Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:601;
C:601;
B:601;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
40.078 Ca [Ca+2...
EDO B:605;
A:605;
B:607;
B:606;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
MES A:604;
B:604;
C:604;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
195.237 C6 H13 N O4 S C1COC...
NGA GCD D:1;
F:1;
E:1;
Valid;
Valid;
Valid;
none;
none;
none;
Kd = 0.635 uM
n/a n/a
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: NGA GCD; Similar ligands found: 0
No: Ligand ECFP6 Tc MDL keys Tc
Similar Ligands (3D)
Ligand no: 1; Ligand: NGA GCD; Similar ligands found: 25
No: Ligand Similarity coefficient
1 NGA GCD 1.0000
2 NAG GCD 0.9776
3 NAG GC4 0.9522
4 NAG GAD 0.9479
5 NGA GAL 0.9412
6 NDG GAD 0.9346
7 A2G GAL 0.9316
8 NAG BDP 0.9250
9 NAG GAL 0.9206
10 MGC GAL 0.9125
11 NOK GAL 0.9097
12 LOG GAL 0.9024
13 ASG GCD 0.9004
14 NG6 GCD 0.8950
15 NDG GCD 0.8828
16 NDG GAL 0.8812
17 NOY BGC 0.8771
18 NGA NAG 0.8758
19 ASG GC4 0.8728
20 BGC Z9D 0.8726
21 NGK GCD 0.8706
22 BGC GAL 0.8686
23 GAL NGT 0.8645
24 BGC BGC 0.8641
25 NGT GAL 0.8562
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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