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 C:602;
A:602;
B:602;
Valid;
Valid;
Valid;
none;
none;
none;
Kd = 0.635 uM
378.31 n/a O=C(N...
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 (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 510 families.
1 5XS8 - GCD 8EX n/a n/a
2 5GX7 Kd = 2.76 uM GCD NG6 n/a n/a
3 5GX6 Kd = 1.6 uM GCD ASG n/a n/a
4 5GUB Kd = 0.635 uM NGA GCD n/a n/a
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 391 families.
1 5XS8 - GCD 8EX n/a n/a
2 5GX7 Kd = 2.76 uM GCD NG6 n/a n/a
3 5GX6 Kd = 1.6 uM GCD ASG n/a n/a
4 5GUB Kd = 0.635 uM NGA GCD n/a n/a
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 298 families.
1 1Y3P Kd = 15 uM BEM MAV LGU MAV n/a n/a
2 1Y3N Kd = 2.8 uM BEM MAV n/a n/a
3 1J1N - BEM MAV LGU MAV n/a n/a
4 5XS8 - GCD 8EX n/a n/a
5 5GX7 Kd = 2.76 uM GCD NG6 n/a n/a
6 5GX6 Kd = 1.6 uM GCD ASG n/a n/a
7 5GUB Kd = 0.635 uM NGA GCD n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NGA GCD; Similar ligands found: 37
No: Ligand ECFP6 Tc MDL keys Tc
1 GCD NGA 1 1
2 NGA GCD 1 1
3 GAD NDG 1 1
4 NAG GAD 1 1
5 UCD 0.782609 0.979592
6 NG6 GCD 0.746667 0.75
7 GCD NG6 0.746667 0.75
8 GCD ASG 0.692308 0.734375
9 NGK GCD 0.692308 0.734375
10 GCD 8EX 0.607143 0.707692
11 GAL NGA 0.577465 0.88
12 GAL A2G 0.577465 0.88
13 A2G GAL 0.577465 0.88
14 NAG BDP 0.552632 0.959184
15 L42 0.547619 0.707692
16 HS2 0.5375 0.959184
17 NAG A2G 0.533333 0.865385
18 NAG NGA 0.533333 0.865385
19 ASG BDP ASG GCD 0.529412 0.701493
20 GC4 NAG 0.525 0.92
21 BGC RAM BGC GAD 0.494624 0.76
22 RAM GAD 0.486842 0.632653
23 DR3 0.470588 0.862745
24 NAG BDP NAG BDP 0.464646 0.924528
25 BEM MAV 0.461538 0.632653
26 NAG BDP NAG BDP NAG BDP 0.460784 0.942308
27 NAG BDP NAG BDP NAG BDP NAG 0.442105 0.903846
28 NAG A2G GAL 0.438202 0.865385
29 AMU 0.434211 0.84
30 ACY 1GN GAL 1GN BGC ACY GAL BGC 0.43299 0.865385
31 1GN ACY GAL ACY 1GN BGC GAL BGC 0.43299 0.865385
32 AQA RAM GTR 0.426966 0.653061
33 MAW MAV GCU 0.413793 0.62
34 MAW LGU BEM BEM 0.413793 0.62
35 MAW BEM BEM BEM 0.413793 0.62
36 BEM MAV LGU MAV 0.413793 0.62
37 H3S 0.402174 0.661765
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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