Receptor
PDB id Resolution Class Description Source Keywords
6BMK 2.43 Å NON-ENZYME: IMMUNE CRYSTAL STRUCTURE OF MHC-I LIKE PROTEIN MUS MUSCULUS MAJOR HISTOCOMPATIBILITY COMPLEX MHC-I CD1D ANTIGEN IMMU
Ref.: DIFFERING ROLES OF CD1D2 AND CD1D1 PROTEINS IN TYPE NATURAL KILLER T CELL DEVELOPMENT AND FUNCTION. PROC. NATL. ACAD. SCI. V. 115 E1204 2018 U.S.A.
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAG NAG F:1;
E:1;
Invalid;
Invalid;
none;
none;
submit data
408.404 n/a O=C(N...
NAG C:501;
A:501;
Invalid;
Invalid;
none;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
F57 C:504;
A:504;
Valid;
Valid;
none;
none;
submit data
592.785 C31 H61 O8 P 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 (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: F57; Similar ligands found: 108
No: Ligand ECFP6 Tc MDL keys Tc
1 6PH 1 1
2 3PH 1 1
3 F57 1 1
4 LPP 1 1
5 7PH 1 1
6 7P9 0.980392 1
7 PD7 0.921569 1
8 D21 0.847458 0.976744
9 M7U 0.847458 1
10 44E 0.846154 1
11 PX8 0.803571 0.930233
12 PX2 0.803571 0.930233
13 PA8 0.785714 0.930233
14 TGL 0.745098 0.690476
15 CD4 0.725806 0.953488
16 8PE 0.714286 0.788462
17 PEH 0.714286 0.788462
18 PEV 0.714286 0.788462
19 PTY 0.714286 0.788462
20 PEF 0.714286 0.788462
21 9PE 0.703125 0.788462
22 PEE 0.703125 0.773585
23 PGT 0.703125 0.911111
24 LHG 0.703125 0.911111
25 CDL 0.6875 0.863636
26 P5S 0.681818 0.803922
27 HGX 0.681818 0.727273
28 PX4 0.681818 0.727273
29 LIO 0.681818 0.727273
30 PLD 0.681818 0.727273
31 HGP 0.681818 0.727273
32 6PL 0.681818 0.727273
33 PC7 0.681818 0.727273
34 PII 0.661765 0.836735
35 PIF 0.642857 0.857143
36 CN3 0.642857 0.953488
37 3PE 0.641791 0.711538
38 L2C 0.631579 0.697674
39 1EM 0.631579 0.697674
40 FAW 0.631579 0.697674
41 DGA 0.631579 0.697674
42 DDR 0.631579 0.697674
43 PIZ 0.630137 0.875
44 XP5 0.626866 0.727273
45 LOP 0.625 0.773585
46 6OU 0.625 0.773585
47 L9Q 0.625 0.773585
48 PC1 0.623188 0.685185
49 PCF 0.623188 0.685185
50 MC3 0.623188 0.685185
51 IP9 0.616438 0.875
52 52N 0.616438 0.857143
53 PIO 0.616438 0.857143
54 D3D 0.616438 0.891304
55 PGW 0.616438 0.891304
56 CN6 0.614286 0.953488
57 NKN 0.610169 0.953488
58 NKO 0.610169 0.953488
59 AGA 0.608696 0.869565
60 PGV 0.608108 0.891304
61 DR9 0.608108 0.891304
62 PCW 0.6 0.714286
63 PGK 0.6 0.854167
64 P6L 0.6 0.891304
65 OZ2 0.592105 0.891304
66 P50 0.592105 0.803922
67 44G 0.590909 0.911111
68 ZPE 0.586667 0.773585
69 B7N 0.584416 0.82
70 PCK 0.584416 0.689655
71 DGG 0.576923 0.854167
72 HXG 0.573529 0.727273
73 PSF 0.573529 0.803922
74 LBR 0.5625 0.644444
75 GP7 0.5625 0.773585
76 PEK 0.556962 0.773585
77 PIE 0.556962 0.764706
78 P3A 0.556962 0.851064
79 L9R 0.551282 0.672727
80 POV 0.551282 0.672727
81 PSC 0.548781 0.714286
82 NKP 0.529412 0.931818
83 2JT 0.527273 0.659091
84 G2A 0.527273 0.659091
85 T7X 0.517647 0.82
86 PDK 0.505618 0.683333
87 SQD 0.5 0.609375
88 GYM 0.491525 0.644444
89 1QW 0.491525 0.644444
90 BQ9 0.486486 0.681818
91 DLP 0.482353 0.672727
92 EPH 0.466667 0.773585
93 LPC 0.465753 0.732143
94 LAP 0.465753 0.732143
95 LP3 0.465753 0.732143
96 PGM 0.457143 0.847826
97 87O 0.45614 0.813953
98 PC5 0.432432 0.603448
99 3PC 0.428571 0.666667
100 OLB 0.426471 0.630435
101 OLC 0.426471 0.630435
102 PVC 0.426471 0.625
103 CN5 0.421053 0.931818
104 42H 0.414634 0.719298
105 DB4 0.413333 0.795918
106 PBU 0.410256 0.795918
107 MVC 0.405797 0.630435
108 S12 0.402439 0.769231
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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