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 = 0.258;
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 MG 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 1068 families.
1 4XJ6 - GH3 C10 H16 N5 O13 P3 c1nc2c(n1[....
2 4XJ3 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
3 4TY0 - 38V MG 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 922 families.
1 4XJ6 - GH3 C10 H16 N5 O13 P3 c1nc2c(n1[....
2 4XJ3 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
3 4TY0 - 38V MG 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: 86
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 GAV 0.57 0.935897
10 G4P 0.57 0.986486
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 G 0.542553 0.96
18 5GP 0.542553 0.96
19 GCP 0.54 0.973684
20 GPX 0.533981 0.946667
21 GPD 0.531532 0.925
22 G5P 0.527273 0.948052
23 GTG 0.522936 0.9125
24 G2P 0.519608 0.961039
25 6CK 0.518182 0.9125
26 G3A 0.518182 0.948052
27 DGP 0.515789 0.935065
28 DG 0.515789 0.935065
29 GP2 0.515152 0.961039
30 GMV 0.514852 0.948052
31 GDC 0.513761 0.935897
32 GDD 0.513761 0.935897
33 GKE 0.513761 0.935897
34 2GP 0.505263 0.96
35 3GP 0.505263 0.946667
36 Y9Z 0.5 0.902439
37 GDR 0.495495 0.935897
38 GFB 0.495495 0.935897
39 GPG 0.490741 0.935897
40 GDP MG 0.490196 0.898734
41 GMP 0.488889 0.855263
42 GDP BEF 0.485437 0.876543
43 JB2 0.482456 0.935897
44 GKD 0.482456 0.935897
45 GCP G 0.481132 0.910256
46 P2G 0.479592 0.883117
47 NGD 0.478992 0.935897
48 GDX 0.478261 0.948052
49 GTP MG 0.471698 0.898734
50 BEF GDP 0.471698 0.865854
51 ALF 5GP 0.471154 0.865854
52 P1G 0.47 0.896104
53 BGO 0.466667 0.924051
54 YGP 0.464286 0.878049
55 GDP AF3 0.458716 0.865854
56 GDP ALF 0.458716 0.865854
57 JB3 0.458333 0.924051
58 TPG 0.457364 0.820225
59 CAG 0.456 0.858824
60 G1G 0.448819 0.901235
61 2MD 0.443548 0.869048
62 PGD 0.44186 0.901235
63 DG DG 0.4375 0.888889
64 MGP 0.433962 0.935897
65 G G 0.433628 0.910256
66 MGD 0.433071 0.869048
67 GGM 0.432 0.901235
68 U2G 0.430894 0.9125
69 MD1 0.430769 0.891566
70 6G0 0.429907 0.935897
71 CG2 0.424 0.9125
72 GDP 7MG 0.423729 0.8875
73 SGP 0.421569 0.82716
74 FEG 0.419355 0.879518
75 ZGP 0.416 0.869048
76 01G 0.413793 0.879518
77 DBG 0.413534 0.924051
78 CGP 0.412698 0.890244
79 GPC 0.410853 0.857143
80 G G U 0.408333 0.935065
81 I2C FE2 CMO CMO 0.407692 0.788889
82 5GP 5GP 0.401869 0.883117
83 DDS 0.401869 0.810127
84 DTP 0.401869 0.858974
85 FE9 0.401515 0.757895
86 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: 6
This union binding pocket(no: 1) in the query (biounit: 4u03.bio1) has 54 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5C3R AKG 0.03579 0.40622 2.62391
2 5C3R HMU 0.03579 0.40622 2.62391
3 2ZHL NAG GAL GAL NAG 0.03972 0.41304 3.37838
4 3P7N FMN 0.02219 0.41363 5.03876
5 3JYY PPV 0.008601 0.46122 5.22648
6 1GEG GLC 0.02354 0.44209 7.42188
Pocket No.: 2; Query (leader) PDB : 4U03; Ligand: GTP; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4U03; Ligand: TLL; Similar sites found: 6
This union binding pocket(no: 3) in the query (biounit: 4u03.bio1) has 54 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5C3R HMU 0.03579 0.40622 2.62391
2 5C3R AKG 0.03579 0.40622 2.62391
3 2ZHL NAG GAL GAL NAG 0.03972 0.41304 3.37838
4 3P7N FMN 0.02219 0.41363 5.03876
5 3JYY PPV 0.008601 0.46122 5.22648
6 1GEG GLC 0.02354 0.44209 7.42188
Pocket No.: 4; Query (leader) PDB : 4U03; Ligand: GTP; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 4U03; Ligand: TLL; Similar sites found: 14
This union binding pocket(no: 5) in the query (biounit: 4u03.bio2) has 46 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4COQ SAN 0.0406 0.41779 2.02429
2 4KBA 1QM 0.03199 0.41947 2.41692
3 1B74 DGN 0.02639 0.42695 2.75591
4 2OFD NGA 0.03371 0.42136 2.8169
5 2XG5 EC2 0.01231 0.46325 4.04624
6 2XG5 EC5 0.01231 0.46325 4.04624
7 4N14 WR7 0.02871 0.42237 6.36943
8 3I7V B4P 0.002208 0.4093 8.20895
9 3SJK LYS PRO VAL LEU ARG THR ALA 0.04161 0.41836 10.5263
10 2QQD AG2 0.04857 0.41323 10.7143
11 4I67 G G G RPC 0.03226 0.41555 12.6437
12 1RL4 BL5 0.04376 0.42139 13.8298
13 2VWA PTY 0.04016 0.42654 13.8614
14 4LO2 GAL BGC 0.04918 0.40219 14.966
Pocket No.: 6; Query (leader) PDB : 4U03; Ligand: GTP; Similar sites found: 13
This union binding pocket(no: 6) in the query (biounit: 4u03.bio2) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2B56 U5P 0.001565 0.40833 1.87354
2 2B56 UTP 0.001565 0.40833 1.87354
3 5W0N 2KH 0.000033 0.43362 2.48139
4 5A2Z GTP 0.00004866 0.40384 2.8103
5 2Q0D ATP 0.000007177 0.50934 2.83286
6 3HJ1 UTP 0.0002213 0.4032 3.35917
7 3HIY UTP 0.00007959 0.41255 3.38542
8 3PUR 2HG 0.02679 0.41233 3.74707
9 4NKT 2KH 0.00009288 0.40952 7.03812
10 5AIG VPR 0.02219 0.40707 8
11 1EPB REA 0.01486 0.40481 8.53659
12 4JH6 FCN 0.0107 0.42737 10.8696
13 1W6P NDG GAL 0.02415 0.41536 14.1791
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