Receptor
PDB id Resolution Class Description Source Keywords
2AG2 2 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE ANALYSIS OF GM2-ACTIVATOR PROTEIN COMPLEXE PHOSPHATIDYLCHOLINE HOMO SAPIENS PHOSPHOLIPID-PROTEIN COMPLEX LIPID ACYL CHAIN STACKING PACLIPID BINDING PROTEIN
Ref.: CRYSTAL STRUCTURE ANALYSIS OF PHOSPHATIDYLCHOLINE-GM2-ACTIVATOR PRODUCT COMPLEXES EVIDENCE FOR HYDROLASE ACTIVITY. BIOCHEMISTRY V. 44 13510 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CH5 B:2341;
C:2342;
Valid;
Valid;
none;
none;
submit data
258.229 C8 H21 N O6 P C[N+]...
CL A:801;
B:802;
C:803;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
35.453 Cl [Cl-]
DAO B:1364;
Valid;
none;
submit data
200.318 C12 H24 O2 CCCCC...
EPE A:900;
C:901;
Invalid;
Invalid;
none;
none;
submit data
238.305 C8 H18 N2 O4 S C1CN(...
IPA A:1502;
A:1504;
B:1508;
B:1509;
B:1515;
C:1510;
C:1511;
C:1512;
C:1513;
C:1514;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
60.095 C3 H8 O CC(C)...
LP3 A:2344;
A:2345;
B:2343;
C:2346;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
524.691 C26 H55 N O7 P CCCCC...
MYR B:3046;
C:3045;
Valid;
Valid;
none;
none;
submit data
228.371 C14 H28 O2 CCCCC...
OLA B:3628;
C:3629;
Valid;
Valid;
none;
none;
submit data
282.461 C18 H34 O2 CCCCC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2AG4 1.8 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE ANALYSIS OF GM2-ACTIVATOR PROTEIN COMPLEXE PHOSPHATIDYLCHOLINE HOMO SAPIENS COMPLEX OF SINGLE CHAIN LIPID AND FATTY ACIDS LIPID BINDING
Ref.: CRYSTAL STRUCTURE ANALYSIS OF PHOSPHATIDYLCHOLINE-GM2-ACTIVATOR PRODUCT COMPLEXES EVIDENCE FOR HYDROLASE ACTIVITY. BIOCHEMISTRY V. 44 13510 2005
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 263 families.
1 2AG4 - LP3 C26 H55 N O7 P CCCCCCCCCC....
2 1TJJ - DAO C12 H24 O2 CCCCCCCCCC....
3 2AG9 - MYR C14 H28 O2 CCCCCCCCCC....
4 2AF9 - MYR C14 H28 O2 CCCCCCCCCC....
5 2AG2 - DAO C12 H24 O2 CCCCCCCCCC....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 196 families.
1 2AG4 - LP3 C26 H55 N O7 P CCCCCCCCCC....
2 1TJJ - DAO C12 H24 O2 CCCCCCCCCC....
3 2AG9 - MYR C14 H28 O2 CCCCCCCCCC....
4 2AF9 - MYR C14 H28 O2 CCCCCCCCCC....
5 2AG2 - DAO C12 H24 O2 CCCCCCCCCC....
6 2AGC - MYR C14 H28 O2 CCCCCCCCCC....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 171 families.
1 2AG4 - LP3 C26 H55 N O7 P CCCCCCCCCC....
2 1TJJ - DAO C12 H24 O2 CCCCCCCCCC....
3 2AG9 - MYR C14 H28 O2 CCCCCCCCCC....
4 2AF9 - MYR C14 H28 O2 CCCCCCCCCC....
5 2AG2 - DAO C12 H24 O2 CCCCCCCCCC....
