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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 1443 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 1205 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 1039 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: 93
No: Ligand ECFP6 Tc MDL keys Tc
1 2BA 1 1
2 CMP 1 0.984848
3 RP1 0.757143 0.915493
4 SP1 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 N6R 0.535354 0.901408
14 N6S 0.535354 0.901408
15 PCG 0.534091 0.902778
16 35G 0.534091 0.902778
17 C2E 0.534091 0.916667
18 1YC 0.53 0.888889
19 Y3J 0.506667 0.742857
20 XYA 0.5 0.814286
21 5CD 0.5 0.8
22 ACK 0.5 0.884058
23 RAB 0.5 0.814286
24 ADN 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 LMS 0.447059 0.8
37 AMP 0.447059 0.914286
38 QQY 0.447059 0.835616
39 A 0.447059 0.914286
40 3DH 0.440476 0.767123
41 3AM 0.435294 0.9
42 A2D 0.431818 0.942857
43 J7C 0.431818 0.74026
44 ABM 0.431818 0.888889
45 ZAS 0.430233 0.76
46 7D7 0.428571 0.760563
47 S4M 0.426966 0.658824
48 SRA 0.425287 0.864865
49 6RE 0.425287 0.730769
50 3AD 0.425 0.826087
51 2AM 0.423529 0.887324
52 BA3 0.422222 0.942857
53 A12 0.422222 0.878378
54 AP2 0.422222 0.878378
55 MAO 0.422222 0.731707
56 DSH 0.420455 0.717949
57 NEC 0.420455 0.716216
58 AOC 0.420455 0.791667
59 A3G 0.420455 0.77027
60 SFG 0.419355 0.743243
61 6JR 0.419048 0.942029
62 ADP 0.417582 0.915493
63 AP5 0.417582 0.942857
64 5AS 0.417582 0.752941
65 B4P 0.417582 0.942857
66 A3N 0.41573 0.756757
67 APC 0.414894 0.878378
68 AN2 0.413043 0.902778
69 SON 0.413043 0.878378
70 AT4 0.413043 0.878378
71 EEM 0.412371 0.682927
72 GJV 0.411111 0.721519
73 GGZ 0.41 0.797468
74 OVE 0.409091 0.851351
75 M33 0.408602 0.902778
76 ADX 0.408602 0.822785
77 AU1 0.408602 0.890411
78 CA0 0.408602 0.890411
79 A3P 0.406593 0.942029
80 5X8 0.404255 0.756757
81 ATP 0.404255 0.915493
82 ACP 0.404255 0.890411
83 HEJ 0.404255 0.915493
84 50T 0.404255 0.876712
85 ADP VO4 0.40404 0.902778
86 VO4 ADP 0.40404 0.902778
87 SAM 0.402062 0.682927
88 0UM 0.401961 0.691358
89 AR6 0.4 0.915493
90 AQP 0.4 0.915493
91 5FA 0.4 0.915493
92 APR 0.4 0.915493
93 PRX 0.4 0.864865
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4S1B; Ligand: 2BA; Similar sites found with APoc: 56
This union binding pocket(no: 1) in the query (biounit: 4s1b.bio2) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 5M36 9SZ None
2 5M37 9SZ None
3 3NGU ADP None
4 5D4Y BXP 1.35135
5 4CSD MFU 1.8018
6 3OBT SLB 2.25225
7 4FGC PQ0 2.42424
8 4AQ4 G3P 2.7027
9 3SCH TB6 3.0303
10 1ZPD CIT 3.15315
11 2UW1 GVM 3.15315
12 5EY0 GTP 3.15315
13 4WOE 3S5 3.15315
14 5UGW GSH 4
15 1GEG GLC 4.05405
16 5IM3 DTP 4.05405
17 5ZMY TAR 4.14013
18 5W7B MYR 4.25532
19 6F7X MFU 4.44444
20 6DWD HDV 4.5045
21 5LX9 OLB 4.5045
22 4ZO3 C6L 4.5045
23 2BCG GER 4.95496
24 3N7S 3N7 5.20833
25 1R6N 434 5.21327
26 1NU4 MLA 6.18557
27 3JRS A8S 6.25
28 1ZED PNP 6.30631
29 3F8C HT1 6.34921
30 3KDJ A8S 6.43564
31 4O4Z N2O 7.14286
32 4PMZ BXP 7.20721
33 4I90 CHT 7.65766
34 1V0L XIF XYP 8.55856
35 1B3X XYP XYP XYP 8.55856
36 5KD8 TNR 8.55856
37 2Y69 CHD 9.45946
38 4OGQ 7PH 10
39 2AJH MET 10.2041
40 4A59 AMP 10.3604
41 5Z84 CHD 10.6383
42 5W97 CHD 10.6383
43 5ZCO CHD 10.6383
44 1DRJ RIP 11.2613
45 1FH8 XYP XIF 11.7117
46 4J6C STR 11.7117
47 3EMZ HXH 13.0631
48 2WZE XYP XYP XYP 13.0631
49 4N6W FLC 13.5135
50 1VBR XYS XYP 13.5135
51 2W5F XYP XYP XYP 13.5135
52 3W25 XYP XYP 13.964
53 3ZW0 FUC 16.092
54 2FGL XYS XYS XYS 26.5766
55 1B74 DGN 30.1802
56 5SWI BMA 35.1351
Pocket No.: 2; Query (leader) PDB : 4S1B; Ligand: 2BA; Similar sites found with APoc: 24
This union binding pocket(no: 2) in the query (biounit: 4s1b.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 4ZGM 32M None
2 3E70 GDP 1.35135
3 5ZKC 3C0 2.7027
4 1Y13 BIO 2.76243
5 2RFY CBI 3.15315
6 1KAE HSO 4.05405
7 3QP8 HL0 4.34783
8 2BS5 BGC GAL FUC 4.44444
9 3ETG GWD 4.5045
10 4CPB GAL CN8 4.95868
11 1XZ3 ICF 5.17241
12 5U9J GER 6.50888
13 3M3E GAL A2G NPO 6.8323
14 5VLC HSO 7.20721
15 5XK9 GST 7.65766
16 2UXI G50 8.09524
17 1U25 IHS 8.10811
18 2ZZV LAC 9.00901
19 3KLL MAL 9.90991
20 4CQB MLI 12.6126
21 1PIG GLC GLC 13.964
22 4MLN ODV 15.3061
23 3ZW2 NAG GAL FUC 16.092
24 2PAR TMP 17.9104
Pocket No.: 3; Query (leader) PDB : 4S1B; Ligand: 2BA; Similar sites found with APoc: 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 Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4S1B; Ligand: 2BA; Similar sites found with APoc: 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 Sequence Similarity
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