Receptor
PDB id Resolution Class Description Source Keywords
6PC3 2.1 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF HELICOBACTER PYLORI PPX/GPPA IN COMPLEX HELICOBACTER PYLORI (STRAIN G27) PPPGPP PPGPP PPX GPPA POLYPHOSPHATE HYDROLASE
Ref.: STRUCTURE AND ACTIVITY OF PPX/GPPA HOMOLOGS FROM ES COLI AND HELICOBACTER PYLORI. FEBS J. V. 287 1865 2020
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:508;
Invalid;
none;
submit data
62.068 C2 H6 O2 C(CO)...
CL A:506;
B:506;
A:507;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
35.453 Cl [Cl-]
K A:505;
B:505;
Part of Protein;
Part of Protein;
none;
none;
submit data
39.098 K [K+]
MG B:504;
B:503;
A:503;
A:504;
Part of Protein;
Invalid;
Invalid;
Part of Protein;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
TS6 B:507;
A:509;
Invalid;
Invalid;
none;
none;
submit data
114.061 H3 O3 P S OP(=O...
GSP A:501;
B:501;
Valid;
Valid;
none;
none;
submit data
539.246 C10 H16 N5 O13 P3 S c1nc2...
PO4 A:502;
B:502;
Invalid;
Invalid;
none;
none;
submit data
94.971 O4 P [O-]P...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6PC3 2.1 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF HELICOBACTER PYLORI PPX/GPPA IN COMPLEX HELICOBACTER PYLORI (STRAIN G27) PPPGPP PPGPP PPX GPPA POLYPHOSPHATE HYDROLASE
Ref.: STRUCTURE AND ACTIVITY OF PPX/GPPA HOMOLOGS FROM ES COLI AND HELICOBACTER PYLORI. FEBS J. V. 287 1865 2020
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 312 families.
1 6PC3 - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 261 families.
1 6PC3 - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 214 families.
1 6PC3 - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: GSP; Similar ligands found: 135
No: Ligand ECFP6 Tc MDL keys Tc
1 GSP 1 1
2 GP3 0.897436 0.925
3 GTP 0.853659 0.948718
4 GNH 0.829268 0.936709
5 GDP 0.817073 0.948718
6 G1R 0.8 0.936709
7 GCP 0.77907 0.925
8 9GM 0.770115 0.925
9 GNP 0.770115 0.925
10 GMV 0.767442 0.925
11 G 0.756098 0.935897
12 5GP 0.756098 0.935897
13 G2R 0.747253 0.91358
14 GDD 0.744681 0.91358
15 GDC 0.744681 0.91358
16 GKE 0.744681 0.91358
17 GPG 0.73913 0.91358
18 GTG 0.736842 0.891566
19 G3A 0.729167 0.925
20 G5P 0.721649 0.925
21 GDR 0.71875 0.91358
22 GFB 0.71875 0.91358
23 GAV 0.714286 0.987179
24 GP2 0.712644 0.91358
25 6CK 0.71134 0.891566
26 Y9Z 0.708333 0.860465
27 JB2 0.69697 0.91358
28 GKD 0.69697 0.91358
29 G2P 0.692308 0.91358
30 GPD 0.69 0.880952
31 GDX 0.69 0.925
32 GDP BEF 0.681319 0.888889
33 GTP MG 0.673913 0.911392
34 ALF 5GP 0.67033 0.847059
35 0O2 0.666667 0.935897
36 YGP 0.663265 0.858824
37 JB3 0.657143 0.902439
38 GDP AF3 0.645833 0.847059
39 GDP ALF 0.645833 0.847059
40 GMP 0.641975 0.835443
41 G3D 0.638298 0.935897
42 NGD 0.635514 0.91358
43 2MD 0.633027 0.894118
44 CAG 0.630631 0.840909
45 G4P 0.625 0.935897
46 FEG 0.62037 0.83908
47 U2G 0.62037 0.891566
