Receptor
PDB id Resolution Class Description Source Keywords
3N75 2 Å EC: 4.1.1.18 X-RAY CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI INDUCIBLE LY DECARBOXYLASE LDCI ESCHERICHIA COLI PYRIDOXAL-5-prime -PHOSPHATE DEPENDENT DECARBOXYLASE ACID STRESS STRINGENT RESPONSE GUANOSINE TETRAPHOSPHATE (PPGPP) LYASE
Ref.: LINKAGE BETWEEN THE BACTERIAL ACID STRESS AND STRIN RESPONSES: THE STRUCTURE OF THE INDUCIBLE LYSINE DECARBOXYLASE. EMBO J. V. 30 931 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
G4P A:716;
B:716;
C:716;
D:716;
E:716;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
Kd = 684.9 nM
603.16 C10 H17 N5 O17 P4 c1nc2...
GOL A:718;
B:718;
C:718;
D:718;
E:718;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
P6G A:717;
B:717;
C:717;
D:717;
E:717;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
282.331 C12 H26 O7 C(COC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3N75 2 Å EC: 4.1.1.18 X-RAY CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI INDUCIBLE LY DECARBOXYLASE LDCI ESCHERICHIA COLI PYRIDOXAL-5-prime -PHOSPHATE DEPENDENT DECARBOXYLASE ACID STRESS STRINGENT RESPONSE GUANOSINE TETRAPHOSPHATE (PPGPP) LYASE
Ref.: LINKAGE BETWEEN THE BACTERIAL ACID STRESS AND STRIN RESPONSES: THE STRUCTURE OF THE INDUCIBLE LYSINE DECARBOXYLASE. EMBO J. V. 30 931 2011
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3N75 Kd = 684.9 nM G4P C10 H17 N5 O17 P4 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 2 families.
1 3N75 Kd = 684.9 nM G4P C10 H17 N5 O17 P4 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 1 families.
1 3N75 Kd = 684.9 nM G4P C10 H17 N5 O17 P4 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 BGO 0.638889 0.935897
8 GNH 0.634409 0.973333
9 GP3 0.630435 0.960526
10 G G 0.63 0.922078
11 GNP 0.625 0.960526
12 GSP 0.625 0.935897
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 GDC 0.596154 0.948052
20 GKE 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 GDP MG 0.57732 0.910256
26 G2P 0.575758 0.948052
27 G G U 0.574074 0.947368
28 GMV 0.571429 0.960526
29 GDP BEF 0.571429 0.8875
30 GH3 0.57 0.986486
31 GGM 0.565217 0.9125
32 2GP 0.565217 0.972973
33 G2R 0.563107 0.948052
34 GFB 0.560748 0.948052
35 GDR 0.560748 0.948052
36 GP2 0.556701 0.948052
37 6CK 0.555556 0.924051
38 ALF 5GP 0.555556 0.876543
39 BEF GDP 0.554455 0.876543
40 GTP MG 0.554455 0.910256
41 DGT 0.55 0.935065
42 GCP G 0.54902 0.922078
43 G A A A 0.547009 0.910256
44 GKD 0.545455 0.948052
45 JB2 0.545455 0.948052
46 CG2 0.543103 0.924051
47 GDX 0.540541 0.960526
48 GPD 0.540541 0.9125
49 GDP AF3 0.538462 0.876543
50 GDP ALF 0.538462 0.876543
51 G G G RPC 0.538462 0.886076
52 G C 0.538462 0.8875
53 Y9Z 0.537037 0.890244
54 G5P 0.536364 0.960526
55 GTG 0.53211 0.924051
56 U A G G 0.529412 0.922078
57 G3A 0.527273 0.960526
58 U2G 0.525862 0.924051
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 DGP 0.494845 0.922078
67 DG 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 U G A 0.467153 0.876543
82 TPG 0.465116 0.829545
83 UCG 0.461538 0.923077
84 MD1 0.460938 0.879518
85 DG DG 0.459459 0.876543
86 G1G 0.456693 0.9125
87 PGD 0.449612 0.9125
88 I2C FE2 CMO CMO 0.448819 0.797753
89 IDP 0.446602 0.959459
90 CGP 0.443548 0.878049
91 G4M 0.442029 0.869048
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 C2E 0.415094 0.933333
99 PCG 0.415094 0.945946
100 35G 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 : 3N75; Ligand: G4P; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3n75.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3N75; Ligand: G4P; 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: 3n75.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3N75; Ligand: G4P; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 3n75.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3N75; Ligand: G4P; 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: 3n75.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 3N75; Ligand: G4P; Similar sites found: 20
This union binding pocket(no: 5) in the query (biounit: 3n75.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3UR0 SVR 0.03978 0.41197 1.35922
2 2V3A FAD 0.03198 0.41606 2.60417
3 1HG4 LPP 0.03121 0.40758 2.7972
4 4BV6 FAD 0.04848 0.40735 4.46247
5 1MO9 FAD 0.01215 0.46682 4.78011
6 1MO9 KPC 0.01421 0.46296 4.78011
7 5FLJ QUE 0.02958 0.40015 5.37634
8 3TE4 ACO 0.01151 0.42626 5.5814
9 1XSE NDP 0.01699 0.43478 6.44068
10 2H5Z CTO 0.008183 0.41089 6.55738
11 1BB6 UMG 0.01337 0.42106 6.97674
12 3R96 ACO 0.03955 0.41038 7.44681
13 3R96 AMP 0.03955 0.41038 7.44681
14 4KOT CE3 0.008645 0.44806 8.02469
15 1LSZ NDG NAG NAG NAG 0.003125 0.44491 8.16327
16 4HP0 NOJ NAG NAG NAG 0.01021 0.43711 9.30233
17 1I0S NAP 0.0338 0.40763 9.46746
18 1I0S FMN 0.02543 0.40763 9.46746
19 4K30 NLG 0.002175 0.4079 11.875
20 4EOY ASN ASP TRP LEU LEU PRO SER TYR 0.01108 0.41026 21.875
Pocket No.: 6; Query (leader) PDB : 3N75; Ligand: G4P; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 3n75.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 3N75; Ligand: G4P; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 3n75.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 3N75; Ligand: G4P; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 3n75.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 9; Query (leader) PDB : 3N75; Ligand: G4P; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 9) in the query (biounit: 3n75.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 10; Query (leader) PDB : 3N75; Ligand: G4P; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 10) in the query (biounit: 3n75.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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