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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:

4ira

2.200 Å

X-ray

2013-01-14

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:4-hydroxyphenylacetate 3-monooxygenase
ID:Q8YHT7_BRUME
AC:Q8YHT7
Organism:Brucella melitensis biotype 1
Reign:Bacteria
TaxID:224914
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:17.843
Number of residues:17
Including
Standard Amino Acids: 16
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors: FAD
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.678398.250

% Hydrophobic% Polar
44.9255.08
According to VolSite

Ligand :
4ira_1 Structure
HET Code: FAD
Formula: C27H31N9O15P2
Molecular weight: 783.534 g/mol
DrugBank ID: DB03147
Buried Surface Area:35.44 %
Polar Surface area: 381.7 Å2
Number of
H-Bond Acceptors: 22
H-Bond Donors: 7
Rings: 6
Aromatic rings: 3
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 3
Rotatable Bonds: 13

Mass center Coordinates

XYZ
-12.7392-37.015.78228


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
C5'CBARG- 203.950Hydrophobic
O4NE2HIS- 1423.48167.32H-Bond
(Protein Donor)
O1PNEARG- 1663.28170.69H-Bond
(Protein Donor)
O1PCZARG- 1663.960Ionic
(Protein Cationic)
C6C1'FAD- 2024.120Hydrophobic
C7MC9FAD- 2024.260Hydrophobic
C9C7MFAD- 2024.250Hydrophobic
C1'C6FAD- 2024.350Hydrophobic
C8MC8MFAD- 2023.810Hydrophobic