Receptor
PDB id Resolution Class Description Source Keywords
6MJI 2.3 Å NON-ENZYME: IMMUNE CRYSTAL STRUCTURE OF THE MCD1D/XXS (JJ304) /INKTCR TERNARY C MUS MUSCULUS, HOMO SAPIENS MHC-FOLD IG-FOLD GLYCOLIPID ANTIGEN PRESENTATION T CELL RIMMUNE SYSTEM
Ref.: 4"-O-ALKYLATED ALPHA-GALACTOSYLCERAMIDE ANALOGUES A INKT-CELL ANTIGENS: SYNTHETIC, BIOLOGICAL, AND STRU STUDIES. CHEMMEDCHEM V. 14 147 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL D:604;
D:602;
A:301;
D:603;
B:101;
D:601;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
NAG NAG FUC BMA MAN F:1;
 Invalid;
 none;
 submit data
n/a n/a
NAG A:302;
 Invalid;
 none;
 submit data
221.208 C8 H15 N O6 CC(=O...
NA C:301;
D:605;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
22.99 Na [Na+]
NAG NAG E:1;
 Invalid;
 none;
 submit data
408.404 n/a O=C(N...
JTD A:310;
 Valid;
 none;
 submit data
912.413 C54 H105 N O9 CCCCC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3QUZ 2.3 Å NON-ENZYME: IMMUNE STRUCTURE OF THE MOUSE CD1D-NU-ALPHA-GALCER-INKT TCR COMPLEX MUS MUSCULUS ANTIGEN PRESENTATION GLYCOLIPID NKT CELLS IMMUNE SYSTEM
Ref.: GALACTOSE-MODIFIED INKT CELL AGONISTS STABILIZED BY INDUCED FIT OF CD1D PREVENT TUMOUR METASTASIS. EMBO J. V. 30 2294 2011
Members (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 222 families.
1 6CXE - EM4 C52 H94 N2 O10 CCCCCCCCCC....
2 6CXF - ELS C51 H92 N2 O10 CCCCCCCCCC....
3 6CX9 - EM4 C52 H94 N2 O10 CCCCCCCCCC....
4 6MJI - JTD C54 H105 N O9 CCCCCCCCCC....
5 6CW9 - 7LM C36 H63 N O9 CCCCCCCC(=....
6 6MJ4 - JTG C53 H103 N O9 CCCCCCCCCC....
7 6MIV - JU1 C61 H113 N O9 CCCCCCCCCC....
8 3QUZ Kd = 39.6 nM QUV C61 H107 N3 O9 CCCCCCCCCC....
9 6MJA - JTJ C58 H107 N O9 CCCCCCCCCC....
10 6MJ6 - JTM C57 H104 Cl N O9 CCCCCCCCCC....
11 6CX5 - FJM C36 H62 N2 O10 CCCCCCCC(=....
12 3QUY Kd = 187 nM QUY C57 H104 N2 O9 CCCCCCCCCC....
13 6MJJ - JU4 C57 H103 Cl2 N O9 CCCCCCCCCC....
70% Homology Family (18)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 67 families.
1 4WO4 - JLS C48 H93 N O9 CCCCCCCCCC....
2 3RUG Kd = 4.4 uM DB6 C44 H83 N O9 CCCCCCCCCC....
3 3HUJ - AGH C50 H99 N O9 CCCCCCCCCC....
4 3QI9 - PII C42 H81 O13 P CCCCCCCCCC....
5 3SCM - LGN C62 H117 N O18 CCCCCCCCCC....
6 6CXE - EM4 C52 H94 N2 O10 CCCCCCCCCC....
7 6CXF - ELS C51 H92 N2 O10 CCCCCCCCCC....
8 6CX9 - EM4 C52 H94 N2 O10 CCCCCCCCCC....
9 6MJI - JTD C54 H105 N O9 CCCCCCCCCC....
10 6CW9 - 7LM C36 H63 N O9 CCCCCCCC(=....
11 6MJ4 - JTG C53 H103 N O9 CCCCCCCCCC....
