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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:

2vhq

2.150 Å

X-ray

2007-11-22

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:NTPase P4
ID:Q94M05_9VIRU
AC:Q94M05
Organism:Pseudomonas phage phi12
Reign:Viruses
TaxID:161736
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B40 %
C60 %


Ligand binding site composition:

B-Factor:51.133
Number of residues:40
Including
Standard Amino Acids: 34
Non Standard Amino Acids: 1
Water Molecules: 5
Cofactors:
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.466702.000

% Hydrophobic% Polar
37.5062.50
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median2vhqHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
2vhq_2 Structure
HET Code: ATP
Formula: C10H12N5O13P3
Molecular weight: 503.149 g/mol
DrugBank ID: DB00171
Buried Surface Area:57.91 %
Polar Surface area: 319.88 Å2
Number of
H-Bond Acceptors: 17
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
32.380552.193627.2349
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median2vhqRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation801020Highcharts.com


Binding mode :
What is Poseview ?
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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
O2BNTHR- 1372.92161.59H-Bond
(Protein Donor)
C5'CGPRO- 1384.020Hydrophobic
O3GND2ASN- 2342.75140.66H-Bond
(Protein Donor)
O1GCZARG- 2723.810Ionic
(Protein Cationic)
O2GCZARG- 2793.650Ionic
(Protein Cationic)
O1ACZARG- 2793.750Ionic
(Protein Cationic)
O1ANH2ARG- 2793.28137.63H-Bond
(Protein Donor)
O1ANEARG- 2793.41135.35H-Bond
(Protein Donor)
O3ANH2ARG- 2793.26158.42H-Bond
(Protein Donor)
C3'CGARG- 2794.480Hydrophobic
C1'CZTYR- 2884.10Hydrophobic
DuArDuArTYR- 2883.480Aromatic Face/Face
N7OGSER- 2922.78146.96H-Bond
(Protein Donor)
O1GMG MG- 13282.320Metal Acceptor
O2BMG MG- 13282.40Metal Acceptor
O3BMG MG- 13282.790Metal Acceptor
O2AMG MG- 13282.030Metal Acceptor
O3GOHOH- 21293.44179.98H-Bond
(Protein Donor)
O1AOHOH- 21702.77149.51H-Bond
(Protein Donor)