Receptor
PDB id Resolution Class Description Source Keywords
3ILQ 2.05 Å NON-ENZYME: IMMUNE STRUCTURE OF MCD1D WITH BOUND GLYCOLIPID BBGL-2C FROM BORREL BURGDORFERI MUS MUSCULUS ANTIGEN PRESENTATION INKT CELLS HOST DEFENSE BORRELIA BURCD1 CELL MEMBRANE DISULFIDE BOND ENDOSOME GLYCOPROTEINRESPONSE IMMUNOGLOBULIN DOMAIN INNATE IMMUNITY LYSOSOMEMEMBRANE TRANSMEMBRANE 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
1O2 C:286;
 Valid;
 none;
 Kd = 6.2 uM
757.089 C43 H80 O10 CCCCC...
NAG C:501;
C:510;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
221.208 C8 H15 N O6 CC(=O...
NAG NAG A: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 225 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 (37)
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 6NUX - FOF C15 H26 O CC(=CCC/C(....
35 4F7E - 0SH C40 H79 N O9 CCCCCCCCCC....
36 5C9J - STE C18 H36 O2 CCCCCCCCCC....
37 3L9R - L9Q C41 H80 N O8 P CCCCCCCCCC....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 1O2; Similar ligands found: 68
No: Ligand ECFP6 Tc MDL keys Tc
1 1O2 1 1
2 3TF 0.986842 1
3 1L2 0.903614 1
4 GGD 0.811111 0.956522
5 DGD 0.776471 0.934783
6 SQD 0.686047 0.666667
7 LTC 0.6 0.745763
8 B7N 0.580645 0.722222
9 PIE 0.574468 0.703704
10 03F 0.556701 0.781818
11 PGW 0.554348 0.618182
12 D3D 0.554348 0.618182
13 PGV 0.548387 0.618182
14 DR9 0.548387 0.618182
15 P6L 0.542553 0.618182
16 OZ2 0.536842 0.618182
17 GAL SPH NER 0.535354 0.763636
18 JLS 0.534653 0.781818
19 J7Z 0.533333 0.913043
20 P3A 0.510204 0.618182
21 GAL SPH EIC 0.5 0.75
22 TGL 0.5 0.622222
23 DB6 0.486239 0.781818
24 PII 0.483871 0.703704
25 T7X 0.480769 0.722222
26 OLC 0.46988 0.711111
27 OLB 0.46988 0.711111
28 GM3 0.469388 0.777778
29 PIZ 0.469388 0.672727
30 IP9 0.459184 0.672727
31 PIF 0.458333 0.690909
32 FAW 0.45679 0.704545
33 DGA 0.45679 0.704545
34 L2C 0.45679 0.704545
35 1EM 0.45679 0.704545
36 DDR 0.45679 0.704545
37 PGT 0.456522 0.6
38 LHG 0.456522 0.6
39 BGC 18C GAL 0.454545 0.754386
40 BGC SPH GAL OCA 0.454545 0.724138
41 MVC 0.452381 0.711111
42 AGH 0.445545 0.763636
43 PBS 0.445545 0.763636
44 F61 0.445545 0.763636
45 FEE 0.445545 0.763636
46 0SH 0.445545 0.763636
47 PIO 0.444444 0.690909
48 52N 0.444444 0.690909
49 78M 0.440476 0.711111
50 78N 0.440476 0.711111
51 LBR 0.436782 0.652174
52 LGN 0.435897 0.754386
53 IGC 0.435897 0.754386
54 DR4 0.426966 0.866667
55 XNS 0.426966 0.866667
56 PG8 0.425532 0.6
57 CIS 0.423423 0.611111
58 BOG 0.421687 0.909091
59 BNG 0.421687 0.909091
60 HSJ 0.421687 0.909091
61 BQ9 0.421053 0.727273
62 1WV 0.411765 0.711111
63 KGM 0.409639 0.909091
64 B7G 0.409639 0.909091
65 DGG 0.409524 0.625
66 AGA 0.402062 0.6
67 BGC ERA GAL 0.401639 0.741379
68 CQX 0.4 0.888889
Similar Ligands (3D)
Ligand no: 1; Ligand: 1O2; Similar ligands found: 0
No: Ligand Similarity coefficient
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: 2
This union binding pocket(no: 1) in the query (biounit: 3g08.bio1) has 85 residues
No: Leader PDB Ligand Sequence Similarity
1 6LM1 D10 6.94981
2 6LM1 OCT 6.94981
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