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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:

3t4h

1.650 Å

X-ray

2011-07-26

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Alpha-ketoglutarate-dependent dioxygenase AlkB
ID:ALKB_ECOLI
AC:P05050
Organism:Escherichia coli
Reign:Bacteria
TaxID:83333
EC Number:1.14.11.33


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:21.556
Number of residues:40
Including
Standard Amino Acids: 37
Non Standard Amino Acids: 1
Water Molecules: 2
Cofactors:
Metals: FE

Cavity properties

LigandabilityVolume (Å3)
0.842617.625

% Hydrophobic% Polar
48.0951.91
According to VolSite

Ligand :
3t4h_1 Structure
HET Code: MD5
Formula: C12H10N2O7S
Molecular weight: 326.282 g/mol
DrugBank ID: -
Buried Surface Area:78.82 %
Polar Surface area: 180.48 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 1
Rings: 1
Aromatic rings: 1
Anionic atoms: 3
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 8

Mass center Coordinates

XYZ
-2.930142.668363.50059


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
OAJND2ASN- 1203.11143.9H-Bond
(Protein Donor)
OND2ASN- 1202.85165.84H-Bond
(Protein Donor)
OOHTYR- 1222.5163.18H-Bond
(Protein Donor)
CAOCG2ILE- 1434.140Hydrophobic
CAPCD1ILE- 1433.970Hydrophobic
SALCBSER- 1453.940Hydrophobic
CAMCE1PHE- 1543.550Hydrophobic
CASCZPHE- 1543.360Hydrophobic
CAMCE2TRP- 1784.160Hydrophobic
CASCE2TRP- 1783.470Hydrophobic
CAQCBTRP- 1783.770Hydrophobic
CASCBHIS- 1874.050Hydrophobic
DuArDuArHIS- 1873.60Aromatic Face/Face
OXTNH1ARG- 2042.9152.88H-Bond
(Protein Donor)
OXTNH2ARG- 2043.11140.94H-Bond
(Protein Donor)
OXTCZARG- 2043.440Ionic
(Protein Cationic)
CBCG2THR- 2083.520Hydrophobic
OAHFE FE- 3002.180Metal Acceptor
OAIFE FE- 3002.170Metal Acceptor