Receptor
PDB id Resolution Class Description Source Keywords
6G14 1.8 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF PPGPP BOUND RBGA FROM S. AUREUS STAPHYLOCOCCUS AUREUS (STRAIN USA300) CPGTPASE RNA BINDING PROTEIN
Ref.: STRUCTURAL BASIS FOR (P)PPGPP-MEDIATED INHIBITION O GTPASE RBGA. J. BIOL. CHEM. V. 293 19699 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
G4P A:301;
B:301;
Valid;
Valid;
none;
none;
Kd = 3.26 uM
603.16 C10 H17 N5 O17 P4 c1nc2...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6G14 1.8 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF PPGPP BOUND RBGA FROM S. AUREUS STAPHYLOCOCCUS AUREUS (STRAIN USA300) CPGTPASE RNA BINDING PROTEIN
Ref.: STRUCTURAL BASIS FOR (P)PPGPP-MEDIATED INHIBITION O GTPASE RBGA. J. BIOL. CHEM. V. 293 19699 2018
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 253 families.
1 6G12 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
2 6G14 Kd = 3.26 uM G4P C10 H17 N5 O17 P4 c1nc2c(n1[....
3 6G15 Kd = 4.31 uM C1Z C10 H18 N5 O20 P5 c1nc2c(n1[....
4 6G0Z Kd = 4.84 uM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 209 families.
1 6G12 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
2 6G14 Kd = 3.26 uM G4P C10 H17 N5 O17 P4 c1nc2c(n1[....
3 6G15 Kd = 4.31 uM C1Z C10 H18 N5 O20 P5 c1nc2c(n1[....
4 6G0Z Kd = 4.84 uM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
5 1PUJ - GNP C10 H17 N6 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 173 families.
1 6G12 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
2 6G14 Kd = 3.26 uM G4P C10 H17 N5 O17 P4 c1nc2c(n1[....
3 6G15 Kd = 4.31 uM C1Z C10 H18 N5 O20 P5 c1nc2c(n1[....
4 6G0Z Kd = 4.84 uM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
5 1PUJ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
6 3CNN - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
7 3CNL - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
8 3CNO - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: G4P; Similar ligands found: 103
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 GCP G 0.646465 0.933333
8 BGO 0.638889 0.935897
9 GNH 0.634409 0.973333
10 GP3 0.630435 0.960526
11 GSP 0.625 0.935897
12 GNP 0.625 0.960526
13 9GM 0.625 0.960526
14 DGI 0.606383 0.935065
15 5GP 0.604396 0.972973
16 G 0.604396 0.972973
17 G1R 0.597938 0.973333
18 GCP 0.597938 0.960526
19 GDC 0.596154 0.948052
20 GKE 0.596154 0.948052
21 GDD 0.596154 0.948052
22 GAV 0.59596 0.948052
23 G G 0.590476 0.935065
24 GPX 0.59 0.959459
25 GPG 0.588235 0.948052
26 GMP 0.588235 0.866667
27 G2P 0.575758 0.948052
28 C1Z 0.572816 1
29 GMV 0.571429 0.960526
30 GH3 0.57 0.986486
31 2GP 0.565217 0.972973
32 GGM 0.565217 0.9125
33 G2R 0.563107 0.948052
34 GDR 0.560748 0.948052
35 GFB 0.560748 0.948052
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 G A A A 0.547009 0.910256
41 GKD 0.545455 0.948052
42 JB2 0.545455 0.948052
43 CG2 0.543103 0.924051
44 GPD 0.540541 0.9125
45 GDX 0.540541 0.960526
46 GDP AF3 0.538462 0.876543
47 G G G RPC 0.538462 0.886076
48 G C 0.538462 0.8875
49 GDP ALF 0.538462 0.876543
50 ALF GDP 0.538462 0.876543
51 Y9Z 0.537037 0.890244
52 G5P 0.536364 0.960526
53 A G 0.533898 0.922078
54 GTG 0.53211 0.924051
55 U A G G 0.529412 0.922078
56 G3A 0.527273 0.960526
57 U2G 0.525862 0.924051
58 G U 0.521368 0.8875
59 APC G U 0.520661 0.897436
60 JB3 0.517241 0.935897
61 YGP 0.513761 0.888889
62 G G G C 0.512195 0.9
63 A G C C 0.508065 0.898734
64 NGD 0.5 0.948052
65 GDP 7MG 0.495575 0.898734
66 DG 0.494845 0.922078
67 DGP 0.494845 0.922078
68 G C C C 0.492188 0.911392
69 P2G 0.489796 0.894737
70 CAG 0.487805 0.869048
71 GPC 0.487805 0.86747
72 2MD 0.487603 0.879518
