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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:

4zvy

1.900 Å

X-ray

2015-05-18

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Alpha-aminoadipic semialdehyde dehydrogenase
ID:AL7A1_HUMAN
AC:P49419
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:1.2.1.31


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:22.677
Number of residues:28
Including
Standard Amino Acids: 27
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.452266.625

% Hydrophobic% Polar
62.0337.97
According to VolSite

Ligand :
4zvy_1 Structure
HET Code: NAD
Formula: C21H26N7O14P2
Molecular weight: 662.417 g/mol
DrugBank ID: -
Buried Surface Area:60.43 %
Polar Surface area: 343.54 Å2
Number of
H-Bond Acceptors: 18
H-Bond Donors: 6
Rings: 5
Aromatic rings: 3
Anionic atoms: 2
Cationic atoms: 1
Rule of Five Violation: 3
Rotatable Bonds: 11

Mass center Coordinates

XYZ
29.1627-50.0698-32.8858


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
C1BCG2ILE- 1633.880Hydrophobic
C4BCG2ILE- 1633.660Hydrophobic
O3BOTHR- 1642.66176.57H-Bond
(Ligand Donor)
C5BCBALA- 1654.430Hydrophobic
C5BCZPHE- 2444.060Hydrophobic
C4BCE1PHE- 2443.890Hydrophobic
C1BCE1PHE- 2444.380Hydrophobic
O2ANSER- 2472.93167.04H-Bond
(Protein Donor)
O2AOGSER- 2473.26142.02H-Bond
(Protein Donor)