Receptor
PDB id Resolution Class Description Source Keywords
3E80 2.35 Å EC: 3.-.-.- STRUCTURE OF HEPARINASE II COMPLEXED WITH HEPARAN SULFATE DE DISACCHARIDE PRODUCT PEDOBACTER HEPARINUS ALPHA AND BETA LYASE FOLD ALPHA6/ALPHA6 INCOMPLETE TOROID BINDING PROTEIN LYASE
Ref.: CATALYTIC MECHANISM OF HEPARINASE II INVESTIGATED B SITE-DIRECTED MUTAGENESIS AND THE CRYSTAL STRUCTURE SUBSTRATE. J.BIOL.CHEM. V. 285 20051 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PO4 A:2;
A:3;
A:5;
A:9;
B:1;
B:7;
B:8;
C:4;
C:6;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
94.971 O4 P [O-]P...
ZN A:1;
B:2;
C:3;
 Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
 submit data
65.409 Zn [Zn+2...
NDG GCD H:1;
G:1;
I:1;
 Valid;
Valid;
Valid;
 none;
none;
none;
 submit data
381.334 n/a O=C([...
MAN GCU RAM XYS F:1;
E:1;
D:1;
 Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
 submit data
n/a n/a
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3E7J 2.1 Å EC: 3.-.-.- HEPARINASEII H202A/Y257A DOUBLE MUTANT COMPLEXED WITH A HEPA SULFATE TETRASACCHARIDE SUBSTRATE PEDOBACTER HEPARINUS ALPHA AND BETA LYASE ALPHA6/ALPHA6 INCOMPLETE TOROID SUGARPROTEIN LYASE
Ref.: CATALYTIC MECHANISM OF HEPARINASE II INVESTIGATED B SITE-DIRECTED MUTAGENESIS AND THE CRYSTAL STRUCTURE SUBSTRATE. J.BIOL.CHEM. V. 285 20051 2010
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 312 families.
1 3E80 - NDG GCD n/a n/a
2 2FUT - SGN UAP n/a n/a
3 3E7J - NAG GCU NAG GCD n/a n/a
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 261 families.
1 3E80 - NDG GCD n/a n/a
2 2FUT - SGN UAP n/a n/a
3 3E7J - NAG GCU NAG GCD n/a n/a
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 214 families.
1 3E80 - NDG GCD n/a n/a
2 2FUT - SGN UAP n/a n/a
3 3E7J - NAG GCU NAG GCD n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: NDG GCD; Similar ligands found: 11
No: Ligand ECFP6 Tc MDL keys Tc
1 NDG GCD 1 1
2 NAG GAD 0.53012 0.921569
3 NDG NAG NAG NAG 0.487805 0.867925
4 ASG GCD 0.483516 0.707692
5 BGC RAM BGC GAD 0.479167 0.72549
6 RAM GAD 0.468354 0.632653
7 LGU MAW 0.4625 0.6
8 NG6 GCD 0.44086 0.69697
9 GTR RAM AQA 0.413043 0.62
10 8EX GCD 0.408163 0.681818
11 GNS UAP 0.404255 0.637681
Similar Ligands (3D)
Ligand no: 1; Ligand: NDG GCD; Similar ligands found: 5
No: Ligand Similarity coefficient
1 NDG GAL 0.9497
2 NGA GCD 0.8828
3 NAG GCD 0.8793
4 NAG GC4 0.8791
5 NDG GAD 0.8704
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3E7J; Ligand: NAG GCU NAG 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: 3e7j.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3E7J; Ligand: NAG GCU NAG GCD; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3e7j.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback