Receptor
PDB id Resolution Class Description Source Keywords
5GX6 1.81 Å NON-ENZYME: BINDING CRYSTAL STRUCTURE OF SOLUTE-BINDING PROTEIN COMPLEXED WITH U CHONDROITIN DISACCHARIDE WITH A SULFATE GROUP AT C-4 POSITIG ALNAC STREPTOBACILLUS MONILIFORMIS DSM 12112ORGANISM_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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:606;
A:604;
B:605;
A:608;
C:604;
B:604;
B:610;
B:606;
B:609;
A:607;
C:606;
A:605;
B:608;
C:605;
B:607;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
CA C:601;
A:601;
B:601;
 Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
 submit data
40.078 Ca [Ca+2...
ASG GCD F:1;
D:1;
E:1;
 Valid;
Valid;
Valid;
 none;
none;
none;
 Kd = 1.6 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: ASG GCD; Similar ligands found: 14
No: Ligand ECFP6 Tc MDL keys Tc
1 ASG GCD 1 1
2 8EX GCD 0.7875 0.968254
3 ASG BDP ASG GCD 0.744681 0.953846
4 NAG GAD 0.692308 0.734375
5 NG6 GCD 0.635294 0.953125
6 ASG GC4 0.586207 0.9375
7 ASG IDR ASG IDR 0.515152 0.909091
8 GNS UAP 0.48913 0.880597
9 NDG GCD 0.483516 0.707692
10 MAG SGA FUC 0.474227 0.893939
11 NAG G6S 0.434783 0.907692
12 NAG FUC GAL 0.423913 0.636364
13 83Y BDP 83Y GCD 0.407407 0.71875
14 ASG 0.402439 0.875
Similar Ligands (3D)
Ligand no: 1; Ligand: ASG GCD; Similar ligands found: 3
No: Ligand Similarity coefficient
1 NGK GCD 0.9456
2 NGA GCD 0.9004
3 NAG GCD 0.8654
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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