48 MGD 0.616071 0.894118
49 ZGP 0.614679 0.872093
50 CG2 0.609091 0.891566
51 TPG 0.598291 0.804348
52 KB7 0.595745 0.788235
53 3GP 0.595506 0.898734
54 GDP 7MG 0.590476 0.86747
55 GH3 0.581633 0.924051
56 PGD 0.581197 0.926829
57 MD1 0.581197 0.894118
58 2GP 0.577778 0.911392
59 DGT 0.561224 0.878049
60 DBG 0.558333 0.902439
61 KBD 0.553398 0.788235
62 G1G 0.550847 0.880952
63 AGS 0.547368 0.924051
64 QBQ 0.546392 0.935897
65 FE9 0.546219 0.8
66 G4M 0.539062 0.840909
67 KBJ 0.53271 0.761364
68 MGP 0.525253 0.91358
69 GPX 0.524272 0.898734
70 BGO 0.521739 0.879518
71 I2C FE2 CMO CMO 0.520661 0.774194
72 DGI 0.520408 0.878049
73 6G0 0.52 0.91358
74 IDP 0.515464 0.923077
75 R5I 0.51 0.898734
76 R7I 0.51 0.898734
77 GGM 0.508475 0.858824
78 G1R G1R 0.508065 0.879518
79 PGD O 0.504 0.875
80 AKW 0.495726 0.915663
81 CZF 0.49 0.886076
82 GTA 0.486726 0.891566
83 P2G 0.484536 0.839506
84 GPC 0.483607 0.83908
85 G C 0.483333 0.857143
86 P1G 0.474747 0.829268
87 DGP 0.474227 0.865854
88 DG 0.474227 0.865854
89 BA3 0.46875 0.85
90 AP5 0.463918 0.85
91 B4P 0.463918 0.85
92 IMP 0.463918 0.910256
93 G2Q 0.462963 0.91358
94 APC G U 0.456693 0.843373
95 ATP 0.45 0.873418
96 HEJ 0.45 0.873418
97 A2D 0.447917 0.85
98 5FA 0.445545 0.873418
99 AQP 0.445545 0.873418
100 G7M 0.444444 0.901235
101 01G 0.442478 0.860465
102 SGP 0.44 0.876543
103 ITT 0.44 0.825
104 JSQ 0.436893 0.831325
105 HFD 0.436893 0.831325
106 GZ0 0.433333 0.902439
107 AT4 0.43 0.911392
108 AN2 0.43 0.8625
109 A4P 0.42623 0.829545
110 UCG 0.424242 0.86747
111 C2E 0.423077 0.875
112 PCG 0.423077 0.886076
113 35G 0.423077 0.886076
114 MGO 0.420561 0.823529
115 ADP 0.42 0.873418
116 ANP 0.419048 0.851852
117 5GP 5GP 0.419048 0.839506
118 M7G A2M G 0.418301 0.774194
119 ADQ 0.418182 0.829268
120 APR 0.417476 0.85
121 7DT 0.417476 0.860759
122 AR6 0.417476 0.85
123 PRT 0.417391 0.910256
124 HQG 0.416667 0.8625
125 C1Z 0.415929 0.935897
126 AD9 0.413462 0.851852
127 UP5 0.413223 0.831325
128 A22 0.412844 0.8625
129 25L 0.412281 0.8625
130 M33 0.411765 0.839506
131 JBT 0.410405 0.783505
132 ACP 0.407767 0.851852
133 6YZ 0.407407 0.851852
134 ACQ 0.40566 0.851852
135 A1R 0.405405 0.8
Similar Ligands (3D)
Ligand no: 1; Ligand: GSP; Similar ligands found: 18
No: Ligand Similarity coefficient
1 BEF GDP 0.9951
2 ALF GDP 0.9840
3 BEF ADP 0.9761
4 DTP 0.9655
5 ADP ALF 0.9598
6 GDP MG 0.9446
7 ADP AF3 0.9389
8 UTP 0.9143
9 CTP 0.9100
10 ATF 0.9078
11 ADP MG 0.8998
12 DSZ 0.8805
13 APC 0.8789
14 AMO 0.8780
15 DAT 0.8737
16 ADP BEF 0.8685
17 AV2 0.8567
18 SAM 0.8566
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6PC3; Ligand: GSP; 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: 6pc3.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6PC3; Ligand: GSP; 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: 6pc3.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback