Receptor
PDB id Resolution Class Description Source Keywords
5J48 1.49 Å EC: 2.7.11.12 PKG I'S CARBOYL TERMINAL CYCLIC NUCLEOTIDE BINDING DOMAIN (C COMPLEX WITH 8-PCPT-CGMP HOMO SAPIENS BINDING SITES CYCLIC AMP CYCLIC GMP CYCLIC GMP-DEPENDENT KINASE TYPE II MUTAGENESIS SITE-DIRECTED PROTEIN BINDING
Ref.: STRUCTURAL BASIS OF ANALOG SPECIFICITY IN PKG I AND ACS CHEM. BIOL. V. 12 2388 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:401;
B:402;
B:401;
A:405;
B:403;
A:403;
B:404;
A:402;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
NA A:406;
B:407;
Part of Protein;
Part of Protein;
none;
none;
submit data
22.99 Na [Na+]
CA B:406;
Invalid;
none;
submit data
40.078 Ca [Ca+2...
6FW B:405;
A:404;
Valid;
Valid;
none;
none;
submit data
487.811 C16 H15 Cl N5 O7 P S c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5JAX 1.49 Å EC: 2.7.11.12 PKG I'S CARBOYL TERMINAL CYCLIC NUCLEOTIDE BINDING DOMAIN (C COMPLEX WITH 8-BR-CGMP HOMO SAPIENS BINDING SITES CYCLIC AMP CYCLIC GMP CYCLIC GMP-DEPENDENT KINASE TYPE II MUTAGENESIS SITE-DIRECTED PROTEIN BINDINGANALOGS TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: STRUCTURAL BASIS OF ANALOG SPECIFICITY IN PKG I AND ACS CHEM. BIOL. V. 12 2388 2017
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 5JAX - 6J7 C10 H11 Br N5 O7 P C1[C@@H]2[....
2 5J48 - 6FW C16 H15 Cl N5 O7 P S c1cc(ccc1S....
3 5JD7 - 6JR C18 H16 N5 O7 P c1ccc(cc1)....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 5JAX - 6J7 C10 H11 Br N5 O7 P C1[C@@H]2[....
2 5J48 - 6FW C16 H15 Cl N5 O7 P S c1cc(ccc1S....
3 5JD7 - 6JR C18 H16 N5 O7 P c1ccc(cc1)....
4 4QX5 - CMP C10 H12 N5 O6 P c1nc(c2c(n....
5 4KU7 Kd = 12 nM PCG C10 H12 N5 O7 P c1nc2c(n1[....
50% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 12 families.
1 5J48 - 6FW C16 H15 Cl N5 O7 P S c1cc(ccc1S....
2 3PNA - CMP C10 H12 N5 O6 P c1nc(c2c(n....
3 5KJY - CMP C10 H12 N5 O6 P c1nc(c2c(n....
4 5T3N Kd = 9.1 nM 75G C10 H11 Cl N5 O5 P S c1nc2c(nc(....
5 5JIX - 6J7 C10 H11 Br N5 O7 P C1[C@@H]2[....
6 1NE6 - SP1 C10 H12 N5 O5 P S c1nc(c2c(n....
7 1NE4 - RP1 C10 H12 N5 O5 P S c1nc(c2c(n....
8 5KBF Kd = 1.2 nM CMP C10 H12 N5 O6 P c1nc(c2c(n....
