Receptor
PDB id Resolution Class Description Source Keywords
6D9S 2.11 Å EC: 2.4.2.8 THE (P)PPGPP-BOUND CRYSTAL STRUCTURE OF HPRT (HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE) BACILLUS ANTHRACIS HPRT HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE TRANSFERASE
Ref.: EVOLUTION OF (P)PPGPP-HPRT REGULATION THROUGH DIVERSIFICATION OF AN ALLOSTERIC OLIGOMERIC INTERAC ELIFE V. 8 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PEG A:204;
B:204;
A:203;
B:203;
A:205;
A:206;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
 submit data
106.12 C4 H10 O3 C(COC...
G4P B:201;
A:201;
 Valid;
Valid;
 none;
none;
 submit data
603.16 C10 H17 N5 O17 P4 c1nc2...
MG A:202;
B:202;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6D9R 1.64 Å EC: 2.4.2.8 THE SUBSTRATE-BOUND CRYSTAL STRUCTURE OF HPRT (HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE) BACILLUS ANTHRACIS HPRT HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE TRANSFERASE
Ref.: EVOLUTION OF (P)PPGPP-HPRT REGULATION THROUGH DIVERSIFICATION OF AN ALLOSTERIC OLIGOMERIC INTERAC ELIFE V. 8 2019
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 12 families.
1 6D9S - G4P C10 H17 N5 O17 P4 c1nc2c(n1[....
2 6D9R - PRP C5 H13 O14 P3 C([C@@H]1[....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 6D9S - G4P C10 H17 N5 O17 P4 c1nc2c(n1[....
2 6D9R - PRP C5 H13 O14 P3 C([C@@H]1[....
50% Homology Family (24)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1PZM - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
2 5KAM Ki = 77.3 uM IMP C10 H13 N4 O8 P c1nc2c(n1[....
3 6APS Ki = 0.22 uM SV2 C11 H19 N5 O9 P2 c1nc2c(n1C....
4 6APU Ki = 13.46 uM 3L6 C12 H22 N7 O4 P c1nc2c(n1C....
5 5JSQ Ki = 21.3 uM 6MS C11 H18 N5 O4 P c1nc2c(n1C....
6 6MXG - XMP C10 H14 N4 O9 P c1[nH+]c2c....
7 6APV Ki = 0.11 uM 3L4 C12 H20 N6 O8 P2 c1nc2c(n1C....
8 6APT Ki = 0.89 uM 45T C12 H21 N5 O9 P2 c1nc2c(n1C....
9 4RHY Ki = 1.13 uM 3QG C15 H29 N6 O10 P3 c1nc2c(n1C....
10 4RHX Ki = 1.6 uM 3QF C15 H27 N7 O8 P2 c1nc2c(n1C....
11 1HGX - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
12 1I0L - PRP C5 H13 O14 P3 C([C@@H]1[....
13 1TC2 - PRP C5 H13 O14 P3 C([C@@H]1[....
14 1I0I - PRP C5 H13 O14 P3 C([C@@H]1[....
15 1P19 Kd = 76.8 uM IMP C10 H13 N4 O8 P c1nc2c(n1[....
16 1P18 - PRP C5 H13 O14 P3 C([C@@H]1[....
17 1TC1 ic50 > 2 mM FMB C10 H12 N4 O5 C1=Nc2c(n[....
18 1I14 - PRP C5 H13 O14 P3 C([C@@H]1[....
19 1I13 - PRP C5 H13 O14 P3 C([C@@H]1[....
20 3ACD - IMP C10 H13 N4 O8 P c1nc2c(n1[....
21 3ACC - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
22 1YFZ Ki = 45 uM IMP C10 H13 N4 O8 P c1nc2c(n1[....
23 6D9S - G4P C10 H17 N5 O17 P4 c1nc2c(n1[....
