Receptor
PDB id Resolution Class Description Source Keywords
5G6U 1.84 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF LANGERIN CARBOHYDRATE RECOGNITION DOMAI GLCNS6S HOMO SAPIENS CARBOHYDRATE BINDING PROTEIN LANGERIN CD207 CLEC4K C-TYPLECTINS CLRS SULFATED CARBOHYDRATES
Ref.: RATIONAL-DIFFERENTIAL DESIGN OF HIGHLY SPECIFIC GLY LIGANDS: TARGETING DC-SIGN AND EXCLUDING LANGERIN RECOGNITION. ACS CHEM. BIOL. V. 13 600 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
YJM C:1326;
A:1327;
B:1326;
D:1325;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
ic50 = 0.22 uM
339.298 C6 H13 N O11 S2 C([C@...
TRP A:1331;
D:1330;
B:1334;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
204.225 C11 H12 N2 O2 c1ccc...
EU A:1328;
A:2000;
C:1329;
B:2000;
C:1328;
B:1327;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
151.964 Eu [Eu+2...
CL D:1327;
C:1332;
B:1333;
A:1330;
B:1330;
B:1331;
B:1329;
B:1332;
C:1331;
D:1329;
D:1328;
C:1330;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
35.453 Cl [Cl-]
CA A:1329;
B:1328;
C:1327;
D:1326;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
40.078 Ca [Ca+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5G6U 1.84 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF LANGERIN CARBOHYDRATE RECOGNITION DOMAI GLCNS6S HOMO SAPIENS CARBOHYDRATE BINDING PROTEIN LANGERIN CD207 CLEC4K C-TYPLECTINS CLRS SULFATED CARBOHYDRATES
Ref.: RATIONAL-DIFFERENTIAL DESIGN OF HIGHLY SPECIFIC GLY LIGANDS: TARGETING DC-SIGN AND EXCLUDING LANGERIN RECOGNITION. ACS CHEM. BIOL. V. 13 600 2018
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1579 families.
1 5G6U ic50 = 0.22 uM YJM C6 H13 N O11 S2 C([C@@H]1[....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1312 families.
1 5G6U ic50 = 0.22 uM YJM C6 H13 N O11 S2 C([C@@H]1[....
50% Homology Family (27)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 319 families.
1 3P5I - G6S NAG n/a n/a
2 3P5H - BGC BGC n/a n/a
3 4N37 - MMA C7 H14 O6 CO[C@@H]1[....
4 4N34 - 2F8 C9 H17 N O6 CC(=O)N[C@....
5 3P5E - MAN C6 H12 O6 C([C@@H]1[....
6 6PWR - NAG MAN n/a n/a
7 6PWS Ki = 1.6 mM MMA C7 H14 O6 CO[C@@H]1[....
8 5G6U ic50 = 0.22 uM YJM C6 H13 N O11 S2 C([C@@H]1[....
9 5VYB - MAN MAN MAN BMA MAN MAN MAN n/a n/a
10 1SL5 - GAL NAG GAL FUC n/a n/a
11 2IT5 - MAN MAN MAN n/a n/a
12 1K9J - NAG MAN MAN MAN NAG n/a n/a
13 1SL4 - MAN MAN MAN MAN n/a n/a
14 2IT6 - MAN MAN n/a n/a
15 1K9I - NAG MAN MAN MAN NAG n/a n/a
16 6GHV Kd = 52 uM EZ8 C35 H48 Cl N6 O10 c1cc(ccc1C....
17 3VYK Kd = 0.000023 M MMA MAN NAG MAN NAG NAG n/a n/a
18 4KZV - TRE C12 H22 O11 C([C@@H]1[....
19 4ZRV - 4RS C16 H28 O12 CCCC(=O)OC....
20 5KTH - TRE 6X7 6X7 n/a n/a
21 5KTI - TRE 6X6 n/a n/a
22 2OX9 - GAL NAG FUC n/a n/a
23 4ZES Ki = 9.4 mM MMA C7 H14 O6 CO[C@@H]1[....
24 3WH2 - FLC C6 H5 O7 C(C(=O)[O-....
25 5JPV - LBT C12 H22 O11 C([C@@H]1[....
26 5JQ1 - ZPF C9 H15 N O6 CC(=O)N[C@....
27 1SL6 - GAL NDG FUC n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: YJM; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 YJM 1 1
2 SGN 1 1
3 NGS 0.603774 0.870968
4 3LJ 0.5 0.898305
Ligand no: 2; Ligand: TRP; Similar ligands found: 30
No: Ligand ECFP6 Tc MDL keys Tc
1 DTR 1 1
2 TRP 1 1
3 LTN 0.765957 0.777778
4 3IL 0.666667 0.75
5 TR7 0.666667 0.833333
6 4Z9 0.666667 0.75
7 FT6 0.561404 0.888889
8 IAC 0.538462 0.787879
9 TSR 0.529412 0.722222
10 IOP 0.518519 0.764706
11 R38 0.515152 0.72093
12 R59 0.515152 0.72093
13 ZIQ 0.491525 0.864865
14 3IB 0.491228 0.742857
15 ITW 0.491228 0.694444
16 IAD 0.484375 0.738095
17 TRP GLY 0.476923 0.704545
18 TSS 0.471698 0.666667
19 CTE 0.467742 0.888889
20 DTE 0.467742 0.888889
21 IAV 0.461538 0.738095
22 IAG 0.459016 0.738095
23 LYS TRP 0.432432 0.673913
24 78U 0.42623 0.794118
25 0ZN 0.421687 0.673913
26 4OG 0.416667 0.8
27 X95 0.411765 0.680851
28 LSW 0.411765 0.680851
29 ASP TRP ASN 0.405063 0.673913
30 GLU ASP ASN ASP TRP ASN 0.405063 0.673913
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5G6U; Ligand: YJM; Similar sites found with APoc: 3
This union binding pocket(no: 1) in the query (biounit: 5g6u.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 4WQQ MAN 39.0071
2 1RDL MMA 45.1327
3 1RDL MMA 45.1327
Pocket No.: 2; Query (leader) PDB : 5G6U; Ligand: YJM; Similar sites found with APoc: 2
This union binding pocket(no: 2) in the query (biounit: 5g6u.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 1RDL MMA 45.1327
2 1RDL MMA 45.1327
Pocket No.: 3; Query (leader) PDB : 5G6U; Ligand: TRP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5g6u.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5G6U; Ligand: TRP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5g6u.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5G6U; Ligand: YJM; Similar sites found with APoc: 3
This union binding pocket(no: 5) in the query (biounit: 5g6u.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 4WQQ MAN 39.0071
2 1RDL MMA 45.1327
3 1RDL MMA 45.1327
Pocket No.: 6; Query (leader) PDB : 5G6U; Ligand: TRP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 5g6u.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 5G6U; Ligand: YJM; Similar sites found with APoc: 9
This union binding pocket(no: 7) in the query (biounit: 5g6u.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 2MSB NAG BMA MAN MAN MAN MAN MAN 32.1739
2 4WQQ MAN 39.0071
3 4WQQ MAN 39.0071
4 4WQQ MAN 39.0071
5 4WQQ MAN 39.0071
6 1PWB GLC 40.678
7 1PWB GLC GLC 40.678
8 1RDL MMA 45.1327
9 1RDL MMA 45.1327
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