Receptor
PDB id Resolution Class Description Source Keywords
3ILQ 2.05 Å NON-ENZYME: IMMUNE STRUCTURE OF MCD1D WITH BOUND GLYCOLIPID BBGL-2C FROM BORRELIA BURGDORFERI MUS MUSCULUS ANTIGEN PRESENTATION INKT CELLS HOST DEFENSE BORRELIA BURGDORFERI CD1 CELL MEMBRANE DISULFIDE BOND ENDOSOME GLYCOPROTEIN IMMUNE RESPONSE IMMUNOGLOBULIN DOMAIN INNATE IMMUNITY LYSOSOME MEMBRANE TRANSMEMBRANE MHC I IMMUNE SYSTEM
Ref.: LIPID BINDING ORIENTATION WITHIN CD1D AFFECTS RECOGNITION OF 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 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: 1O2; Similar ligands found: 67
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 DR9 0.548387 0.618182
14 PGV 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 TGL 0.5 0.622222
22 GAL SPH EIC 0.5 0.75
23 T6D 0.488889 0.891304
24 DB6 0.486239 0.781818
25 PII 0.483871 0.703704
26 T7X 0.480769 0.722222
27 OLC 0.46988 0.711111
28 OLB 0.46988 0.711111
29 GM3 0.469388 0.777778
30 PIZ 0.469388 0.672727
31 IP9 0.459184 0.672727
32 PIF 0.458333 0.690909
33 1EM 0.45679 0.704545
34 DDR 0.45679 0.704545
35 FAW 0.45679 0.704545
36 DGA 0.45679 0.704545
37 L2C 0.45679 0.704545
38 PGT 0.456522 0.6
39 LHG 0.456522 0.6
40 BGC 18C GAL 0.454545 0.754386
41 LAT SPH OCA 0.454545 0.724138
42 MVC 0.452381 0.711111
43 PBS 0.445545 0.763636
44 0SH 0.445545 0.763636
45 AGH 0.445545 0.763636
46 F61 0.445545 0.763636
47 FEE 0.445545 0.763636
48 52N 0.444444 0.690909
49 PIO 0.444444 0.690909
50 78N 0.440476 0.711111
51 78M 0.440476 0.711111
52 LBR 0.436782 0.652174
53 IGC 0.435897 0.754386
54 LGN 0.435897 0.754386
55 DR4 0.426966 0.866667
56 XNS 0.426966 0.866667
57 CIS 0.423423 0.611111
58 HSJ 0.421687 0.909091
59 BOG 0.421687 0.909091
60 BNG 0.421687 0.909091
61 BQ9 0.421053 0.727273
62 KGM 0.409639 0.909091
63 B7G 0.409639 0.909091
64 DGG 0.409524 0.625
65 AGA 0.402062 0.6
66 ERA BGC GAL 0.401639 0.741379
67 CQX 0.4 0.888889
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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