6 2AGC - MYR C14 H28 O2 CCCCCCCCCC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: CH5; Similar ligands found: 13
No: Ligand ECFP6 Tc MDL keys Tc
1 CH5 1 1
2 GPE 0.65 0.745098
3 LPE 0.526316 0.87037
4 LP3 0.483871 0.824561
5 LAP 0.483871 0.824561
6 LPC 0.483871 0.824561
7 PC 0.45 0.84
8 GSE 0.44898 0.636364
9 G3P 0.425 0.6
10 1GP 0.425 0.6
11 SPU 0.424242 0.79661
12 42H 0.422535 0.810345
13 XP5 0.402985 0.789474
Ligand no: 2; Ligand: DAO; Similar ligands found: 52
No: Ligand ECFP6 Tc MDL keys Tc
1 MYR 1 1
2 F23 1 1
3 11A 1 1
4 STE 1 1
5 KNA 1 1
6 TDA 1 1
7 DCR 1 1
8 DAO 1 1
9 DKA 1 1
10 PLM 1 1
11 F15 1 1
12 OCA 0.956522 1
13 SHV 0.833333 0.952381
14 KTC 0.793103 0.875
15 AZ1 0.73913 0.64
16 6NA 0.72 0.904762
17 NER 0.71875 0.954545
18 OLA 0.71875 0.954545
19 ELA 0.71875 0.954545
20 VCA 0.666667 0.954545
21 PAM 0.666667 0.954545
22 PML 0.625 0.6
23 3LA 0.606061 0.8
24 LEA 0.6 0.809524
25 MYZ 0.588235 0.909091
26 12H 0.586207 0.615385
27 ODD 0.567568 0.913043
28 BRC 0.566667 0.666667
29 14V 0.555556 0.740741
30 M12 0.545455 0.869565
31 14U 0.542857 0.703704
32 EIC 0.538462 0.913043
33 EOD 0.538462 0.7
34 BUA 0.48 0.666667
35 RCL 0.468085 0.84
36 HXD 0.459459 0.807692
37 56S 0.459459 0.653846
38 ODT 0.452381 0.782609
39 3X1 0.444444 0.818182
40 LNL 0.44186 0.826087
41 CNS 0.435897 0.68
42 6UL 0.435897 0.68
43 5UF 0.432432 0.807692
44 243 0.428571 0.807692
45 GYM 0.418605 0.606061
46 PL3 0.413793 0.75
47 O8N 0.413793 0.75
48 1DO 0.413793 0.75
49 F09 0.413793 0.75
50 OC9 0.413793 0.75
51 DE1 0.413793 0.75
52 T25 0.403846 0.677419
Ligand no: 3; Ligand: LP3; Similar ligands found: 74
No: Ligand ECFP6 Tc MDL keys Tc
1 LAP 1 1
2 LP3 1 1
3 LPC 1 1
4 42H 0.863636 0.982143
5 LIO 0.685714 0.963636
6 HGX 0.685714 0.963636
7 PC7 0.685714 0.963636
8 HGP 0.685714 0.963636
9 6PL 0.685714 0.963636
10 PLD 0.685714 0.963636
11 NKN 0.645161 0.732143
12 XP5 0.633803 0.963636
13 PCW 0.607595 0.946429
14 LPE 0.602941 0.945455
15 PCK 0.592593 0.913793
16 S12 0.584416 0.75
17 CD4 0.583333 0.763636
18 CN5 0.575342 0.781818
19 NKP 0.56338 0.719298
20 PSC 0.55814 0.946429
21 PGM 0.557143 0.719298
22 CN6 0.538462 0.763636
23 PEH 0.533333 0.827586
24 PEV 0.533333 0.827586
25 8PE 0.533333 0.827586
26 PEF 0.533333 0.827586
27 PTY 0.533333 0.827586
28 9PE 0.526316 0.827586
29 LHG 0.526316 0.736842
30 PGT 0.526316 0.736842
31 PCF 0.525641 0.890909
