Receptor
PDB id Resolution Class Description Source Keywords
3ILP 1.85 Å NON-ENZYME: IMMUNE STRUCTURE OF MCD1D WITH BOUND GLYCOLIPID BBGL-2F FROM BORREL BURGDORFERI MUS MUSCULUS ANTIGEN PRESENTATION. INKT CELLS GLYCOLIPID HOST DEFENSE MEMBRANE DISULFIDE BOND ENDOSOME GLYCOPROTEIN IMMUNE REIMMUNOGLOBULIN DOMAIN INNATE IMMUNITY LYSOSOME MEMBRANETRANSMEMBRANE MHC I IMMUNE SYSTEM
Ref.: LIPID BINDING ORIENTATION WITHIN CD1D AFFECTS RECOG BORRELIA BURGORFERI ANTIGENS BY NKT CELLS. PROC.NATL.ACAD.SCI.USA V. 107 1535 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
1L2 A:286;
Valid;
none;
submit data
781.111 C45 H80 O10 CCCCC...
DMS A:3092;
Invalid;
none;
submit data
78.133 C2 H6 O S CS(=O...
NAG A:501;
Part of Protein;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
NAG NAG C:1;
Part of Protein;
none;
submit data
408.404 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3G08 1.6 Å NON-ENZYME: IMMUNE CRYSTAL STRUCTURE OF THE ALPHA-GALACTOSYLCERAMIDE ANALOG OCH COMPLEX WITH MOUSE CD1D MUS MUSCULUS ANTIGEN PRESENTATION GLYCOLIPID NKT CELLS CELL MEMBRANE GLYCOPROTEIN IMMUNE RESPONSE IMMUNOGLOBULIN DOMAIN INNATIMMUNITY LYSOSOME MEMBRANE TRANSMEMBRANE MHC I SECRETESYSTEM
Ref.: MECHANISMS FOR GLYCOLIPID ANTIGEN-DRIVEN CYTOKINE POLARIZATION BY VALPHA14I NKT CELLS. J.IMMUNOL. V. 184 141 2010
Members (23)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 222 families.
1 3GMM - PLM C16 H32 O2 CCCCCCCCCC....
2 3G08 Kd = 6.843 nM FEE C39 H77 N O9 CCCCCCCCCC....
3 3MA7 - CD4 C65 H126 O17 P2 CCCCCCCCCC....
4 1Z5L - PBS C32 H63 N O9 CCCCCCCCCC....
5 5TW5 - PLM C16 H32 O2 CCCCCCCCCC....
6 6CYW - FO4 C47 H94 N2 O6 P CCCCCCCCCC....
7 3ILQ Kd = 6.2 uM 1O2 C43 H80 O10 CCCCCCCCCC....
8 3GMR - PLM C16 H32 O2 CCCCCCCCCC....
9 3T1F - 3TF C43 H80 O10 CCCCCCCCCC....
10 3GMQ - PLM C16 H32 O2 CCCCCCCCCC....
11 6BMH - F61 C35 H69 N O9 CCCCCCCCCC....
12 6OJP - 7LP C34 H58 N2 O10 CCCCCCCC(=....
13 2AKR - CIS C48 H91 N O11 S CCCCCCCCCC....
14 3GMP - PBS C32 H63 N O9 CCCCCCCCCC....
15 3AU1 - BGC ERA GAL n/a n/a
16 3GMN - PLM C16 H32 O2 CCCCCCCCCC....
17 5TW2 - 7LP C34 H58 N2 O10 CCCCCCCC(=....
18 3GML - PLM C16 H32 O2 CCCCCCCCCC....
19 2Q7Y - IGC C44 H81 N O18 CCCCCCCCCC....
20 6BMK - F57 C31 H61 O8 P CCCCCCCCCC....
21 3ILP - 1L2 C45 H80 O10 CCCCCCCC/C....
22 3GMO - PLM C16 H32 O2 CCCCCCCCCC....
23 2FIK - PLM C16 H32 O2 CCCCCCCCCC....
70% Homology Family (24)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 67 families.
1 3GMM - PLM C16 H32 O2 CCCCCCCCCC....
2 3G08 Kd = 6.843 nM FEE C39 H77 N O9 CCCCCCCCCC....
3 3MA7 - CD4 C65 H126 O17 P2 CCCCCCCCCC....
4 1Z5L - PBS C32 H63 N O9 CCCCCCCCCC....
5 5TW5 - PLM C16 H32 O2 CCCCCCCCCC....
6 6CYW - FO4 C47 H94 N2 O6 P CCCCCCCCCC....
7 3ILQ Kd = 6.2 uM 1O2 C43 H80 O10 CCCCCCCCCC....
8 3GMR - PLM C16 H32 O2 CCCCCCCCCC....
9 3T1F - 3TF C43 H80 O10 CCCCCCCCCC....
10 3GMQ - PLM C16 H32 O2 CCCCCCCCCC....
11 6BMH - F61 C35 H69 N O9 CCCCCCCCCC....
12 6OJP - 7LP C34 H58 N2 O10 CCCCCCCC(=....
13 2AKR - CIS C48 H91 N O11 S CCCCCCCCCC....
14 3GMP - PBS C32 H63 N O9 CCCCCCCCCC....
15 3AU1 - BGC ERA GAL n/a n/a
16 3GMN - PLM C16 H32 O2 CCCCCCCCCC....
17 5TW2 - 7LP C34 H58 N2 O10 CCCCCCCC(=....
18 3GML - PLM C16 H32 O2 CCCCCCCCCC....
19 2Q7Y - IGC C44 H81 N O18 CCCCCCCCCC....
20 6BMK - F57 C31 H61 O8 P CCCCCCCCCC....
