Receptor
PDB id Resolution Class Description Source Keywords
4XJ5 1.55 Å EC: 2.7.7.86 CRYSTAL STRUCTURE OF VIBRIO CHOLERAE DNCV 3'-DEOXY GTP BOUND VIBRIO CHOLERAE O1 BIOVAR EL TOR STR. ORGANISM_TAXID: 243277 CYCLIC GMP-AMP SYNTHASE BACTERIAL VIRULENCE NUCLEOTIDYLTRATRANSFERASE
Ref.: STRUCTURAL BASIS FOR THE CATALYTIC MECHANISM OF DNC BACTERIAL HOMOLOG OF CYCLIC GMP-AMP SYNTHASE STRUCTURE V. 23 843 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:1007;
A:1005;
A:1011;
A:1008;
A:1003;
A:1012;
A:1006;
A:1009;
A:1004;
A:1010;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
MG A:1002;
A:1001;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
NA A:1015;
Part of Protein;
none;
submit data
22.99 Na [Na+]
GH3 A:1013;
A:1014;
Valid;
Valid;
Atoms found LESS than expected: % Diff = 0;
none;
submit data
507.181 C10 H16 N5 O13 P3 c1nc2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4U03 2.04 Å EC: 2.7.7.86 STRUCTURE OF THE VIBRIO CHOLERAE DI-NUCLEOTIDE CYCLASE (DNCV COMPLEX WITH GTP AND 5MTHFGLU2 VIBRIO CHOLERAE EL TOR N16961 REGULATION TRANSFERASE
Ref.: STRUCTURAL BIOCHEMISTRY OF A VIBRIO CHOLERAE DINUCL CYCLASE REVEALS CYCLASE ACTIVITY REGULATION BY FOLA MOL.CELL V. 55 931 2014
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4XJ3 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
2 4TY0 - 38V n/a n/a
3 4U0M - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
4 4U0N - TLL C25 H32 N8 O9 CN1[C@H](C....
5 4U03 ic50 = 1.69 uM TLL C25 H32 N8 O9 CN1[C@H](C....
6 4XJ4 - 3AT C10 H16 N5 O12 P3 c1nc(c2c(n....
7 4XJ5 - GH3 C10 H16 N5 O13 P3 c1nc2c(n1[....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1312 families.
1 4XJ6 - GH3 C10 H16 N5 O13 P3 c1nc2c(n1[....
2 4XJ3 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
3 4TY0 - 38V n/a n/a
4 4U0M - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
5 4U0N - TLL C25 H32 N8 O9 CN1[C@H](C....
6 4U03 ic50 = 1.69 uM TLL C25 H32 N8 O9 CN1[C@H](C....
7 4XJ4 - 3AT C10 H16 N5 O12 P3 c1nc(c2c(n....
8 4XJ5 - GH3 C10 H16 N5 O13 P3 c1nc2c(n1[....
50% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1130 families.
1 4XJ6 - GH3 C10 H16 N5 O13 P3 c1nc2c(n1[....
2 4XJ3 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
3 4TY0 - 38V n/a n/a
4 4U0M - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
5 4U0N - TLL C25 H32 N8 O9 CN1[C@H](C....
6 4U03 ic50 = 1.69 uM TLL C25 H32 N8 O9 CN1[C@H](C....
7 4XJ4 - 3AT C10 H16 N5 O12 P3 c1nc(c2c(n....