32 PC1 0.525641 0.890909
33 MC3 0.525641 0.890909
34 CN3 0.525 0.763636
35 PEE 0.506494 0.844828
36 OPC 0.494253 0.929825
37 SPU 0.487179 0.836066
38 CH5 0.483871 0.824561
39 PX2 0.479452 0.745455
40 3XU 0.477273 0.84127
41 LOP 0.47619 0.813559
42 L9Q 0.47619 0.813559
43 P5S 0.475 0.779661
44 CDL 0.474359 0.727273
45 L9R 0.471264 0.875
46 PGW 0.470588 0.724138
47 7PH 0.465753 0.732143
48 6PH 0.465753 0.732143
49 3PH 0.465753 0.732143
50 LPP 0.465753 0.732143
51 DR9 0.465116 0.724138
52 PGV 0.465116 0.724138
53 ZPE 0.465116 0.813559
54 PGK 0.45977 0.7
55 P6L 0.45977 0.724138
56 7P9 0.459459 0.732143
57 OZ2 0.454545 0.724138
58 PEK 0.444444 0.813559
59 3PC 0.444444 0.872727
60 DGG 0.444444 0.7
61 44G 0.435897 0.736842
62 GP7 0.434783 0.813559
63 PII 0.428571 0.66129
64 PD7 0.418919 0.732143
65 PIF 0.418605 0.650794
66 PIZ 0.41573 0.66129
67 DLP 0.414894 0.875
68 M7U 0.414634 0.732143
69 3PE 0.409639 0.758621
70 8ND 0.407895 0.62069
71 AGA 0.404762 0.736842
72 PIO 0.404494 0.650794
73 IP9 0.404494 0.66129
74 52N 0.404494 0.650794
Ligand no: 4; Ligand: MYR; Similar ligands found: 52
No: Ligand ECFP6 Tc MDL keys Tc
1 MYR 1 1
2 F23 1 1
3 11A 1 1
4 STE 1 1
5 KNA 1 1
6 TDA 1 1
7 DCR 1 1
8 DAO 1 1
9 DKA 1 1
10 PLM 1 1
11 F15 1 1
12 OCA 0.956522 1
13 SHV 0.833333 0.952381
14 KTC 0.793103 0.875
15 AZ1 0.73913 0.64
16 6NA 0.72 0.904762
17 NER 0.71875 0.954545
18 OLA 0.71875 0.954545
19 ELA 0.71875 0.954545
20 VCA 0.666667 0.954545
21 PAM 0.666667 0.954545
22 PML 0.625 0.6
23 3LA 0.606061 0.8
24 LEA 0.6 0.809524
25 MYZ 0.588235 0.909091
26 12H 0.586207 0.615385
27 ODD 0.567568 0.913043
28 BRC 0.566667 0.666667
29 14V 0.555556 0.740741
30 M12 0.545455 0.869565
31 14U 0.542857 0.703704
32 EIC 0.538462 0.913043
33 EOD 0.538462 0.7
34 BUA 0.48 0.666667
35 RCL 0.468085 0.84
36 HXD 0.459459 0.807692
37 56S 0.459459 0.653846
38 ODT 0.452381 0.782609
39 3X1 0.444444 0.818182
40 LNL 0.44186 0.826087
41 CNS 0.435897 0.68
42 6UL 0.435897 0.68
43 5UF 0.432432 0.807692
44 243 0.428571 0.807692
45 GYM 0.418605 0.606061
46 PL3 0.413793 0.75
47 O8N 0.413793 0.75
48 1DO 0.413793 0.75
49 F09 0.413793 0.75
50 OC9 0.413793 0.75
51 DE1 0.413793 0.75
52 T25 0.403846 0.677419
Ligand no: 5; Ligand: OLA; Similar ligands found: 51
No: Ligand ECFP6 Tc MDL keys Tc
1 NER 1 1
2 OLA 1 1
3 ELA 1 1
4 PAM 0.939394 1
5 VCA 0.939394 1
6 MYZ 0.852941 0.954545
