Receptor
PDB id Resolution Class Description Source Keywords
3MA7 2.29 Å NON-ENZYME: IMMUNE CRYSTAL STRUCTURE OF CARDIOLIPIN BOUND TO MOUSE CD1D MUS MUSCULUS GAMMA DELTA T CELLS GLYCOLIPID PRESENTATION MHC CD1 CELLMEMBRANE ENDOSOME GLYCOPROTEIN IMMUNE RESPONSE IMMUNOGLDOMAIN INNATE IMMUNITY LYSOSOME MEMBRANE TRANSMEMBRANESECRETED IMMUNE SYSTEM DISULFIDE BOND IMMUNITY
Ref.: CARDIOLIPIN BINDS TO CD1D AND STIMULATES CD1D-RESTR {GAMMA}{DELTA} T CELLS IN THE NORMAL MURINE REPERTO J.IMMUNOL. V. 186 4771 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CD4 A:2089;
C:2089;
Valid;
Valid;
none;
none;
submit data
1241.63 C65 H126 O17 P2 CCCCC...
NAG C:501;
Part of Protein;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
NAG NAG A:501;
A:511;
C:511;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
408.404 n/a O=C(N...
PLM A:286;
C:286;
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: CD4; Similar ligands found: 101
No: Ligand ECFP6 Tc MDL keys Tc
1 CD4 1 1
2 CN3 0.876923 1
3 PGT 0.870968 0.954545
4 LHG 0.870968 0.954545
5 CN6 0.846154 1
6 P5S 0.787879 0.84
7 PEH 0.769231 0.823529
8 PTY 0.769231 0.823529
9 PEF 0.769231 0.823529
10 8PE 0.769231 0.823529
11 PEV 0.769231 0.823529
12 D3D 0.760563 0.933333
13 PGW 0.760563 0.933333
14 9PE 0.757576 0.823529
15 PEE 0.757576 0.807692
16 PGV 0.75 0.933333
17 44G 0.75 0.954545
18 DR9 0.75 0.933333
19 PX2 0.741935 0.930233
20 PX8 0.741935 0.930233
21 P6L 0.739726 0.933333
22 PGK 0.739726 0.893617
23 HGX 0.735294 0.727273
24 6PL 0.735294 0.727273
25 PLD 0.735294 0.727273
26 LIO 0.735294 0.727273
27 PC7 0.735294 0.727273
28 HGP 0.735294 0.727273
29 OZ2 0.72973 0.933333
30 7PH 0.725806 0.953488
31 6PH 0.725806 0.953488
32 3PH 0.725806 0.953488
33 LPP 0.725806 0.953488
34 F57 0.725806 0.953488
35 CDL 0.716418 0.906977
36 7P9 0.714286 0.953488
37 DGG 0.710526 0.893617
38 XP5 0.681159 0.727273
39 PSF 0.676471 0.84
40 6OU 0.675676 0.807692
41 LOP 0.675676 0.807692
42 L9Q 0.675676 0.807692
43 PD7 0.666667 0.953488
44 PII 0.666667 0.836735
45 P50 0.662338 0.84
46 TGL 0.655172 0.690476
47 PCW 0.649351 0.714286
48 ZPE 0.636364 0.807692
49 M7U 0.633803 0.953488
50 D21 0.633803 0.931818
51 PCK 0.632911 0.689655
52 PIF 0.626667 0.82
53 PIZ 0.615385 0.836735
54 GP7 0.609756 0.807692
55 44E 0.609375 0.953488
56 PEK 0.604938 0.807692
57 PIO 0.602564 0.82
58 52N 0.602564 0.82
59 IP9 0.602564 0.836735
60 PSC 0.595238 0.714286
61 AGA 0.594595 0.911111
62 B7N 0.592593 0.82
63 P3A 0.585366 0.891304
64 LAP 0.583333 0.763636
65 LP3 0.583333 0.763636
66 LPC 0.583333 0.763636
67 3PE 0.581081 0.745098
68 MC3 0.565789 0.685185
69 PCF 0.565789 0.685185
70 PC1 0.565789 0.685185
71 DDR 0.5625 0.697674
72 FAW 0.5625 0.697674
73 DGA 0.5625 0.697674
74 L2C 0.5625 0.697674
75 CN5 0.554054 0.976744
76 PDK 0.549451 0.711864
77 NKN 0.545455 0.953488
78 NKO 0.545455 0.953488
79 S12 0.544304 0.803922
80 PIE 0.529412 0.764706
81 T7X 0.52809 0.82
82 42H 0.518519 0.75
83 EPH 0.51087 0.807692
84 LBR 0.507042 0.644444
85 L9R 0.505882 0.672727
86 POV 0.505882 0.672727
87 SQD 0.494118 0.634921
88 NKP 0.48 0.931818
89 PGM 0.472973 0.888889
90 2JT 0.467742 0.659091
91 G2A 0.467742 0.659091
92 GYM 0.461538 0.681818
93 1QW 0.461538 0.681818
94 DLP 0.445652 0.672727
95 LPS 0.417722 0.803922
96 PC5 0.4125 0.603448
97 DB4 0.4125 0.76
98 PBU 0.409639 0.76
99 OLC 0.405405 0.666667
100 PVC 0.405405 0.659574
101 OLB 0.405405 0.666667
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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