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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:

4gl4

1.800 Å

X-ray

2012-08-13

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Alcohol dehydrogenase class-3
ID:ADHX_ARATH
AC:Q96533
Organism:Arabidopsis thaliana
Reign:Eukaryota
TaxID:3702
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A98 %
B2 %


Ligand binding site composition:

B-Factor:34.156
Number of residues:44
Including
Standard Amino Acids: 42
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals: ZN

Cavity properties

LigandabilityVolume (Å3)
0.4712048.625

% Hydrophobic% Polar
47.7852.22
According to VolSite

Ligand :
4gl4_1 Structure
HET Code: NAI
Formula: C21H27N7O14P2
Molecular weight: 663.425 g/mol
DrugBank ID: DB00157
Buried Surface Area:58.41 %
Polar Surface area: 342.9 Å2
Number of
H-Bond Acceptors: 19
H-Bond Donors: 6
Rings: 5
Aromatic rings: 2
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 3
Rotatable Bonds: 11

Mass center Coordinates

XYZ
65.129519.010743.1592


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
C4NCG2THR- 1813.640Hydrophobic
O2NNVAL- 2063.07159.1H-Bond
(Protein Donor)
C5DCG2VAL- 2063.870Hydrophobic
O3BOD2ASP- 2262.68155.08H-Bond
(Ligand Donor)
O2BOD2ASP- 2263.26157.29H-Bond
(Ligand Donor)
N3ANILE- 2273.45140.73H-Bond
(Protein Donor)
C1BCG1ILE- 2724.290Hydrophobic
N7NOVAL- 2952.87167.47H-Bond
(Ligand Donor)
O3DNVAL- 2972.95167.96H-Bond
(Protein Donor)
C1DCG2VAL- 2974.420Hydrophobic
N7NOTHR- 3202.97157.38H-Bond
(Ligand Donor)
O7NNPHE- 3222.86173.37H-Bond
(Protein Donor)
O2NOHOH- 5162.57179.99H-Bond
(Protein Donor)