7 EIC 0.725 0.956522
8 STE 0.71875 0.954545
9 MYR 0.71875 0.954545
10 F23 0.71875 0.954545
11 DAO 0.71875 0.954545
12 11A 0.71875 0.954545
13 TDA 0.71875 0.954545
14 KNA 0.71875 0.954545
15 F15 0.71875 0.954545
16 DKA 0.71875 0.954545
17 DCR 0.71875 0.954545
18 PLM 0.71875 0.954545
19 OCA 0.6875 0.954545
20 ODD 0.675 0.956522
21 RCL 0.625 0.88
22 LNL 0.613636 0.869565
23 SHV 0.606061 0.909091
24 KTC 0.605263 0.84
25 3X1 0.564103 0.863636
26 ODT 0.555556 0.826087
27 T25 0.54717 0.709677
28 AZ1 0.53125 0.615385
29 6NA 0.529412 0.863636
30 10Y 0.529412 0.645161
31 10X 0.529412 0.645161
32 243 0.519231 0.846154
33 OLC 0.519231 0.617647
34 OLB 0.519231 0.617647
35 MVC 0.490566 0.617647
36 ACD 0.488889 0.956522
37 VA 0.478261 0.692308
38 3LA 0.47619 0.769231
39 78N 0.471698 0.617647
40 78M 0.471698 0.617647
41 EOD 0.468085 0.677419
42 MPG 0.45283 0.617647
43 14V 0.444444 0.714286
44 LEA 0.441176 0.772727
45 T24 0.438596 0.769231
46 BRC 0.435897 0.64
47 14U 0.431818 0.678571
48 M12 0.428571 0.833333
49 UNA 0.421053 0.636364
50 8YP 0.421053 0.636364
51 OCD 0.421053 0.636364
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2AG4; Ligand: OLA; Similar sites found: 59
This union binding pocket(no: 1) in the query (biounit: 2ag4.bio2) has 54 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5F6U 5VK 0.02074 0.43037 None
2 5D48 L96 0.004929 0.42691 None
3 4WVW SLT 0.001819 0.49621 2.08333
4 5HZ5 65X 0.01566 0.40989 2.23881
5 4WCX MET 0.02654 0.4291 2.43902
6 5C5T AKG 0.03854 0.42077 2.43902
7 5H9Q TD2 0.003685 0.47491 2.58065
8 5DG2 GAL GLC 0.00345 0.4576 2.96296
9 5C3R HMU 0.03653 0.40578 3.04878
10 5C3R AKG 0.03653 0.40578 3.04878
11 3TAY MN0 0.01131 0.40874 3.06748
12 4WUJ FMN 0.005146 0.4445 3.40136
13 4YVN EBS 0.01569 0.44921 3.65854
14 4YGF AZM 0.00471 0.44637 3.65854
15 5T7I LAT NAG GAL 0.00362 0.48546 3.87097
16 4XMF HSM 0.003405 0.48909 4.26829
17 5D9G GLU ASN LEU TYR PHE GLN 0.007947 0.45876 4.26829
18 5T96 79J 0.02559 0.43738 4.26829
19 4D4U FUC NDG GAL FUC 0.01279 0.45272 4.87805
20 4CJN QNZ 0.04111 0.42324 4.87805
21 5V1B 8UY 0.04208 0.42246 4.87805
22 4D4U FUC GAL NDG FUC 0.0376 0.41773 4.87805
23 2ZHL NAG GAL GAL NAG 0.004662 0.46224 5.40541
24 4RF7 ARG 0.0007453 0.47317 5.4878
25 4WOE ADP 0.001033 0.45974 5.4878
26 2Y3S TIR 0.01141 0.42462 5.4878
27 5F7Y GLC GAL NAG GAL FUC A2G 0.04629 0.40947 5.4878
