Receptor
PDB id Resolution Class Description Source Keywords
2Q7Y 1.95 Å NON-ENZYME: IMMUNE STRUCTURE OF THE ENDOGENOUS INKT CELL LIGAND IGB3 BOUND TO M MUS MUSCULUS ANTIGEN PRESENTING MOLECULE MHC FOLD NKT CELLS IMMUNE SYS
Ref.: CRYSTAL STRUCTURES OF MOUSE CD1D-IGB3 COMPLEX AND I COGNATE VALPHA14 T CELL RECEPTOR SUGGEST A MODEL FO RECOGNITION OF FOREIGN AND SELF GLYCOLIPIDS. J.MOL.BIOL. V. 377 1104 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
IGC A:601;
C:602;
Valid;
Valid;
none;
none;
submit data
912.11 C44 H81 N O18 CCCCC...
NAG A:500;
C:500;
C:501;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
NAG NAG A:501;
C:502;
Invalid;
Invalid;
none;
none;
submit data
408.404 n/a O=C(N...
NAG NAG BMA MAN MAN A:511;
Invalid;
none;
submit data
910.826 n/a O=C(N...
PLM A:701;
C:702;
Invalid;
Invalid;
none;
none;
submit data
256.424 C16 H32 O2 CCCCC...
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 (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 208 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 3ILQ Kd = 6.2 uM 1O2 C43 H80 O10 CCCCCCCCCC....
7 3GMR - PLM C16 H32 O2 CCCCCCCCCC....
8 3T1F - 3TF C43 H80 O10 CCCCCCCCCC....
9 3GMQ - PLM C16 H32 O2 CCCCCCCCCC....
10 6BMH - F61 C35 H69 N O9 CCCCCCCCCC....
11 2AKR - CIS C48 H91 N O11 S CCCCCCCCCC....
12 3GMP - PBS C32 H63 N O9 CCCCCCCCCC....
13 3AU1 - ERA BGC GAL n/a n/a
14 3GMN - PLM C16 H32 O2 CCCCCCCCCC....
15 5TW2 - 7LP C34 H58 N2 O10 CCCCCCCC(=....
16 3GML - PLM C16 H32 O2 CCCCCCCCCC....
17 2Q7Y - IGC C44 H81 N O18 CCCCCCCCCC....
18 6BMK - F57 C31 H61 O8 P CCCCCCCCCC....
19 3ILP - 1L2 C45 H80 O10 CCCCCCCC/C....
20 3GMO - PLM C16 H32 O2 CCCCCCCCCC....
21 2FIK - PLM C16 H32 O2 CCCCCCCCCC....
70% Homology Family (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 62 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 3ILQ Kd = 6.2 uM 1O2 C43 H80 O10 CCCCCCCCCC....
7 3GMR - PLM C16 H32 O2 CCCCCCCCCC....
8 3T1F - 3TF C43 H80 O10 CCCCCCCCCC....
9 3GMQ - PLM C16 H32 O2 CCCCCCCCCC....
10 6BMH - F61 C35 H69 N O9 CCCCCCCCCC....
11 2AKR - CIS C48 H91 N O11 S CCCCCCCCCC....
12 3GMP - PBS C32 H63 N O9 CCCCCCCCCC....
13 3AU1 - ERA BGC GAL n/a n/a
14 3GMN - PLM C16 H32 O2 CCCCCCCCCC....
15 5TW2 - 7LP C34 H58 N2 O10 CCCCCCCC(=....
16 3GML - PLM C16 H32 O2 CCCCCCCCCC....
17 2Q7Y - IGC C44 H81 N O18 CCCCCCCCCC....
18 6BMK - F57 C31 H61 O8 P CCCCCCCCCC....
19 3ILP - 1L2 C45 H80 O10 CCCCCCCC/C....
20 3GMO - PLM C16 H32 O2 CCCCCCCCCC....
21 2FIK - PLM C16 H32 O2 CCCCCCCCCC....
22 4F7E - 0SH C40 H79 N O9 CCCCCCCCCC....
50% Homology Family (33)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 42 families.
1 5WKE - P50 C40 H76 N O9 P CCCCCCCCCC....
2 1GZQ - PII C42 H81 O13 P CCCCCCCCCC....
3 5L2J - 70E C42 H82 O8 CCCCCCCCCC....
4 5WL1 - D3D C40 H77 O10 P CCCCCCCCCC....
5 5WKG - CUY C42 H84 O2 CCCCCCCCCC....
6 2H26 - 6UL C40 H80 O2 CCCCCCCCCC....
7 3GMM - PLM C16 H32 O2 CCCCCCCCCC....
8 3G08 Kd = 6.843 nM FEE C39 H77 N O9 CCCCCCCCCC....
