Receptor
PDB id Resolution Class Description Source Keywords
3HUJ 2.5 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF HUMAN CD1D-ALPHA-GALACTOSYLCERAMIDE IN WITH SEMI-INVARIANT NKT CELL RECEPTOR HOMO SAPIENS CD1D NKT T CELL RECEPTOR ALPHA-GALACTOSYLCERAMIDE PROTEINCOMPLEX CELL MEMBRANE DISULFIDE BOND ENDOSOME GLYCOPROTHOST-VIRUS INTERACTION IMMUNE RESPONSE IMMUNOGLOBULIN DOMINNATE IMMUNITY LYSOSOME MEMBRANE TRANSMEMBRANE DISEASEMUTATION GLYCATION MHC I PYRROLIDONE CARBOXYLIC ACID SEIMMUNE SYSTEM
Ref.: DIFFERENTIAL RECOGNITION OF CD1D-ALPHA-GALACTOSYL C BY THE V BETA 8.2 AND V BETA 7 SEMI-INVARIANT NKT T RECEPTORS IMMUNITY V. 31 47 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
AGH A:3000;
C:3000;
 Valid;
Valid;
 none;
none;
 submit data
858.322 C50 H99 N O9 CCCCC...
MG H:1000;
 Part of Protein;
 none;
 submit data
24.305 Mg [Mg+2...
NAG A:2000;
C:2000;
 Invalid;
Invalid;
 none;
none;
 submit data
221.208 C8 H15 N O6 CC(=O...
NAG NDG BMA J:1;
 Invalid;
 none;
 submit data
570.545 n/a O=C(N...
NAG BMA I:1;
 Invalid;
 none;
 submit data
367.351 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3HUJ 2.5 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF HUMAN CD1D-ALPHA-GALACTOSYLCERAMIDE IN WITH SEMI-INVARIANT NKT CELL RECEPTOR HOMO SAPIENS CD1D NKT T CELL RECEPTOR ALPHA-GALACTOSYLCERAMIDE PROTEINCOMPLEX CELL MEMBRANE DISULFIDE BOND ENDOSOME GLYCOPROTHOST-VIRUS INTERACTION IMMUNE RESPONSE IMMUNOGLOBULIN DOMINNATE IMMUNITY LYSOSOME MEMBRANE TRANSMEMBRANE DISEASEMUTATION GLYCATION MHC I PYRROLIDONE CARBOXYLIC ACID SEIMMUNE SYSTEM
Ref.: DIFFERENTIAL RECOGNITION OF CD1D-ALPHA-GALACTOSYL C BY THE V BETA 8.2 AND V BETA 7 SEMI-INVARIANT NKT T RECEPTORS IMMUNITY V. 31 47 2009
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1579 families.
1 3HUJ - AGH C50 H99 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: AGH; Similar ligands found: 58
No: Ligand ECFP6 Tc MDL keys Tc
1 AGH 1 1
2 0SH 1 1
3 F61 1 1
4 PBS 1 1
5 FEE 0.945205 1
6 JLS 0.8875 0.981481
7 GM3 0.818182 0.981132
8 DB6 0.816092 0.981481
9 C8F 0.788889 0.866667
10 C8P 0.788889 0.928571
11 7LM 0.788889 0.928571
12 C1Q 0.788889 0.928571
13 C6Q 0.777778 0.928571
14 JTG 0.727273 0.963636
15 JTD 0.719101 0.981481
16 ELS 0.683673 0.883333
17 JTJ 0.666667 0.946429
18 JTM 0.659794 0.883333
19 JU1 0.653061 0.898305
20 EM4 0.650485 0.881356
21 FJM 0.650485 0.881356
22 7LP 0.640777 0.881356
23 JU4 0.64 0.868852
24 03F 0.633333 0.945455
25 QUV 0.616822 0.791045
26 QUY 0.6 0.883333
27 GSL 0.579545 0.892857
28 BGC 18C GAL 0.544554 0.912281
29 GAL SPH NER 0.510204 0.892857
30 LGN 0.504587 0.912281
31 IGC 0.504587 0.912281
32 EIS 0.49505 0.712329
33 SLF 0.49505 0.712329
34 CIS 0.480769 0.712329
35 LAT SPH DAO 0.470588 0.877193
36 LAT SPH OLA 0.470588 0.877193
37 BOG 0.461538 0.754717
38 BNG 0.461538 0.754717
39 HSJ 0.461538 0.754717
40 DGD 0.455446 0.75
41 B7G 0.448718 0.754717
42 KGM 0.448718 0.754717
43 1O2 0.445545 0.763636
44 3TF 0.441176 0.763636
45 GLC HEX 0.435897 0.735849
46 JZR 0.435897 0.735849
47 BHG 0.435897 0.735849
48 GAL SPH EIC 0.435185 0.877193
49 0SG 0.422018 0.69863
50 XNS 0.413793 0.722222
51 DR4 0.413793 0.722222
52 T6D 0.413043 0.745455
53 1L2 0.412844 0.763636
54 LAT SPH OCA 0.405405 0.847458
55 SFT 0.405405 0.712329
56 AFO 0.405063 0.690909
57 SER MAN 0.402439 0.678571
58 CQX 0.402299 0.740741
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3HUJ; Ligand: AGH; Similar sites found with APoc: 3
This union binding pocket(no: 1) in the query (biounit: 3huj.bio1) has 46 residues
No: Leader PDB Ligand Sequence Similarity
1 1NU4 MLA 11.3402
2 1NU4 MLA 11.3402
3 1NU4 MLA 11.3402
Pocket No.: 2; Query (leader) PDB : 3HUJ; Ligand: AGH; Similar sites found with APoc: 3
This union binding pocket(no: 2) in the query (biounit: 3huj.bio2) has 48 residues
No: Leader PDB Ligand Sequence Similarity
1 1NU4 MLA 11.3402
2 1NU4 MLA 11.3402
3 1NU4 MLA 11.3402
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