9 1CX4 - CMP C10 H12 N5 O6 P c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 6FW; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 6FW 1 1
2 6J7 0.462963 0.902439
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5JAX; Ligand: 6J7; Similar sites found: 81
This union binding pocket(no: 1) in the query (biounit: 5jax.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1WD4 AHR 0.01462 0.40421 2.22222
2 5ML3 DL3 0.02515 0.40301 2.96296
3 4ASE AV9 0.00142 0.45103 3.7037
4 4CLI 5P8 0.01139 0.42465 3.7037
5 3TAY MN0 0.00978 0.41198 3.7037
6 4CKU P2F 0.01936 0.40537 3.7037
7 2WSA MYA 0.02758 0.42744 4.44444
8 2WSA 646 0.02758 0.42744 4.44444
9 1RE8 BD2 0.02365 0.41074 4.44444
10 2X4Z X4Z 0.02147 0.40321 4.44444
11 2VUT NAD 0.01069 0.4025 4.44444
12 5EOB 5QQ 0.008693 0.43808 5.18518
13 3SXS PP2 0.001792 0.43583 5.18518
14 4XLI 1N1 0.005133 0.40919 5.18518
15 3FU7 3DM 0.008692 0.4087 5.18518
16 1RYO OXL 0.004097 0.44332 5.92593
17 5JFS 6K0 0.004985 0.4392 5.92593
18 1YY5 FAD 0.02976 0.40658 5.92593
19 2J5V PCA 0.001293 0.46964 6.66667
20 5DRB 5FJ 0.003725 0.45037 6.66667
21 4F4P 0SB 0.01341 0.43153 6.66667
22 5DQ8 FLF 0.007386 0.41314 6.66667
23 3PE2 E1B 0.03489 0.40232 6.66667
24 2IHU TP9 0.02662 0.40081 6.66667
25 5N87 N66 0.002079 0.45296 7.40741
26 5FBN 5WF 0.004793 0.4344 7.40741
27 4U0I 0LI 0.009907 0.41571 7.40741
28 4NFN 2KC 0.003866 0.41465 7.40741
29 5USZ SKE 0.01157 0.40856 7.40741
30 4WHZ 3NL 0.008194 0.43527 8.14815
31 5HES 032 0.002926 0.4281 8.14815
32 1TT8 PHB 0.007771 0.41519 8.14815
33 3MTX PGT 0.01408 0.40969 8.14815
34 3E7O 35F 0.01489 0.40732 8.14815
35 4YZC STU 0.002053 0.45443 8.88889
36 3THR C2F 0.005667 0.40729 8.88889
37 3TTC ADP 0.01376 0.40068 8.88889
38 4Y8D 49J 0.0009332 0.43378 9.62963
39 2HK5 1BM 0.007402 0.40799 9.62963
40 2CDO GAL AAL GAL AAL GAL AAL 0.01698 0.40493 10.3704
41 4P5Z Q7M 0.004323 0.44003 11.1111
42 1PN0 IPH 0.02139 0.41691 11.1111
43 1M13 HYF 0.01831 0.40426 11.1111
44 3LA3 2FT 0.002008 0.40105 11.1111
45 5JKG 6LF 0.00127 0.46566 11.8519
46 4FWE FAD 0.03305 0.42858 11.8519
47 3FGC FMN 0.007682 0.40726 11.8519
48 2PZI AXX 0.009165 0.40561 11.8519
49 1VJY 460 0.02223 0.40023 11.8519
50 2Y6O 1N1 0.002498 0.43122 12.5926
51 2WEI VGG 0.001947 0.42221 12.5926
52 2XKO AKG 0.001668 0.45643 13.3333
53 2XHK AKG 0.002054 0.40841 13.3333
54 4CQE CQE 0.008545 0.40692 13.3333
55 2XMY CDK 0.001257 0.48734 14.0741
56 5BYZ 4WE 0.00907 0.41752 15.5556
57 5DA3 58V 0.00519 0.42155 17.7778
58 5H2U 1N1 0.008844 0.40265 17.7778
59 4USF 6UI 0.005636 0.41854 18.5185
60 4Y7U 2KH 0.01774 0.40119 19.2593
61 5K2M ADP 0.01128 0.40467 20
62 1NM5 NAP 0.03528 0.4074 20.7407
63 5JGA 6KC 0.002019 0.44969 22.2222
64 4QYS PLP SEP 0.01284 0.40359 24.4444
65 1DZK PRZ 0.009843 0.40029 27.4074
66 5H5O PCG 0.00001636 0.52635 32.5581
67 4N9I PCG 0.0000002768 0.65317 33.3333
68 3KCC CMP 0.000000043 0.64103 33.3333
69 4CYD CMP 0.0000002297 0.60179 35.5556
70 4NVP 7CH 0.03853 0.41779 36.2963
71 3I59 N6S 0.0000003345 0.60108 38.5185
72 3I59 N6R 0.0000007534 0.58526 38.5185
73 3I54 CMP 0.000001192 0.57013 38.5185
74 3PNA CMP 0.00000000001992 0.70624 39.2593
75 4AVB CMP 0.00000003803 0.65556 39.2593
76 3CF6 SP1 0.0000003474 0.59385 41.4815
77 4MUV PCG 0.00000000007368 0.75648 42.2222
78 1CX4 CMP 0.000000004293 0.68221 45.1852
79 5KBF CMP 0.000000001331 0.68631 46.6667
80 5K8S CMP 0.000000001615 0.67789 47.4074
81 3OF1 CMP 0.0000000003601 0.76235 48.1481
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