9 3MA7 - CD4 C65 H126 O17 P2 CCCCCCCCCC....
10 1Z5L - PBS C32 H63 N O9 CCCCCCCCCC....
11 5TW5 - PLM C16 H32 O2 CCCCCCCCCC....
12 3ILQ Kd = 6.2 uM 1O2 C43 H80 O10 CCCCCCCCCC....
13 3GMR - PLM C16 H32 O2 CCCCCCCCCC....
14 3T1F - 3TF C43 H80 O10 CCCCCCCCCC....
15 3GMQ - PLM C16 H32 O2 CCCCCCCCCC....
16 6BMH - F61 C35 H69 N O9 CCCCCCCCCC....
17 2AKR - CIS C48 H91 N O11 S CCCCCCCCCC....
18 3GMP - PBS C32 H63 N O9 CCCCCCCCCC....
19 3AU1 - ERA BGC GAL n/a n/a
20 3GMN - PLM C16 H32 O2 CCCCCCCCCC....
21 5TW2 - 7LP C34 H58 N2 O10 CCCCCCCC(=....
22 3GML - PLM C16 H32 O2 CCCCCCCCCC....
23 2Q7Y - IGC C44 H81 N O18 CCCCCCCCCC....
24 6BMK - F57 C31 H61 O8 P CCCCCCCCCC....
25 3ILP - 1L2 C45 H80 O10 CCCCCCCC/C....
26 3GMO - PLM C16 H32 O2 CCCCCCCCCC....
27 2FIK - PLM C16 H32 O2 CCCCCCCCCC....
28 1ONQ - SLF C42 H81 N O11 S CCCCCCCCCC....
29 4X6E - 42H C26 H53 N O7 P CCCCCCCC/C....
30 4X6F - 3XU C47 H94 N2 O6 P CCCCCCCCCC....
31 4F7E - 0SH C40 H79 N O9 CCCCCCCCCC....
32 5C9J - STE C18 H36 O2 CCCCCCCCCC....
33 3L9R - L9Q C41 H80 N O8 P CCCCCCCCCC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: IGC; Similar ligands found: 55
No: Ligand ECFP6 Tc MDL keys Tc
1 IGC 1 1
2 LGN 1 1
3 BGC 18C GAL 0.913979 1
4 03F 0.72449 0.964286
5 EIS 0.647619 0.753425
6 SLF 0.647619 0.753425
7 BGC 18C GAL SIA 0.634328 0.903226
8 LAT SPH OCA 0.633027 0.931035
9 CIS 0.62963 0.753425
10 BGC 18C GAL NGA SIA GAL 0.594595 0.903226
11 SIA GAL BGC 16C 0.583942 0.903226
12 0SG 0.580357 0.739726
13 JLS 0.544643 0.929825
14 GGD 0.533898 0.789474
15 DB6 0.525424 0.929825
16 LAT SPH DAO 0.522124 0.896552
17 LAT SPH OLA 0.522124 0.896552
18 GM3 0.514019 0.928571
19 F61 0.504587 0.912281
20 0SH 0.504587 0.912281
21 AGH 0.504587 0.912281
22 PBS 0.504587 0.912281
23 FEE 0.504587 0.912281
24 SFT 0.495798 0.753425
25 LMT 0.48 0.75
26 LMU 0.48 0.75
27 DMU 0.48 0.75
28 UMQ 0.48 0.75
29 GAL SPH EIC 0.475 0.896552
30 1PX 0.456311 0.636364
31 1PZ 0.456311 0.636364
32 ERA BGC GAL 0.442748 0.915254
33 C8P 0.440945 0.913793
34 C1Q 0.440945 0.913793
35 7LM 0.440945 0.913793
36 GAL SPH NER 0.440678 0.87931
37 1O2 0.435897 0.754386
38 C6Q 0.433071 0.913793
39 3TF 0.432203 0.754386
40 C8F 0.429688 0.854839
41 6UZ 0.424528 0.666667
42 16C 0.424242 0.732143
43 SPL 0.424242 0.732143
44 18C 0.424242 0.732143
45 MAN BMA NAG 0.420561 0.741379
46 GLA GAL NAG 0.420561 0.741379
47 1L2 0.419355 0.754386
48 GLA GAL GLC NBU 0.417476 0.696429
49 GLA EGA 0.408163 0.625
50 6CM 0.405941 0.732143
51 GAL NGA GLA BGC GAL 0.405172 0.741379
52 7LP 0.404412 0.868852
53 GLA GAL BGC 5VQ 0.401961 0.660714
54 GLC GAL NAG GAL 0.4 0.741379
55 LAT NAG GAL 0.4 0.741379
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 53 residues
No: Leader PDB Ligand Sequence Similarity
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