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 A:502;
C:502;
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 (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: F57; Similar ligands found: 103
No: Ligand ECFP6 Tc MDL keys Tc
1 7PH 1 1
2 F57 1 1
3 LPP 1 1
4 3PH 1 1
5 6PH 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 TGL 0.745098 0.690476
14 CD4 0.725806 0.953488
15 PTY 0.714286 0.788462
16 PEH 0.714286 0.788462
17 PEF 0.714286 0.788462
18 PEV 0.714286 0.788462
19 8PE 0.714286 0.788462
20 PEE 0.703125 0.773585
21 LHG 0.703125 0.911111
22 PGT 0.703125 0.911111
23 9PE 0.703125 0.788462
24 CDL 0.6875 0.863636
25 PLD 0.681818 0.727273
26 HGX 0.681818 0.727273
27 PC7 0.681818 0.727273
28 LIO 0.681818 0.727273
29 P5S 0.681818 0.803922
30 HGP 0.681818 0.727273
31 6PL 0.681818 0.727273
32 PII 0.661765 0.836735
33 PIF 0.642857 0.857143
34 CN3 0.642857 0.953488
35 3PE 0.641791 0.711538
36 DDR 0.631579 0.697674
37 DGA 0.631579 0.697674
38 FAW 0.631579 0.697674
39 L2C 0.631579 0.697674
40 PIZ 0.630137 0.875
41 XP5 0.626866 0.727273
42 L9Q 0.625 0.773585
43 6OU 0.625 0.773585
44 LOP 0.625 0.773585
45 PCF 0.623188 0.685185
46 PC1 0.623188 0.685185
47 MC3 0.623188 0.685185
48 PIO 0.616438 0.857143
49 PGW 0.616438 0.891304
50 52N 0.616438 0.857143
51 IP9 0.616438 0.875
52 D3D 0.616438 0.891304
53 CN6 0.614286 0.953488
54 NKN 0.610169 0.953488
55 NKO 0.610169 0.953488
56 AGA 0.608696 0.869565
57 PGV 0.608108 0.891304
58 DR9 0.608108 0.891304
59 P6L 0.6 0.891304
60 PGK 0.6 0.854167
61 PCW 0.6 0.714286
62 OZ2 0.592105 0.891304
63 P50 0.592105 0.803922
64 44G 0.590909 0.911111
65 ZPE 0.586667 0.773585
66 B7N 0.584416 0.82
67 PCK 0.584416 0.689655
68 DGG 0.576923 0.854167
69 PSF 0.573529 0.803922
70 GP7 0.5625 0.773585
71 LBR 0.5625 0.644444
72 PIE 0.556962 0.764706
73 PEK 0.556962 0.773585
74 P3A 0.556962 0.851064
75 POV 0.551282 0.672727
76 L9R 0.551282 0.672727
77 PSC 0.548781 0.714286
78 NKP 0.529412 0.931818
79 G2A 0.527273 0.659091
80 2JT 0.527273 0.659091
81 T7X 0.517647 0.82
82 PDK 0.505618 0.683333
83 SQD 0.5 0.609375
84 1QW 0.491525 0.644444
85 GYM 0.491525 0.644444
86 DLP 0.482353 0.672727
87 EPH 0.466667 0.773585
88 LAP 0.465753 0.732143
89 LPC 0.465753 0.732143
90 LP3 0.465753 0.732143
91 PGM 0.457143 0.847826
92 87O 0.45614 0.813953
93 PC5 0.432432 0.603448
94 3PC 0.428571 0.666667
95 PVC 0.426471 0.625
96 OLC 0.426471 0.630435
97 OLB 0.426471 0.630435
98 CN5 0.421053 0.931818
99 42H 0.414634 0.719298
100 DB4 0.413333 0.795918
101 PBU 0.410256 0.795918
102 MVC 0.405797 0.630435
103 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 53 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback