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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:

2bt4

1.700 Å

X-ray

2005-05-26

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:3-dehydroquinate dehydratase
ID:AROQ_STRCO
AC:P15474
Organism:Streptomyces coelicolor / M145)
Reign:Bacteria
TaxID:100226
EC Number:4.2.1.10


Chains:

Chain Name:Percentage of Residues
within binding site
J9 %
L91 %


Ligand binding site composition:

B-Factor:14.690
Number of residues:35
Including
Standard Amino Acids: 34
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.014364.500

% Hydrophobic% Polar
38.8961.11
According to VolSite

Ligand :
2bt4_11 Structure
HET Code: CA2
Formula: C16H21O6
Molecular weight: 309.334 g/mol
DrugBank ID: DB04656
Buried Surface Area:82.11 %
Polar Surface area: 110.05 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 3
Rings: 2
Aromatic rings: 1
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 6

Mass center Coordinates

XYZ
-1.43436-14.047524.5837


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
C10CBASN- 20163.460Hydrophobic
C12CD2LEU- 20174.380Hydrophobic
C9CD2LEU- 20173.840Hydrophobic
C16CBLEU- 20193.670Hydrophobic
C13CD1LEU- 20203.860Hydrophobic
C15CGARG- 20233.650Hydrophobic
C2CE2TYR- 20284.090Hydrophobic
C13CD1TYR- 20283.250Hydrophobic
C14CBTYR- 20283.940Hydrophobic
O2ND2ASN- 20792.74149.29H-Bond
(Protein Donor)
O3OD1ASN- 20792.81130.29H-Bond
(Ligand Donor)
C3CBALA- 20814.050Hydrophobic
C9CBALA- 20814.150Hydrophobic
O5NE2HIS- 20852.6169.56H-Bond
(Ligand Donor)
O2NILE- 21072.84159.78H-Bond
(Protein Donor)
O1OGSER- 21082.8157.09H-Bond
(Protein Donor)
O1NSER- 21082.96160.32H-Bond
(Protein Donor)
C6CG2ILE- 21103.790Hydrophobic
O5NH1ARG- 21173.13155.6H-Bond
(Protein Donor)
O4OD2ASP- 22922.66148.9H-Bond
(Ligand Donor)
C16CG2THR- 22964.350Hydrophobic