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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:

1wy7

2.200 Å

X-ray

2005-02-08

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Uncharacterized protein
ID:O59611_PYRHO
AC:O59611
Organism:Pyrococcus horikoshii
Reign:Archaea
TaxID:70601
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
C100 %


Ligand binding site composition:

B-Factor:46.709
Number of residues:37
Including
Standard Amino Acids: 36
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.201378.000

% Hydrophobic% Polar
42.8657.14
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median1wy7HydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
1wy7_2 Structure
HET Code: SAH
Formula: C14H20N6O5S
Molecular weight: 384.411 g/mol
DrugBank ID: DB01752
Buried Surface Area:78.8 %
Polar Surface area: 212.38 Å2
Number of
H-Bond Acceptors: 10
H-Bond Donors: 4
Rings: 3
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 1
Rule of Five Violation: 1
Rotatable Bonds: 7

Mass center Coordinates

XYZ
12.21217.146586.88219
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median1wy7RingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation80510Highcharts.com


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
CBCZPHE- 184.110Hydrophobic
C3'CZPHE- 184.320Hydrophobic
C2'CBLEU- 254.250Hydrophobic
O2'NE2GLN- 272.99168.65H-Bond
(Protein Donor)
C3'CGGLN- 273.850Hydrophobic
ONLEU- 633.27175.62H-Bond
(Protein Donor)
O3'OE1GLU- 792.96175.35H-Bond
(Ligand Donor)
O2'OE2GLU- 792.66151.7H-Bond
(Ligand Donor)
O2'OE1GLU- 793.42134.66H-Bond
(Ligand Donor)
N3NVAL- 803.48146.06H-Bond
(Protein Donor)
N6OD2ASP- 1052.91148.56H-Bond
(Ligand Donor)
N1NVAL- 1063.1148.87H-Bond
(Protein Donor)
CGCBASN- 1194.320Hydrophobic