8 4XJ5 - GH3 C10 H16 N5 O13 P3 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GH3; Similar ligands found: 85
No: Ligand ECFP6 Tc MDL keys Tc
1 GH3 1 1
2 GTP 0.681319 0.973333
3 DGT 0.673913 0.948052
4 0O2 0.642857 0.986486
5 GP3 0.619565 0.948052
6 GDP 0.612903 0.973333
7 DGI 0.595745 0.948052
8 GSP 0.581633 0.924051
9 G4P 0.57 0.986486
10 GAV 0.57 0.935897
11 G3D 0.565657 0.986486
12 3AT 0.5625 0.92
13 GNH 0.556701 0.960526
14 G1R 0.555556 0.960526
15 G2R 0.553398 0.961039
16 GNP 0.55 0.948052
17 9GM 0.55 0.948052
18 5GP 0.542553 0.96
19 G 0.542553 0.96
20 GCP 0.54 0.973684
21 GPX 0.533981 0.946667
22 GPD 0.531532 0.925
23 G5P 0.527273 0.948052
24 GTG 0.522936 0.9125
25 G2P 0.519608 0.961039
26 G3A 0.518182 0.948052
27 6CK 0.518182 0.9125
28 DG 0.515789 0.935065
29 DGP 0.515789 0.935065
30 GP2 0.515152 0.961039
31 GMV 0.514852 0.948052
32 GDC 0.513761 0.935897
33 GDD 0.513761 0.935897
34 GKE 0.513761 0.935897
35 2GP 0.505263 0.96
36 3GP 0.505263 0.946667
37 Y9Z 0.5 0.902439
38 GDR 0.495495 0.935897
39 GFB 0.495495 0.935897
40 GPG 0.490741 0.935897
41 GMP 0.488889 0.855263
42 GKD 0.482456 0.935897
43 JB2 0.482456 0.935897
44 P2G 0.479592 0.883117
45 NGD 0.478992 0.935897
46 GDX 0.478261 0.948052
47 ALF 5GP 0.471154 0.865854
48 P1G 0.47 0.896104
49 BGO 0.466667 0.924051
50 YGP 0.464286 0.878049
51 ALF GDP 0.458716 0.865854
52 GDP ALF 0.458716 0.865854
53 GDP AF3 0.458716 0.865854
54 JB3 0.458333 0.924051
55 TPG 0.457364 0.820225
56 CAG 0.456 0.858824
57 G1G 0.448819 0.901235
58 GCP G 0.446429 0.921053
59 2MD 0.443548 0.869048
60 PGD 0.44186 0.901235
61 KB7 0.438095 0.804878
62 DG DG 0.4375 0.888889
63 MGP 0.433962 0.935897
64 MGD 0.433071 0.869048
65 GGM 0.432 0.901235
66 U2G 0.430894 0.9125
67 MD1 0.430769 0.891566
68 6G0 0.429907 0.935897
69 CG2 0.424 0.9125
70 GDP 7MG 0.423729 0.8875
71 SGP 0.421569 0.82716
72 FEG 0.419355 0.879518
73 G G 0.418803 0.923077
74 ZGP 0.416 0.869048
75 01G 0.413793 0.879518
76 DBG 0.413534 0.924051
77 CGP 0.412698 0.890244
78 C1Z 0.412281 0.986486
79 KBD 0.412281 0.804878
80 GPC 0.410853 0.857143
81 DTP 0.401869 0.858974
82 5GP 5GP 0.401869 0.883117
83 DDS 0.401869 0.810127
84 FE9 0.401515 0.757895
85 3ZE 0.4 0.884615
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4U03; Ligand: GTP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4u03.bio1) has 54 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4U03; Ligand: GTP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4u03.bio1) has 54 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4U03; Ligand: TLL; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 4u03.bio1) has 54 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4U03; Ligand: GTP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 4u03.bio2) has 27 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 4U03; Ligand: TLL; Similar sites found with APoc: 3
This union binding pocket(no: 5) in the query (biounit: 4u03.bio2) has 46 residues
No: Leader PDB Ligand Sequence Similarity
1 1NU4 MLA 4.12371
2 1NU4 MLA 4.12371
3 1NU4 MLA 4.12371
Pocket No.: 6; Query (leader) PDB : 4U03; Ligand: GTP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 4u03.bio2) has 29 residues
No: Leader PDB Ligand Sequence Similarity
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