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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:

1ad3

2.600 Å

X-ray

1996-06-25

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Aldehyde dehydrogenase, dimeric NADP-preferring
ID:AL3A1_RAT
AC:P11883
Organism:Rattus norvegicus
Reign:Eukaryota
TaxID:10116
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:15.931
Number of residues:43
Including
Standard Amino Acids: 43
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.150783.000

% Hydrophobic% Polar
54.3145.69
According to VolSite

Ligand :
1ad3_2 Structure
HET Code: NAD
Formula: C21H26N7O14P2
Molecular weight: 662.417 g/mol
DrugBank ID: -
Buried Surface Area:51.9 %
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
49.31667.260344.1866


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
O1NNE1TRP- 1133.08156.64H-Bond
(Protein Donor)
O3BOE2GLU- 1403.19129.54H-Bond
(Ligand Donor)
O3BOE1GLU- 1402.63162.62H-Bond
(Ligand Donor)
O2BOE2GLU- 1402.74150.36H-Bond
(Ligand Donor)
C3BCG2VAL- 1414.280Hydrophobic
C2BCG2VAL- 1693.740Hydrophobic
O2ANE2HIS- 2893.46147.26H-Bond
(Protein Donor)
O3NE2HIS- 2893.17136.32H-Bond
(Protein Donor)
C3DCDARG- 2923.920Hydrophobic
C2DCBPHE- 3354.180Hydrophobic