Receptor
PDB id Resolution Class Description Source Keywords
3GMM 1.8 Å NON-ENZYME: IMMUNE STRUCTURE OF MOUSE CD1D IN COMPLEX WITH C8PH MUS MUSCULUS CD1 NKT CELL GLYCOLIPID ANTIGEN PRESENTATION IMMUNE SYST
Ref.: STRUCTURAL EVALUATION OF POTENT NKT CELL AGONISTS: IMPLICATIONS FOR DESIGN OF NOVEL STIMULATORY LIGAND J.MOL.BIOL. V. 394 71 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
C8P A:300;
Valid;
none;
submit data
681.94 C38 H67 N O9 CCCCC...
EDO A:302;
A:303;
B:100;
B:101;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
NAG A:288;
Invalid;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
NAG NAG BMA MAN MAN A:289;
Invalid;
none;
submit data
910.826 n/a O=C(N...
NAG NAG FUC BMA MAN MAN A:294;
Invalid;
none;
submit data n/a n/a n/a n/a
PLM A:301;
Valid;
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: C8P; Similar ligands found: 27
No: Ligand ECFP6 Tc MDL keys Tc
1 C8P 1 1
2 7LM 1 1
3 C1Q 1 1
4 C6Q 0.967033 1
5 C8F 0.836735 0.932203
6 7LP 0.825243 0.948276
7 0SH 0.788889 0.928571
8 PBS 0.788889 0.928571
9 AGH 0.788889 0.928571
10 F61 0.788889 0.928571
11 FEE 0.75 0.928571
12 JLS 0.717172 0.912281
13 GM3 0.673684 0.910714
14 DB6 0.669811 0.912281
15 QUY 0.642202 0.916667
16 QUV 0.6 0.820895
17 03F 0.522936 0.912281
18 GSL 0.504762 0.862069
19 BGC 18C GAL 0.470588 0.913793
20 IGC 0.440945 0.913793
21 LGN 0.440945 0.913793
22 EIS 0.428571 0.693333
23 SLF 0.428571 0.693333
24 GAL SPH NER 0.42735 0.830508
25 CIS 0.418033 0.693333
26 LAT SPH DAO 0.408333 0.847458
27 LAT SPH OLA 0.408333 0.847458
Ligand no: 2; Ligand: PLM; Similar ligands found: 62
No: Ligand ECFP6 Tc MDL keys Tc
1 MYR 1 1
2 EW8 1 1
3 TDA 1 1
4 F15 1 1
5 PLM 1 1
6 STE 1 1
7 X90 1 1
8 DAO 1 1
9 KNA 1 1
10 DCR 1 1
11 F23 1 1
12 11A 1 1
13 DKA 1 1
14 OCA 0.956522 1
15 SHV 0.833333 0.952381
16 KTC 0.793103 0.875
17 AZ1 0.73913 0.64
18 6NA 0.72 0.904762
19 ELA 0.71875 0.954545
20 OLA 0.71875 0.954545
21 NER 0.71875 0.954545
22 VCA 0.666667 0.954545
23 PAM 0.666667 0.954545
24 PML 0.625 0.6
25 3LA 0.606061 0.8
26 LEA 0.6 0.809524
27 MYZ 0.588235 0.909091
28 12H 0.586207 0.615385
29 ODD 0.567568 0.913043
30 BRC 0.566667 0.666667
31 14V 0.555556 0.740741
32 M12 0.545455 0.869565
33 14U 0.542857 0.703704
34 EIC 0.538462 0.913043
35 EOD 0.538462 0.7
36 D0G 0.5 0.954545
37 BMJ 0.5 0.954545
38 BNV 0.5 0.954545
39 BUA 0.48 0.666667
40 RCL 0.468085 0.84
41 FTT 0.459459 0.807692
42 HXD 0.459459 0.807692
43 56S 0.459459 0.653846
44 ODT 0.452381 0.782609
45 3X1 0.444444 0.818182
46 LNL 0.44186 0.826087
47 9J6 0.441176 0.666667
48 OOA 0.441176 0.76
49 CUY 0.435897 0.68
50 6UL 0.435897 0.68
51 CNS 0.435897 0.68
52 5UF 0.432432 0.807692
53 243 0.428571 0.807692
54 1QW 0.418605 0.606061
55 GYM 0.418605 0.606061
56 O8N 0.413793 0.75
57 1DO 0.413793 0.75
58 PL3 0.413793 0.75
59 OC9 0.413793 0.75
60 DE1 0.413793 0.75
61 F09 0.413793 0.75
62 T25 0.403846 0.677419
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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