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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:

1zdw

2.020 Å

X-ray

2005-04-15

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Prenyltransferase
ID:Q4R2T2_STRC1
AC:Q4R2T2
Organism:Streptomyces sp.
Reign:Bacteria
TaxID:93372
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:23.861
Number of residues:21
Including
Standard Amino Acids: 21
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.0861242.000

% Hydrophobic% Polar
50.0050.00
According to VolSite

Ligand :
1zdw_1 Structure
HET Code: FLV
Formula: C10H4O5
Molecular weight: 204.136 g/mol
DrugBank ID: DB02521
Buried Surface Area:54.67 %
Polar Surface area: 100.49 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 1
Rings: 2
Aromatic rings: 1
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 0

Mass center Coordinates

XYZ
30.889129.67649.1218


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
CAKCGGLN- 1614.210Hydrophobic
CAFCEMET- 1623.570Hydrophobic
CAFCBTYR- 1754.180Hydrophobic
OACOGSER- 2142.89163.28H-Bond
(Protein Donor)
CAFCBSER- 2143.470Hydrophobic
OADOHTYR- 2882.71164.79H-Bond
(Ligand Donor)
OADNE2GLN- 2952.53137.62H-Bond
(Protein Donor)
CAOCD1LEU- 2984.350Hydrophobic