Receptor
PDB id Resolution Class Description Source Keywords
4S1B 2.1 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF L. MONOCYTOGENES PHOSPHODIESTERASE PGPH IN COMPLEX WITH CYCLIC-DI-AMP LISTERIA MONOCYTOGENES C-DI-AMP LISTERIA MONOCYTOGENES PHOSPHODIESTERASE HD DOMAHYDROLASE
Ref.: AN HD-DOMAIN PHOSPHODIESTERASE MEDIATES COOPERATIVE HYDROLYSIS OF C-DI-AMP TO AFFECT BACTERIAL GROWTH A VIRULENCE. PROC.NATL.ACAD.SCI.USA V. 112 E747 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FE A:802;
A:801;
D:802;
D:801;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
55.845 Fe [Fe+3...
2BA A:803;
D:803;
Valid;
Valid;
none;
none;
Kd = 0.3 uM
658.412 C20 H24 N10 O12 P2 c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4S1B 2.1 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF L. MONOCYTOGENES PHOSPHODIESTERASE PGPH IN COMPLEX WITH CYCLIC-DI-AMP LISTERIA MONOCYTOGENES C-DI-AMP LISTERIA MONOCYTOGENES PHOSPHODIESTERASE HD DOMAHYDROLASE
Ref.: AN HD-DOMAIN PHOSPHODIESTERASE MEDIATES COOPERATIVE HYDROLYSIS OF C-DI-AMP TO AFFECT BACTERIAL GROWTH A VIRULENCE. PROC.NATL.ACAD.SCI.USA V. 112 E747 2015
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 4S1B Kd = 0.3 uM 2BA C20 H24 N10 O12 P2 c1nc(c2c(n....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 4S1B Kd = 0.3 uM 2BA C20 H24 N10 O12 P2 c1nc(c2c(n....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 4S1B Kd = 0.3 uM 2BA C20 H24 N10 O12 P2 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 2BA; Similar ligands found: 94
No: Ligand ECFP6 Tc MDL keys Tc
1 CMP 1 0.984848
2 2BA 1 1
3 SP1 0.757143 0.915493
4 RP1 0.757143 0.915493
5 1YD 0.727273 0.916667
6 4BW 0.727273 0.916667
7 1SY 0.653061 0.916667
8 1OR 0.635294 0.797468
9 4UR 0.626263 0.916667
10 7CH 0.580247 0.969697
11 6SX 0.573171 0.939394
12 6SZ 0.559524 0.970149
13 N6S 0.535354 0.901408
14 N6R 0.535354 0.901408
15 C2E 0.534091 0.916667
16 35G 0.534091 0.902778
17 PCG 0.534091 0.902778
18 1YC 0.53 0.888889
19 Y3J 0.506667 0.742857
20 5CD 0.5 0.8
21 XYA 0.5 0.814286
22 ACK 0.5 0.884058
23 ADN 0.5 0.814286
24 RAB 0.5 0.814286
25 6SW 0.494382 0.914286
26 5AD 0.493151 0.764706
27 5N5 0.486842 0.788732
28 75G 0.483146 0.878378
29 A4D 0.480519 0.788732
30 M2T 0.475 0.727273
31 MTA 0.469136 0.767123
32 CC5 0.466667 0.838235
33 EP4 0.4625 0.746667
34 DTA 0.45679 0.805556
35 QQX 0.452381 0.824324
36 AMP 0.447059 0.914286
37 A 0.447059 0.914286
38 QQY 0.447059 0.835616
39 3DH 0.440476 0.767123
40 AMP MG 0.436782 0.863014
41 3AM 0.435294 0.9
42 ABM 0.431818 0.888889
43 J7C 0.431818 0.74026
44 A2D 0.431818 0.942857
45 ZAS 0.430233 0.76
46 7D7 0.428571 0.760563
47 S4M 0.426966 0.658824
48 6RE 0.425287 0.730769
49 SRA 0.425287 0.864865
50 3AD 0.425 0.826087
51 2AM 0.423529 0.887324
52 AP2 0.422222 0.878378
53 A12 0.422222 0.878378
54 BA3 0.422222 0.942857
55 MAO 0.422222 0.731707
56 NEC 0.420455 0.716216
57 A3G 0.420455 0.77027
58 DSH 0.420455 0.717949
59 AOC 0.420455 0.791667
60 BEF ADP 0.419355 0.853333
61 SFG 0.419355 0.743243
62 ADP BEF 0.419355 0.853333
63 6JR 0.419048 0.942029
64 B4P 0.417582 0.942857
65 5AS 0.417582 0.752941
66 AP5 0.417582 0.942857
67 ADP 0.417582 0.915493
68 A3N 0.41573 0.756757
69 APC 0.414894 0.878378
70 SON 0.413043 0.878378
71 AN2 0.413043 0.902778
72 EEM 0.412371 0.682927
73 GJV 0.411111 0.721519
74 GGZ 0.41 0.797468
75 OVE 0.409091 0.851351
76 ADP MG 0.408602 0.876712
77 AU1 0.408602 0.890411
78 M33 0.408602 0.902778
79 CA0 0.408602 0.890411
80 ADX 0.408602 0.822785
81 A3P 0.406593 0.942029
82 5X8 0.404255 0.756757
83 50T 0.404255 0.876712
84 ATP 0.404255 0.915493
85 ACP 0.404255 0.890411
86 VO4 ADP 0.40404 0.902778
87 ADP VO4 0.40404 0.902778
88 SAM 0.402062 0.682927
89 0UM 0.401961 0.691358
90 AQP 0.4 0.915493
91 APR 0.4 0.915493
92 PRX 0.4 0.864865
93 AR6 0.4 0.915493
94 5FA 0.4 0.915493
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4S1B; Ligand: 2BA; Similar sites found: 7
This union binding pocket(no: 1) in the query (biounit: 4s1b.bio2) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1GEG GLC 0.00003464 0.58488 4.05405
2 4J6C STR 0.02457 0.40585 11.7117
3 3EMZ HXH 0.0093 0.42777 13.0631
4 4N6W FLC 0.0023 0.44358 13.5135
5 2W5F XYP XYP XYP 0.02997 0.40135 13.5135
6 3W25 XYP XYP 0.006345 0.42681 13.964
7 5SWI BMA 0.02986 0.40758 35.1351
Pocket No.: 2; Query (leader) PDB : 4S1B; Ligand: 2BA; Similar sites found: 4
This union binding pocket(no: 2) in the query (biounit: 4s1b.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1KAE HSO 0.02423 0.40498 4.05405
2 5U9J GER 0.03094 0.40353 6.50888
3 4I90 CHT 0.0453 0.40174 7.65766
4 2ZZV LAC 0.01431 0.4246 9.00901
Pocket No.: 3; Query (leader) PDB : 4S1B; Ligand: 2BA; 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: 4s1b.bio3) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4S1B; Ligand: 2BA; 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: 4s1b.bio3) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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