Receptor
PDB id Resolution Class Description Source Keywords
5GX7 1.99 Å NON-ENZYME: BINDING CRYSTAL STRUCTURE OF SOLUTE-BINDING PROTEIN COMPLEXED WITH U CHONDROITIN DISACCHARIDE WITH A SULFATE GROUP AT C-6 POSITIG ALNAC STREPTOBACILLUS MONILIFORMIS DSM 12112ORGANISM_TAXID: 519441 GLYCOSAMINOGLYCAN ABC TRANSPORTER SOLUTE-BINDING PROTEIN PROTEIN
Ref.: A BACTERIAL ABC TRANSPORTER ENABLES IMPORT OF MAMMA GLYCOSAMINOGLYCANS SCI REP V. 7 1069 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA B:603;
C:603;
A:603;
 Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
 submit data
40.078 Ca [Ca+2...
NG6 GCD F:1;
D:1;
E:1;
 Valid;
Valid;
Valid;
 none;
none;
none;
 Kd = 2.76 uM
457.365 n/a S(=O)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5GUB 1.78 Å NON-ENZYME: BINDING CRYSTAL STRUCTURE OF SOLUTE-BINDING PROTEIN COMPLEXED WITH S GROUP-FREE UNSATURATED CHONDROITIN DISACCHARIDE STREPTOBACILLUS MONILIFORMIS STRAIN DSORGANISM_TAXID: 519441 GLYCOSAMINOGLYCAN ABC TRANSPORTER SOLUTE-BINDING PROTEIN BINDING PROTEIN
Ref.: A BACTERIAL ABC TRANSPORTER ENABLES IMPORT OF MAMMA GLYCOSAMINOGLYCANS SCI REP V. 7 1069 2017
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 552 families.
1 5XS8 - 8EX GCD n/a n/a
2 6INZ Kd = 1.6 uM NAG GCD n/a n/a
3 5GX7 Kd = 2.76 uM NG6 GCD n/a n/a
4 5GX6 Kd = 1.6 uM ASG GCD n/a n/a
5 5GUB Kd = 0.635 uM NGA GCD n/a n/a
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 426 families.
1 5XS8 - 8EX GCD n/a n/a
2 6INZ Kd = 1.6 uM NAG GCD n/a n/a
3 5GX7 Kd = 2.76 uM NG6 GCD n/a n/a
4 5GX6 Kd = 1.6 uM ASG GCD n/a n/a
5 5GUB Kd = 0.635 uM NGA GCD n/a n/a
50% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 322 families.
1 1Y3P Kd = 15 uM MAV LGU MAV BEM n/a n/a
2 1Y3N Kd = 2.8 uM MAV BEM n/a n/a
3 1J1N - MAV LGU MAV BEM n/a n/a
4 5XS8 - 8EX GCD n/a n/a
5 6INZ Kd = 1.6 uM NAG GCD n/a n/a
6 5GX7 Kd = 2.76 uM NG6 GCD n/a n/a
7 5GX6 Kd = 1.6 uM ASG GCD n/a n/a
8 5GUB Kd = 0.635 uM NGA GCD n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: NG6 GCD; Similar ligands found: 11
No: Ligand ECFP6 Tc MDL keys Tc
1 NG6 GCD 1 1
2 NAG GAD 0.746667 0.75
3 8EX GCD 0.710843 0.953125
4 ASG GCD 0.635294 0.953125
5 ASG BDP ASG GCD 0.495413 0.910448
6 NDG GCD 0.44086 0.69697
7 NAG G6S 0.43956 0.923077
8 NG6 BDP ASG GCD 0.423729 0.897059
9 A2G GAL NAG 0.421053 0.656716
10 A2G GAL 0.416667 0.661538
11 NAG BDP 0.404494 0.71875
Similar Ligands (3D)
Ligand no: 1; Ligand: NG6 GCD; Similar ligands found: 3
No: Ligand Similarity coefficient
1 NGA GCD 0.8950
2 NAG GCD 0.8695
3 NGA GAL 0.8531
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5GUB; Ligand: NGA GCD; 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: 5gub.bio3) has 23 residues
No: Leader PDB Ligand Sequence Similarity
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