Receptor
PDB id Resolution Class Description Source Keywords
3CF6 2.2 Å NON-ENZYME: OTHER STRUCTURE OF EPAC2 IN COMPLEX WITH CYCLIC-AMP AND RAP MUS MUSCULUS EPAC RAPGEF4 RAP RAP1B CAMP SP-CAMPS GEF GUNANINE NUCEXCHANGE FACTOR G-PROTEIN GTP-BINDING NUCLEOTIDE-BINDINGSIGNALING PROTEIN REGULATOR-GTP-BINDING PROTEIN COMPLEX SIPROTEIN-GTP-BINDING PROTEIN COMPLEX
Ref.: STRUCTURE OF EPAC2 IN COMPLEX WITH A CYCLIC AMP ANA RAP1B NATURE V. 455 124 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 R:168;
Invalid;
none;
submit data
96.063 O4 S [O-]S...
SP1 E:2;
E:3;
Valid;
Valid;
none;
none;
submit data
345.272 C10 H12 N5 O5 P S c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3CF6 2.2 Å NON-ENZYME: OTHER STRUCTURE OF EPAC2 IN COMPLEX WITH CYCLIC-AMP AND RAP MUS MUSCULUS EPAC RAPGEF4 RAP RAP1B CAMP SP-CAMPS GEF GUNANINE NUCEXCHANGE FACTOR G-PROTEIN GTP-BINDING NUCLEOTIDE-BINDINGSIGNALING PROTEIN REGULATOR-GTP-BINDING PROTEIN COMPLEX SIPROTEIN-GTP-BINDING PROTEIN COMPLEX
Ref.: STRUCTURE OF EPAC2 IN COMPLEX WITH A CYCLIC AMP ANA RAP1B NATURE V. 455 124 2008
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 3CF6 - SP1 C10 H12 N5 O5 P S c1nc(c2c(n....
70% Homology Family (34)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 250 families.
1 5WFO - 5UU C19 H16 Cl F N2 c1cc(ccc1N....
2 6FA3 Kd = 0.038 uM D1Z C30 H36 N4 O5 CN(C)Cc1cc....
3 5WFQ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
4 5O2T Kd = 3.9 nM GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
5 5WPM - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
6 5WFR - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
7 5UFQ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
8 6AMB - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
9 6FA1 - D2Z C20 H25 N2 O4 C[NH+](C)C....
10 5UFE - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
11 5WFP - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
12 5WHB - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
13 5WPL - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
14 5XCO - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
15 1NVU - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
16 5WHE - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
17 3KUC - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
18 1C1Y - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
19 5TAR - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
20 4DXA - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
21 4HDO - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
22 5E95 Kd = 15.7 nM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
23 3CF6 - SP1 C10 H12 N5 O5 P S c1nc(c2c(n....
24 6FA4 Kd = 0.051 uM D1W C23 H25 N3 O3 CN(C)Cc1cc....
25 2C5L - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
26 4K81 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
27 1LFD - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
28 4KVG - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
29 1WQ1 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
30 3DDC - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
31 3KUD - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
32 4URZ Kd = 3 mM VJP C11 H14 N2 O3 S c1cc(ccc1N....
33 4URX Kd = 1.3 mM HXY C11 H14 Br N c1cc(ccc1C....
34 4URY Kd = 6 mM RV1 C10 H12 N2 O3 S c1cc(ccc1N....
50% Homology Family (47)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 204 families.
1 3QBT - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
2 5WFO - 5UU C19 H16 Cl F N2 c1cc(ccc1N....
3 6FA3 Kd = 0.038 uM D1Z C30 H36 N4 O5 CN(C)Cc1cc....
4 5WFQ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
5 5O2T Kd = 3.9 nM GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
6 5WPM - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
7 5WFR - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
8 5UFQ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
9 6AMB - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
10 6FA1 - D2Z C20 H25 N2 O4 C[NH+](C)C....
11 5UFE - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
12 5WFP - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
13 5WHB - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
14 5WPL - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
15 5XCO - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
16 1NVU - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
17 5WHE - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
18 3KUC - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
19 1C1Y - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
20 5TAR - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
21 4DXA - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
22 4HDO - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
23 3MJH - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
24 5E95 Kd = 15.7 nM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
25 3CF6 - SP1 C10 H12 N5 O5 P S c1nc(c2c(n....
26 2CJW Kd = 2.5 uM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
27 6FA4 Kd = 0.051 uM D1W C23 H25 N3 O3 CN(C)Cc1cc....