12 6MIV - JU1 C61 H113 N O9 CCCCCCCCCC....
13 3QUZ Kd = 39.6 nM QUV C61 H107 N3 O9 CCCCCCCCCC....
14 6MJA - JTJ C58 H107 N O9 CCCCCCCCCC....
15 6MJ6 - JTM C57 H104 Cl N O9 CCCCCCCCCC....
16 6CX5 - FJM C36 H62 N2 O10 CCCCCCCC(=....
17 3QUY Kd = 187 nM QUY C57 H104 N2 O9 CCCCCCCCCC....
18 6MJJ - JU4 C57 H103 Cl2 N O9 CCCCCCCCCC....
50% Homology Family (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 45 families.
1 4WO4 - JLS C48 H93 N O9 CCCCCCCCCC....
2 6CUG - CUY C42 H84 O2 CCCCCCCCCC....
3 3RUG Kd = 4.4 uM DB6 C44 H83 N O9 CCCCCCCCCC....
4 3HUJ - AGH C50 H99 N O9 CCCCCCCCCC....
5 3QI9 - PII C42 H81 O13 P CCCCCCCCCC....
6 3SCM - LGN C62 H117 N O18 CCCCCCCCCC....
7 6CXE - EM4 C52 H94 N2 O10 CCCCCCCCCC....
8 6CXF - ELS C51 H92 N2 O10 CCCCCCCCCC....
9 6CX9 - EM4 C52 H94 N2 O10 CCCCCCCCCC....
10 6MJI - JTD C54 H105 N O9 CCCCCCCCCC....
11 6CW9 - 7LM C36 H63 N O9 CCCCCCCC(=....
12 6MJ4 - JTG C53 H103 N O9 CCCCCCCCCC....
13 6MIV - JU1 C61 H113 N O9 CCCCCCCCCC....
14 3QUZ Kd = 39.6 nM QUV C61 H107 N3 O9 CCCCCCCCCC....
15 6MJA - JTJ C58 H107 N O9 CCCCCCCCCC....
16 6MJ6 - JTM C57 H104 Cl N O9 CCCCCCCCCC....
17 6CX5 - FJM C36 H62 N2 O10 CCCCCCCC(=....
18 3QUY Kd = 187 nM QUY C57 H104 N2 O9 CCCCCCCCCC....
19 6MJJ - JU4 C57 H103 Cl2 N O9 CCCCCCCCCC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: JTD; Similar ligands found: 35
No: Ligand ECFP6 Tc MDL keys Tc
1 JTD 1 1
2 JTG 0.752688 0.946429
3 PBS 0.719101 0.981481
4 AGH 0.719101 0.981481
5 F61 0.719101 0.981481
6 0SH 0.719101 0.981481
7 JU1 0.696078 0.883333
8 JTJ 0.693069 0.929825
9 JTM 0.686275 0.868852
10 FEE 0.681319 0.981481
11 JU4 0.666667 0.854839
12 JLS 0.653061 0.963636
13 DB6 0.609524 0.963636
14 C1Q 0.592593 0.912281
15 7LM 0.592593 0.912281
16 C8F 0.592593 0.852459
17 C8P 0.592593 0.912281
18 GM3 0.589474 0.962963
19 C6Q 0.583333 0.912281
20 ELS 0.530435 0.868852
21 QUY 0.513274 0.868852
22 QUV 0.495935 0.779412
23 FJM 0.495868 0.866667
24 EM4 0.495868 0.866667
25 7LP 0.487603 0.866667
26 GSL 0.485149 0.877193
27 BGC 18C GAL 0.464912 0.896552
28 03F 0.462963 0.928571
29 LGN 0.434426 0.896552
30 IGC 0.434426 0.896552
31 EIS 0.421053 0.702703
32 SLF 0.421053 0.702703
33 CIS 0.410256 0.702703
34 LAT SPH DAO 0.4 0.862069
35 LAT SPH OLA 0.4 0.862069
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3QUZ; Ligand: QUV; 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: 3quz.bio1) has 86 residues
No: Leader PDB Ligand Sequence Similarity
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