24 6D9R - PRP C5 H13 O14 P3 C([C@@H]1[....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: G4P; Similar ligands found: 95
No: Ligand ECFP6 Tc MDL keys Tc
1 G4P 1 1
2 0O2 0.905882 1
3 G3D 0.879518 1
4 GDP 0.715909 0.986486
5 3GP 0.674419 0.959459
6 GTP 0.655914 0.986486
7 BGO 0.638889 0.935897
8 GNH 0.634409 0.973333
9 GP3 0.630435 0.960526
10 GSP 0.625 0.935897
11 GNP 0.625 0.960526
12 9GM 0.625 0.960526
13 DGI 0.606383 0.935065
14 G 0.604396 0.972973
15 5GP 0.604396 0.972973
16 G1R 0.597938 0.973333
17 GCP 0.597938 0.960526
18 GDD 0.596154 0.948052
19 GKE 0.596154 0.948052
20 GDC 0.596154 0.948052
21 GAV 0.59596 0.948052
22 GPX 0.59 0.959459
23 GPG 0.588235 0.948052
24 GMP 0.588235 0.866667
25 G2P 0.575758 0.948052
26 C1Z 0.572816 1
27 GMV 0.571429 0.960526
28 GH3 0.57 0.986486
29 GDP BEF 0.565657 0.922078
30 2GP 0.565217 0.972973
31 GGM 0.565217 0.9125
32 G2R 0.563107 0.948052
33 GFB 0.560748 0.948052
34 GDR 0.560748 0.948052
35 GTP MG 0.56 0.946667
36 GP2 0.556701 0.948052
37 6CK 0.555556 0.924051
38 ALF 5GP 0.555556 0.876543
39 DGT 0.55 0.935065
40 JB2 0.545455 0.948052
41 GKD 0.545455 0.948052
42 CG2 0.543103 0.924051
43 GPD 0.540541 0.9125
44 GDX 0.540541 0.960526
45 GDP ALF 0.538462 0.876543
46 GDP AF3 0.538462 0.876543
47 G C 0.538462 0.8875
48 Y9Z 0.537037 0.890244
49 G5P 0.536364 0.960526
50 GTG 0.53211 0.924051
51 G3A 0.527273 0.960526
52 U2G 0.525862 0.924051
53 APC G U 0.520325 0.897436
54 JB3 0.517241 0.935897
55 YGP 0.513761 0.888889
56 NGD 0.5 0.948052
57 GDP 7MG 0.495575 0.898734
58 DG 0.494845 0.922078
59 DGP 0.494845 0.922078
60 KB7 0.490196 0.814815
61 P2G 0.489796 0.894737
62 CAG 0.487805 0.869048
63 GPC 0.487805 0.86747
64 2MD 0.487603 0.879518
65 FEG 0.487395 0.86747
66 ZGP 0.483333 0.857143
67 P1G 0.48 0.883117
68 DBG 0.476562 0.935897
69 MGD 0.475806 0.879518
70 PAP 0.475248 0.918919
71 TPG 0.465116 0.829545
72 UCG 0.461538 0.923077
73 MD1 0.460938 0.879518
74 KBD 0.459459 0.814815
75 G1G 0.456693 0.9125
76 PGD 0.449612 0.9125
77 IDP 0.446602 0.959459
78 CGP 0.443548 0.878049
79 KBJ 0.443478 0.785714
80 G4M 0.442029 0.869048
81 AKW 0.439024 0.878049
82 QBQ 0.433962 0.972973
83 G1R G1R 0.431818 0.911392
84 SGP 0.431373 0.8375
85 FE9 0.430769 0.765957
86 I2C FE2 CMO CMO 0.430769 0.797753
87 PGD O 0.428571 0.83908
88 5GP 5GP 0.424528 0.894737
89 35G 0.415094 0.945946
90 C2E 0.415094 0.933333
91 PCG 0.415094 0.945946
92 AGO 0.414062 0.9
93 G 5MC C U 0.411765 0.878049
94 MGP 0.40367 0.948052
95 6G0 0.4 0.948052
Similar Ligands (3D)
Ligand no: 1; Ligand: G4P; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6D9R; Ligand: 9DG; 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: 6d9r.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6D9R; Ligand: 9DG; Similar sites found with APoc: 2
This union binding pocket(no: 2) in the query (biounit: 6d9r.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 4P83 U5P 20.3297
2 4P83 U5P 20.3297
Pocket No.: 3; Query (leader) PDB : 6D9R; Ligand: PRP; Similar sites found with APoc: 1
This union binding pocket(no: 3) in the query (biounit: 6d9r.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 4P83 U5P 20.3297
Pocket No.: 4; Query (leader) PDB : 6D9R; Ligand: PRP; Similar sites found with APoc: 2
This union binding pocket(no: 4) in the query (biounit: 6d9r.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 4P83 U5P 20.3297
2 4P83 U5P 20.3297
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