73 FEG 0.487395 0.86747
74 G U34 0.483333 0.876543
75 ZGP 0.483333 0.857143
76 P1G 0.48 0.883117
77 DBG 0.476562 0.935897
78 MGD 0.475806 0.879518
79 PAP 0.475248 0.918919
80 A G U 0.470588 0.876543
81 TPG 0.465116 0.829545
82 UCG 0.461538 0.923077
83 MD1 0.460938 0.879518
84 DG DG 0.459459 0.876543
85 G1G 0.456693 0.9125
86 A G U U 0.453901 0.876543
87 PGD 0.449612 0.9125
88 IDP 0.446602 0.959459
89 CGP 0.443548 0.878049
90 G4M 0.442029 0.869048
91 AKW 0.439024 0.878049
92 G1R G1R 0.431818 0.911392
93 SGP 0.431373 0.8375
94 FE9 0.430769 0.765957
95 PGD O 0.428571 0.83908
96 DC DG 0.428571 0.855422
97 5GP 5GP 0.424528 0.894737
98 35G 0.415094 0.945946
99 C2E 0.415094 0.933333
100 PCG 0.415094 0.945946
101 AGO 0.414062 0.9
102 MGP 0.40367 0.948052
103 6G0 0.4 0.948052
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6G14; Ligand: G4P; Similar sites found with APoc: 120
This union binding pocket(no: 1) in the query (biounit: 6g14.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 2XTZ GSP 1.70068
2 4LPS GDP 2.06612
3 3CX8 GSP 2.38095
4 1TQ4 GDP 3.40136
5 1YVD GNP 4.14201
6 1SKQ GDP 4.42177
7 3WYA GDP 4.42177
8 2C78 GNP 4.42177
9 2C77 GNP 4.42177
10 4RD0 GDP 4.42177
11 5M04 GDP 4.42177
12 4ZKD GDP 4.42177
13 3VMF GTP 4.42177
14 5GOE GDP 4.7619
15 1YRB GDP 4.96183
16 5CK5 GDP 5.10204
17 5W7Q GDP 5.44218
18 4DKX GDP 5.55556
19 3PCR GTP 5.78231
20 2RCN GDP 5.78231
21 1U8Z GDP 5.95238
22 5FG3 GDP 6.12245
23 1Z0A GDP 6.32184
24 3GJ7 GDP 6.33484
25 3GJ4 GDP 6.33484
26 3GJ5 GDP 6.33484
27 2QN6 GDP 6.45161
28 1G7S GDP 6.46258
29 3TK1 GDP 6.46258
30 4D0N GDP 6.48649
31 5TB5 GDP 6.48649
32 3Q85 GNP 6.50888
33 3Q72 GNP 6.62651
34 2CJW GDP 6.77083
35 2FFQ GSP 7.01754
36 4HI0 GDP 7.08661
37 1DAR GDP 7.14286
38 1CLU DBG 7.22892
39 1I4D GDP 7.29167
40 2HT6 GDP 7.47126
41 1KK1 GNP 7.82313
42 2ZEJ GDP 8.15217
43 1Z0J GTP 8.47458
44 4BAS GNP 8.54271
45 3CH5 GDP 8.7963
46 1MR3 G3D 8.83978
47 6AU6 GDP 8.84354
48 1CS4 GSP 8.84354
49 3DOE GTP 8.85417
50 2A5J GDP 8.90052
51 3T12 GDP ALF 9.09091
52 3T1O GDP 9.09091
53 1KSH GDP 9.13978
54 5SZH GNP 9.15033
55 1D2E GDP 9.18367
56 1VG1 GDP 9.18919
57 1VG9 GDP 9.18919
58 5OEC GDP 9.28962
59 1YZG GDP 9.49721
60 5W75 GDP 9.52381
61 1F6B GDP 9.59596
62 1ZJ6 G3D 9.62567
63 1ZD9 GDP 10.1064
64 5H7J GCP 10.2041
65 5H7K GDP 10.2041
66 1S9D GDP 10.3659
67 1RE0 GDP 10.3659
68 5EE5 GTP 10.5263
69 4V0K GDP 10.6509
70 1O3Y GTP 10.8434
71 2WIC GNP 11.236
72 4R98 GNH 11.4391
73 3AQ4 GDP 11.9565
74 4YLG GDP 12.1387
75 1FZQ GDP 12.1547
76 3WY9 GDP 12.5
77 3MJH GTP 12.5
78 2F9L GDP 15.0754
79 4B47 GDP 15.6463
80 3RWO GDP 15.6757
81 1R4A GNP 15.6863
82 1OIV GDP 15.7068
83 2W83 GTP 15.7576
84 1ZC3 GNP 15.9292
85 3N5C GDP 16.0494
86 1OIX GDP 16.2304
87 1S8F GDP 16.3842
88 5O2T GSP 16.568
89 3T5G GDP 16.5746
90 5O74 GDP 16.6667
91 1Z0F GDP 16.7598
92 3QBT GNP 17.2414
93 1Z06 GNP 17.4603
94 2WJG GDP 17.5532
95 4NON GDP 17.6923
96 1Z2A GDP 18.4524
97 6CRK GDP 18.7075
98 1BH2 GSP 18.7075
99 5KDO GDP 18.7075
100 1Y3A GDP 18.7075
101 2OM2 GDP 19.4444
102 3W5J GDP 19.6078
103 2WJH GDP 19.8795
104 4J0Q GDP 22.449
105 3U6B GDP 24.3655
106 5JBQ GDP 24.3655
107 4G5G GDP 24.3655
108 4P3Y GDP 24.3655
109 3U6K GDP 24.3655
110 4PC3 GDP 24.3655
111 1D8T GDP 24.4275
112 2BVN GNP 24.4275
113 1MKY GDP 26.5306
114 4DCT GDP 26.5306
115 5LEF GTP 27.7487
116 2HCJ GDP 28.6567
117 5YT0 GDP 33.3333
118 1G7C 5GP 34.0426
119 1J2J GTP 35.5556
120 5W76 GDP 39.4558
Pocket No.: 2; Query (leader) PDB : 6G14; Ligand: G4P; 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: 6g14.bio2) has 19 residues
No: Leader PDB Ligand Sequence Similarity
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