21 3ILP - 1L2 C45 H80 O10 CCCCCCCC/C....
22 3GMO - PLM C16 H32 O2 CCCCCCCCCC....
23 2FIK - PLM C16 H32 O2 CCCCCCCCCC....
24 4F7E - 0SH C40 H79 N O9 CCCCCCCCCC....
50% Homology Family (36)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 45 families.
1 5WKE - P50 C40 H76 N O9 P CCCCCCCCCC....
2 1GZQ - PII C42 H81 O13 P CCCCCCCCCC....
3 6D64 - POV C42 H82 N O8 P CCCCCCCCCC....
4 5L2J - 70E C42 H82 O8 CCCCCCCCCC....
5 5WL1 - D3D C40 H77 O10 P CCCCCCCCCC....
6 5WKG - CUY C42 H84 O2 CCCCCCCCCC....
7 2H26 - 6UL C40 H80 O2 CCCCCCCCCC....
8 3GMM - PLM C16 H32 O2 CCCCCCCCCC....
9 3G08 Kd = 6.843 nM FEE C39 H77 N O9 CCCCCCCCCC....
10 3MA7 - CD4 C65 H126 O17 P2 CCCCCCCCCC....
11 1Z5L - PBS C32 H63 N O9 CCCCCCCCCC....
12 5TW5 - PLM C16 H32 O2 CCCCCCCCCC....
13 6CYW - FO4 C47 H94 N2 O6 P CCCCCCCCCC....
14 3ILQ Kd = 6.2 uM 1O2 C43 H80 O10 CCCCCCCCCC....
15 3GMR - PLM C16 H32 O2 CCCCCCCCCC....
16 3T1F - 3TF C43 H80 O10 CCCCCCCCCC....
17 3GMQ - PLM C16 H32 O2 CCCCCCCCCC....
18 6BMH - F61 C35 H69 N O9 CCCCCCCCCC....
19 6OJP - 7LP C34 H58 N2 O10 CCCCCCCC(=....
20 2AKR - CIS C48 H91 N O11 S CCCCCCCCCC....
21 3GMP - PBS C32 H63 N O9 CCCCCCCCCC....
22 3AU1 - BGC ERA GAL n/a n/a
23 3GMN - PLM C16 H32 O2 CCCCCCCCCC....
24 5TW2 - 7LP C34 H58 N2 O10 CCCCCCCC(=....
25 3GML - PLM C16 H32 O2 CCCCCCCCCC....
26 2Q7Y - IGC C44 H81 N O18 CCCCCCCCCC....
27 6BMK - F57 C31 H61 O8 P CCCCCCCCCC....
28 3ILP - 1L2 C45 H80 O10 CCCCCCCC/C....
29 3GMO - PLM C16 H32 O2 CCCCCCCCCC....
30 2FIK - PLM C16 H32 O2 CCCCCCCCCC....
31 1ONQ - SLF C42 H81 N O11 S CCCCCCCCCC....
32 4X6E - 42H C26 H53 N O7 P CCCCCCCC/C....
33 4X6F - 3XU C47 H94 N2 O6 P CCCCCCCCCC....
34 4F7E - 0SH C40 H79 N O9 CCCCCCCCCC....
35 5C9J - STE C18 H36 O2 CCCCCCCCCC....
36 3L9R - L9Q C41 H80 N O8 P CCCCCCCCCC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 1L2; Similar ligands found: 55
No: Ligand ECFP6 Tc MDL keys Tc
1 1L2 1 1
2 1O2 0.903614 1
3 3TF 0.892857 1
4 GGD 0.762887 0.956522
5 DGD 0.709677 0.934783
6 SQD 0.62766 0.666667
7 J7Z 0.579439 0.913043
8 GAL SPH EIC 0.575472 0.75
9 DB6 0.559633 0.781818
10 LTC 0.559322 0.745763
11 T7X 0.557692 0.722222
12 B7N 0.534653 0.722222
13 PIE 0.529412 0.703704
14 03F 0.514286 0.781818
15 PGW 0.51 0.618182
16 D3D 0.51 0.618182
17 PGV 0.504951 0.618182
18 DR9 0.504951 0.618182
19 P6L 0.5 0.618182
20 JLS 0.495413 0.781818
21 GAL SPH NER 0.495327 0.763636
22 OZ2 0.495146 0.618182
23 BQ9 0.474227 0.727273
24 P3A 0.471698 0.618182
25 TGL 0.452381 0.622222
26 T6D 0.44898 0.891304
27 PII 0.445545 0.703704
28 GM3 0.433962 0.777778
29 PIZ 0.433962 0.672727
30 OLC 0.428571 0.711111
31 OLB 0.428571 0.711111
32 IP9 0.424528 0.672727
33 52N 0.424528 0.690909
34 PIO 0.424528 0.690909
35 LAT SPH OCA 0.423729 0.724138
36 BGC 18C GAL 0.423729 0.754386
37 PIF 0.423077 0.690909
38 LHG 0.42 0.6
39 PGT 0.42 0.6
40 IGC 0.419355 0.754386
41 LGN 0.419355 0.754386
42 L2C 0.41573 0.704545
43 DDR 0.41573 0.704545
44 DGA 0.41573 0.704545
45 FAW 0.41573 0.704545
46 1EM 0.41573 0.704545
47 MVC 0.413043 0.711111
48 AGH 0.412844 0.763636
49 0SH 0.412844 0.763636
50 FEE 0.412844 0.763636
51 PBS 0.412844 0.763636
52 F61 0.412844 0.763636
53 78M 0.402174 0.711111
54 78N 0.402174 0.711111
55 LBR 0.4 0.652174
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3G08; Ligand: FEE; 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: 3g08.bio1) has 81 residues
No: Leader PDB Ligand Sequence Similarity
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