28 2C5L - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
29 4K81 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
30 1LFD - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
31 4KVG - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
32 3TNF - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
33 1ZC4 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
34 1ZC3 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
35 2A9K - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
36 2A78 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
37 1WQ1 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
38 3TKL - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
39 3DDC - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
40 3KUD - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
41 1TU3 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
42 1UAD Ka = 7260000 M^-1 GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
43 5O74 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
44 3SFV - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
45 4URZ Kd = 3 mM VJP C11 H14 N2 O3 S c1cc(ccc1N....
46 4URX Kd = 1.3 mM HXY C11 H14 Br N c1cc(ccc1C....
47 4URY Kd = 6 mM RV1 C10 H12 N2 O3 S c1cc(ccc1N....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SP1; Similar ligands found: 85
No: Ligand ECFP6 Tc MDL keys Tc
1 RP1 1 1
2 SP1 1 1
3 CMP 0.757143 0.928571
4 2BA 0.757143 0.915493
5 1YD 0.580645 0.844156
6 4BW 0.580645 0.844156
7 Y3J 0.542857 0.702703
8 5AD 0.529412 0.722222
9 QQX 0.519481 0.90411
10 RAB 0.514286 0.77027
11 ADN 0.514286 0.77027
12 XYA 0.514286 0.77027
13 5CD 0.513889 0.756757
14 1SY 0.509615 0.844156
15 CC5 0.5 0.791667
16 4UR 0.5 0.844156
17 5N5 0.5 0.746667
18 A4D 0.493151 0.77027
19 MTA 0.480519 0.75
20 75G 0.476744 0.932432
21 EP4 0.473684 0.708861
22 1OR 0.472527 0.759036
23 M2T 0.467532 0.7125
24 DTA 0.467532 0.810811
25 7D7 0.458333 0.72
26 ACK 0.45679 0.835616
27 3AD 0.453333 0.780822
28 SRA 0.451219 0.918919
29 1YC 0.45098 0.818182
30 3DH 0.45 0.75
31 3AM 0.444444 0.851351
32 J7C 0.440476 0.703704
33 AMP 0.439024 0.864865
34 A 0.439024 0.864865
35 LMS 0.439024 0.804878
36 ZAS 0.439024 0.721519
37 QQY 0.439024 0.890411
38 6RE 0.433735 0.695122
39 2AM 0.432099 0.84
40 NEC 0.428571 0.679487
41 AOC 0.428571 0.75
42 DSH 0.428571 0.703704
43 A3G 0.428571 0.730769
44 6SX 0.425287 0.885714
45 A2D 0.423529 0.866667
46 A3N 0.423529 0.717949
47 ABM 0.423529 0.842105
48 EEM 0.419355 0.651163
49 GJV 0.418605 0.686747
50 S4M 0.418605 0.647727
51 OVE 0.416667 0.88
52 6SZ 0.41573 0.915493
53 ADX 0.41573 0.82716
54 7CH 0.413793 0.914286
55 A12 0.413793 0.810127
56 A3P 0.413793 0.864865
57 BA3 0.413793 0.866667
58 AP2 0.413793 0.810127
59 MAO 0.413793 0.697674
60 SFG 0.411111 0.705128
61 50T 0.411111 0.831169
62 5X8 0.411111 0.74026
63 S7M 0.410526 0.670588
64 AP5 0.409091 0.866667
65 5AS 0.409091 0.758621
66 ADP 0.409091 0.842105
67 B4P 0.409091 0.866667
68 APC 0.406593 0.810127
69 5F1 0.405063 0.688312
70 AT4 0.404494 0.881579
71 SON 0.404494 0.810127
72 A3S 0.404494 0.74026
73 A7D 0.404494 0.753247
74 AN2 0.404494 0.831169
75 7D5 0.402439 0.805195
76 AD9 0.402174 0.820513
77 SA8 0.402174 0.666667
78 SAP 0.402174 0.894737
79 AGS 0.402174 0.894737
80 AU1 0.4 0.820513
81 N6R 0.4 0.853333
82 CA0 0.4 0.820513
83 MHZ 0.4 0.659091
84 N6S 0.4 0.853333
85 M33 0.4 0.831169
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3CF6; Ligand: SP1; 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: 3cf6.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3CF6; Ligand: SP1; 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: 3cf6.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3CF6; Ligand: SP1; Similar sites found with APoc: 2
This union binding pocket(no: 3) in the query (biounit: 3cf6.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 5C8W PCG 31.4685
2 3PNA CMP 36.3636
Pocket No.: 4; Query (leader) PDB : 3CF6; Ligand: SP1; 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: 3cf6.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 3CF6; Ligand: SP1; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 3cf6.bio2) has 11 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 3CF6; Ligand: SP1; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 3cf6.bio2) has 19 residues
No: Leader PDB Ligand Sequence Similarity
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