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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

1u30

1.900 Å

X-ray

2004-07-20

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Pancreatic alpha-amylase
ID:AMYP_HUMAN
AC:P04746
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:21.030
Number of residues:19
Including
Standard Amino Acids: 18
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.585583.875

% Hydrophobic% Polar
39.3160.69
According to VolSite

Ligand :
1u30_1 Structure
HET Code: GOX
Formula: C6H13N2O5
Molecular weight: 193.178 g/mol
DrugBank ID: DB02376
Buried Surface Area:47.6 %
Polar Surface area: 127.15 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 7
Rings: 1
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 1
Rotatable Bonds: 1

Mass center Coordinates

XYZ
4.2418514.410641.5127


Binding mode :
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Binding mode
BioSolveIT Image generated by PoseView
Protein
Binding Site
Ligand
Interaction pattern
hydrophobic (CA)
aromatic (CZ)
hydrogen bond acceptor (O)
hydrogen bond acceptor/donor (OG)
hydrogen bond donor (N)
positively ionized (NZ)
negatively ionized (OD1)
metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
C4CZTYR- 1513.860Hydrophobic
C2CD1LEU- 1623.960Hydrophobic
O6NZLYS- 2002.54132.07H-Bond
(Protein Donor)
N1NE2HIS- 2012.7158.91H-Bond
(Protein Donor)
O7NE2HIS- 2012.97124.3H-Bond
(Protein Donor)
C5CBILE- 2354.260Hydrophobic
C6CG2ILE- 2354.240Hydrophobic
O6OE1GLU- 2403.02139.37H-Bond
(Ligand Donor)