28 5E89 TD2 0.003545 0.45999 5.7554
29 4RYV ZEA 0.0005218 0.51776 5.80645
30 4KBA 1QM 0.001062 0.50679 6.09756
31 2XG5 EC2 0.003782 0.48059 6.09756
32 4MVK ACE VAL PHE PHE ALA GLU ASP NH2 0.002214 0.44508 6.70732
33 4P7X YCP 0.04677 0.40037 6.70732
34 4ZU4 4TG 0.01303 0.43146 6.75676
35 5KEW 6SB 0.02393 0.4323 6.94444
36 4BQY FNT 0.008067 0.4318 7.31707
37 5HZX 2GE 0.04604 0.41291 7.31707
38 5M6N 7H9 0.04336 0.42464 7.62712
39 4L9I 8PR 0.006679 0.44612 7.92683
40 5H2U 1N1 0.008668 0.43688 7.92683
41 5MST FUM 0.02868 0.42793 7.92683
42 5TVF CGQ 0.004465 0.46322 8.23529
43 2YMZ LAT 0.001847 0.47402 8.46154
44 5XLY C2E 0.009333 0.43528 8.53659
45 4DXD 9PC 0.0239 0.40926 8.53659
46 4ITH RCM 0.03054 0.40413 8.53659
47 5SVV FMN 0.01271 0.42238 8.75912
48 4D5B ACX 0.02579 0.40501 11.5854
49 5EFW FMN 0.004316 0.4482 11.7241
50 5DJU FMN 0.008005 0.43196 11.7241
51 3ZJX BOG 0.008498 0.46823 12.1951
52 1EPB REA 0.006526 0.44663 12.8049
53 4YBN FAD 0.006813 0.41331 12.8049
54 1GP6 DH2 0.004562 0.43118 14.0244
55 4Z3E GAL NGA GLA BGC GAL 0.03565 0.4237 14.6341
56 5FPX GLY SER SER HIS HIS HIS HIS HIS 0.00899 0.43275 15.0442
57 5DKK FMN 0.002862 0.45684 15.1724
58 5LUN OGA 0.03715 0.41802 15.2439
59 5FUI APY 0.0005741 0.53165 15.9091
Pocket No.: 2; Query (leader) PDB : 2AG4; Ligand: LP3; Similar sites found: 53
This union binding pocket(no: 2) in the query (biounit: 2ag4.bio2) has 57 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5F6U 5VK 0.02231 0.43037 None
2 5D48 L96 0.005536 0.42691 None
3 4WVW SLT 0.001982 0.49621 2.08333
4 5HZ5 65X 0.01537 0.41231 2.23881
5 4WCX MET 0.02845 0.4291 2.43902
6 5C5T AKG 0.04171 0.42077 2.43902
7 5H9Q TD2 0.003991 0.47491 2.58065
8 5DG2 GAL GLC 0.003727 0.4576 2.96296
9 5C3R HMU 0.0399 0.40578 3.04878
10 5C3R AKG 0.0399 0.40578 3.04878
11 3TAY MN0 0.01265 0.40874 3.06748
12 4WUJ FMN 0.006035 0.44334 3.40136
13 4YVN EBS 0.01726 0.44886 3.65854
14 4YGF AZM 0.005231 0.44637 3.65854
15 5T7I LAT NAG GAL 0.003959 0.48546 3.87097
16 4XMF HSM 0.003679 0.48909 4.26829
17 5D9G GLU ASN LEU TYR PHE GLN 0.00474 0.47333 4.26829
18 5T96 79J 0.02761 0.43738 4.26829
19 4D4U FUC NDG GAL FUC 0.01386 0.45272 4.87805
20 4D4U FUC GAL NDG FUC 0.04078 0.41773 4.87805
21 2ZHL NAG GAL GAL NAG 0.005135 0.46224 5.40541
22 4RF7 ARG 0.0008432 0.47317 5.4878
23 4WOE ADP 0.001171 0.45974 5.4878
24 2Y3S TIR 0.01262 0.42462 5.4878
