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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:

2hr8

2.800 Å

X-ray

2006-07-20

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Diphthine synthase
ID:DPHB_PYRHO
AC:O58456
Organism:Pyrococcus horikoshii
Reign:Archaea
TaxID:70601
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A98 %
B2 %


Ligand binding site composition:

B-Factor:47.531
Number of residues:40
Including
Standard Amino Acids: 40
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.129506.250

% Hydrophobic% Polar
42.0058.00
According to VolSite

Ligand :
2hr8_1 Structure
HET Code: SAH
Formula: C14H20N6O5S
Molecular weight: 384.411 g/mol
DrugBank ID: DB01752
Buried Surface Area:73.48 %
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
-14.5622-27.928132.7468


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
N6OLEU- 103.49122.68H-Bond
(Ligand Donor)
C5'CBSER- 374.320Hydrophobic
CGCBSER- 373.610Hydrophobic
ONASP- 873.29130.92H-Bond
(Protein Donor)
NOVAL- 902.8172.29H-Bond
(Ligand Donor)
CBCBALA- 914.330Hydrophobic
SDCBALA- 914.340Hydrophobic
OOGSER- 1152.75148.85H-Bond
(Protein Donor)
OXTOGSER- 1153.17137.18H-Bond
(Protein Donor)
CBCG2ILE- 1164.310Hydrophobic
C1'CG1ILE- 1164.330Hydrophobic
OXTNILE- 1163.21174.67H-Bond
(Protein Donor)
SDCD1PHE- 1653.970Hydrophobic
C4'CD1PHE- 1653.760Hydrophobic
O3'NLEU- 1662.64135.57H-Bond
(Protein Donor)
N6OALA- 2092.51158.84H-Bond
(Ligand Donor)
N1NALA- 2092.77122.8H-Bond
(Protein Donor)
C2'CBPRO- 2333.50Hydrophobic
O3'OHIS- 2343.09158.88H-Bond
(Ligand Donor)
C1'CG1ILE- 2353.970Hydrophobic