Receptor
PDB id Resolution Class Description Source Keywords
3SCM 2.5 Å NON-ENZYME: IMMUNE CRYSTAL STRUCTURE OF AUTOREACTIVE-VALPHA14-VBETA6 NKT TCR IN WITH CD1D-ISOGLOBOTRIHEXOSYLCERAMIDE MUS MUSCULUS TERNARY COMPLEX IMMUNITY APC CELL SURFACE IMMUNE SYSTEM
Ref.: RECOGNITION OF BETA-LINKED SELF GLYCOLIPIDS MEDIATE NATURAL KILLER T CELL ANTIGEN RECEPTORS NAT.IMMUNOL. V. 12 827 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
LGN A:307;
Valid;
none;
submit data
1164.59 C62 H117 N O18 CCCCC...
NAG A:303;
A:304;
Part of Protein;
Part of Protein;
none;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
NAG NAG E:1;
Part of Protein;
none;
submit data
408.404 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3SCM 2.5 Å NON-ENZYME: IMMUNE CRYSTAL STRUCTURE OF AUTOREACTIVE-VALPHA14-VBETA6 NKT TCR IN WITH CD1D-ISOGLOBOTRIHEXOSYLCERAMIDE MUS MUSCULUS TERNARY COMPLEX IMMUNITY APC CELL SURFACE IMMUNE SYSTEM
Ref.: RECOGNITION OF BETA-LINKED SELF GLYCOLIPIDS MEDIATE NATURAL KILLER T CELL ANTIGEN RECEPTORS NAT.IMMUNOL. V. 12 827 2011
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 222 families.
1 3QI9 - PII C42 H81 O13 P CCCCCCCCCC....
2 3SCM - LGN C62 H117 N O18 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: LGN; Similar ligands found: 64
No: Ligand ECFP6 Tc MDL keys Tc
1 IGC 1 1
2 LGN 1 1
3 BGC 18C GAL 0.913979 1
4 03F 0.72449 0.964286
5 SLF 0.647619 0.753425
6 EIS 0.647619 0.753425
7 BGC 18C GAL SIA 0.634328 0.903226
8 LAT SPH OCA 0.633027 0.931035
9 CIS 0.62963 0.753425
10 BGC 18C GAL NGA SIA GAL 0.594595 0.903226
11 SIA GAL BGC 16C 0.583942 0.903226
12 0SG 0.580357 0.739726
13 JLS 0.544643 0.929825
14 GGD 0.533898 0.789474
15 DB6 0.525424 0.929825
16 LAT SPH OLA 0.522124 0.896552
17 LAT SPH DAO 0.522124 0.896552
18 GM3 0.514019 0.928571
19 F61 0.504587 0.912281
20 PBS 0.504587 0.912281
21 FEE 0.504587 0.912281
22 AGH 0.504587 0.912281
23 0SH 0.504587 0.912281
24 SFT 0.495798 0.753425
25 LMU 0.48 0.75
26 UMQ 0.48 0.75
27 DMU 0.48 0.75
28 LMT 0.48 0.75
29 GAL SPH EIC 0.475 0.896552
30 1PZ 0.456311 0.636364
31 1PX 0.456311 0.636364
32 JTG 0.45 0.913793
33 ERA BGC GAL 0.442748 0.915254
34 C8P 0.440945 0.913793
35 C1Q 0.440945 0.913793
36 7LM 0.440945 0.913793
37 GAL SPH NER 0.440678 0.87931
38 1O2 0.435897 0.754386
39 JTD 0.434426 0.896552
40 C6Q 0.433071 0.913793
41 3TF 0.432203 0.754386
42 C8F 0.429688 0.854839
43 ELS 0.427481 0.870968
44 6UZ 0.424528 0.666667
45 16C 0.424242 0.732143
46 18C 0.424242 0.732143
47 SPL 0.424242 0.732143
48 MAN BMA NAG 0.420561 0.741379
49 GLA GAL NAG 0.420561 0.741379
50 1L2 0.419355 0.754386
51 GLA GAL GLC NBU 0.417476 0.696429
52 EM4 0.411765 0.868852
53 FJM 0.411765 0.868852
54 JTJ 0.410853 0.931035
55 GLA EGA 0.408163 0.625
56 JTM 0.407692 0.870968
57 T6D 0.407407 0.767857
58 6CM 0.405941 0.732143
59 GAL NGA GLA BGC GAL 0.405172 0.741379
60 JU1 0.40458 0.885246
61 7LP 0.404412 0.868852
62 GLA GAL BGC 5VQ 0.401961 0.660714
63 GLC GAL NAG GAL 0.4 0.741379
64 LAT NAG GAL 0.4 0.741379
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3SCM; Ligand: LGN; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 3scm.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
1 3TDC 0EU 6.06061
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