25 5E89 TD2 0.003928 0.45999 5.7554
26 4RYV ZEA 0.000581 0.51776 5.80645
27 4KBA 1QM 0.001175 0.50679 6.09756
28 2XG5 EC2 0.004105 0.48059 6.09756
29 4MVK ACE VAL PHE PHE ALA GLU ASP NH2 0.002497 0.44508 6.70732
30 4ZU4 4TG 0.01432 0.43146 6.75676
31 4BQY FNT 0.01838 0.41676 7.31707
32 5HZX 2GE 0.04985 0.41291 7.31707
33 5M6N 7H9 0.04671 0.42464 7.62712
34 4L9I 8PR 0.006776 0.44798 7.92683
35 5H2U 1N1 0.009568 0.43688 7.92683
36 5MST FUM 0.0311 0.42793 7.92683
37 5TVF CGQ 0.005041 0.46266 8.23529
38 2YMZ LAT 0.002001 0.47402 8.46154
39 5XLY C2E 0.01046 0.43494 8.53659
40 4DXD 9PC 0.01176 0.42609 8.53659
41 5SVV FMN 0.01381 0.42273 8.75912
42 4D5B ACX 0.0284 0.40501 11.5854
43 5EFW FMN 0.004796 0.4482 11.7241
44 5DJU FMN 0.008875 0.43196 11.7241
45 3ZJX BOG 0.009229 0.46823 12.1951
46 1EPB REA 0.007203 0.44663 12.8049
47 4YBN FAD 0.007676 0.41331 12.8049
48 1GP6 DH2 0.005117 0.43118 14.0244
49 4Z3E GAL NGA GLA BGC GAL 0.04994 0.41552 14.6341
50 5FPX GLY SER SER HIS HIS HIS HIS HIS 0.002435 0.46255 15.0442
51 5DKK FMN 0.003189 0.45684 15.1724
52 5LUN OGA 0.04029 0.41802 15.2439
53 5FUI APY 0.0006254 0.53165 15.9091
Pocket No.: 3; Query (leader) PDB : 2AG4; Ligand: OLA; Similar sites found: 9
This union binding pocket(no: 3) in the query (biounit: 2ag4.bio1) has 60 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5HA0 LTD 0.02235 0.40148 3.20513
2 5DMZ ADP 0.01842 0.42092 4.26829
3 4QAC KK3 0.01026 0.42442 4.87805
4 4X9X OLA 0.01804 0.40562 4.87805
5 5N2D 8J8 0.04035 0.40404 5.55556
6 4XT2 43L 0.02737 0.40452 9.09091
7 5FQK 6NT 0.0451 0.42536 9.29368
8 4NV7 COA 0.01887 0.40249 9.7561
9 1W6P NDG GAL 0.0198 0.43016 11.9403
Pocket No.: 4; Query (leader) PDB : 2AG4; Ligand: LP3; Similar sites found: 12
This union binding pocket(no: 4) in the query (biounit: 2ag4.bio1) has 60 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5HA0 LTD 0.02235 0.40148 3.20513
2 5F7J ADE 0.03719 0.42949 4.26829
3 5DMZ ADP 0.01842 0.42092 4.26829
4 4QAC KK3 0.01026 0.42442 4.87805
5 4X9X OLA 0.01806 0.4056 4.87805
6 5F7Y GLC GAL NAG GAL FUC A2G 0.04686 0.41231 5.4878
7 4P7X YCP 0.03383 0.41065 6.70732
8 5KEW 6SB 0.02785 0.43189 6.94444
9 4ITH RCM 0.02849 0.40882 8.53659
10 4NV7 COA 0.01931 0.40205 9.7561
11 1W6P NDG GAL 0.0198 0.43016 11.9403
12 2Y2B AH0 0.04753 0.42478 12.1951
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