0.01864 0.40439 2.23881
8 3FAL REA 0.01137 0.40133 2.63158
9 4Y8D 49J 0.002305 0.4248 2.85714
10 1SLT NDG GAL 0.02309 0.41471 2.98507
11 3QH2 3NM 0.0229 0.40249 3.28947
12 3TL1 JRO 0.01997 0.40554 3.94737
13 3THR C2F 0.009381 0.4015 3.94737
14 2DW7 SRT 0.02089 0.4003 3.94737
15 5BTX CMP 0.01008 0.40947 4.10959
16 5V4R MGT 0.006755 0.44322 4.60526
17 2P3I MNA 0.003161 0.43033 4.60526
18 3CHT 4NB 0.01079 0.42451 4.60526
19 1KQR MNA 0.005304 0.4212 4.60526
20 2BP1 FLC 0.0162 0.4104 4.60526
21 3VV1 GAL FUC 0.03435 0.40214 4.60526
22 3BPX SAL 0.02314 0.40493 4.72973
23 1LTT GAL BGC 0.00388 0.41755 4.85437
24 3NW7 LGV 0.003506 0.44401 5.26316
25 4XNV BUR 0.005736 0.43995 5.26316
26 2X1L ADN 0.003277 0.43528 5.26316
27 1Q19 SSC 0.007132 0.43233 5.26316
28 3WV6 GAL BGC 0.01618 0.41092 5.26316
29 4XDA RIB 0.0144 0.40419 5.26316
30 1V0O INR 0.006901 0.40387 5.26316
31 5KL0 G16 0.01846 0.40299 5.26316
32 2DKD NG1 0.01465 0.408 5.92105
33 2V7O DRN 0.0176 0.40402 5.92105
34 1K0E TRP 0.01421 0.40056 5.92105
35 4ZCW 4NG 0.004382 0.41637 6.57895
36 1WNB BTL 0.003889 0.40537 6.57895
37 2Q1H AS4 0.006129 0.40264 6.57895
38 2YFB SIN 0.02602 0.40206 6.57895
39 3PE2 E1B 0.02903 0.40044 6.57895
40 4D2S DYK 0.009917 0.40794 7.23684
41 4YEE 4CQ 0.02376 0.40357 7.77778
42 4Z7X 3CX 0.003512 0.45079 7.89474
43 1FM9 9CR 0.002343 0.41492 7.89474
44 3KYQ DPV 0.01939 0.4062 7.89474
45 1RYO OXL 0.005939 0.44698 9.21053
46 4YZC STU 0.00528 0.42742 9.21053
47 2CYC TYR 0.01306 0.41691 9.21053
48 5DA3 58V 0.005494 0.42445 9.86842
49 1DQN IMU 0.02009 0.40115 9.86842
50 4H4D 10E 0.01211 0.40007 9.86842
51 3H9R TAK 0.01707 0.40468 10.5263
52 5JKG 6LF 0.0008289 0.46571 11.1842
53 4X1B MLI 0.005096 0.44287 11.1842
54 4QXB OGA 0.01606 0.406 11.8421
55 5JFS 6K0 0.01881 0.4049 11.8421
56 5ML3 DL3 0.009886 0.41591 12.0805
57 3HW5 AMP 0.02004 0.40823 12.5
58 4CNO 9PY 0.02434 0.40114 12.5
59 3SXS PP2 0.003109 0.40916 13.1579
60 1LOX RS7 0.006742 0.40796 13.1579
61 2YMZ LAT 0.005666 0.43191 14.6154
62 5OCA 9QZ 0.001868 0.47945 15.1316
63 3LA3 2FT 0.002123 0.45574 15.1316
64 2FVK DUC 0.0134 0.41681 15.1316
65 3GGF GVD 0.009908 0.40409 15.1316
66 1Z0N BCD 0.01456 0.41253 15.625
67 4RW3 TDA 0.02421 0.42377 15.7895
68 2W3L DRO 0.01665 0.41024 15.9722
69 2F7A BEZ 0.02337 0.40243 16.4474
70 4XV1 904 0.01077 0.40971 17.1053
71 2F57 23D 0.01139 0.40129 17.7632
72 2XKO AKG 0.002217 0.45565 18.4211
73 2XHK AKG 0.002795 0.44909 18.4211
74 1LCF OXL 0.01011 0.43339 19.7368
75 5H5O PCG 0.000009341 0.54305 21.7054
76 4AVB CMP 0.000000009045 0.69193 26.9737
77 1XPJ TLA 0.01708 0.41642 27.7778
78 4N9I PCG 0.0000002323 0.64117 28.9474
79 4CYD CMP 0.0000004413 0.59568 28.9474
80 3I54 CMP 0.0000005803 0.59034 28.9474
81 3I59 N6S 0.0000005983 0.5748 28.9474
82 3I59 N6R 0.000003428 0.54226 28.9474
83 4MUV PCG 0.00000000004778 0.77353 32.3944
84 3KCC CMP 0.00000002238 0.63604 33.5526
85 2WEI VGG 0.003495 0.42492 33.5526
86 1BYG STU 0.004882 0.41825 34.2105
87 3CF6 SP1 0.00000008532 0.62769 34.8684
88 3PNA CMP 0.00000000002875 0.83847 38.1579
89 1NE6 SP1 0.0000000003268 0.6861 47.3684
90 1CX4 CMP 0.00000001948 0.62756 47.3684
91 5KJZ PCG 0.000000001014 0.71402 48.6667
92 3OF1 CMP 0.0000000001456 0.7895 50
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