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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:

4dbu

2.530 Å

X-ray

2012-01-16

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Aldo-keto reductase family 1 member C3
ID:AK1C3_HUMAN
AC:P42330
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:30.426
Number of residues:27
Including
Standard Amino Acids: 25
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors: NAP
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.127833.625

% Hydrophobic% Polar
67.6132.39
According to VolSite

Ligand :
4dbu_2 Structure
HET Code: BT9
Formula: C14H9F3NO2
Molecular weight: 280.222 g/mol
DrugBank ID: -
Buried Surface Area:67.62 %
Polar Surface area: 52.16 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 1
Rings: 2
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
-16.64143.39-17.0021


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
C05CD2LEU- 543.640Hydrophobic
O15OHTYR- 552.53154.06H-Bond
(Protein Donor)
O15NE2HIS- 1173.1125.48H-Bond
(Protein Donor)
C10CEMET- 1203.90Hydrophobic
F20CEMET- 1203.510Hydrophobic
F18CBASN- 1673.70Hydrophobic
C03CH2TRP- 2273.330Hydrophobic
F18CD2PHE- 3064.350Hydrophobic
F20CE2PHE- 3063.490Hydrophobic
DuArDuArPHE- 3063.480Aromatic Face/Face
F19CGPRO- 3183.920Hydrophobic
F20CGPRO- 3184.330Hydrophobic
F18CE2TYR- 3193.60Hydrophobic