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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:

5fit

2.300 Å

X-ray

1997-09-25

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Bis(5'-adenosyl)-triphosphatase
ID:FHIT_HUMAN
AC:P49789
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:3.6.1.29


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:30.645
Number of residues:27
Including
Standard Amino Acids: 27
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.690442.125

% Hydrophobic% Polar
51.9148.09
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median5fitHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
5fit_1 Structure
HET Code: AP2
Formula: C11H14N5O9P2
Molecular weight: 422.204 g/mol
DrugBank ID: DB03148
Buried Surface Area:58.16 %
Polar Surface area: 251.48 Å2
Number of
H-Bond Acceptors: 13
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 3
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 6

Mass center Coordinates

XYZ
8.3124821.618124.7723
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median5fitRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation8051015Highcharts.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
O3'ND2ASN- 272.74132.13H-Bond
(Protein Donor)
C4'CD1LEU- 374.140Hydrophobic
C1'CD1LEU- 373.860Hydrophobic
O1ANE2GLN- 832.54143.34H-Bond
(Protein Donor)
C3ACG2THR- 9140Hydrophobic
O2ANTHR- 913.16145.4H-Bond
(Protein Donor)
O2ANVAL- 923.32143.5H-Bond
(Protein Donor)
C5'CG1VAL- 923.760Hydrophobic
O5'NE2HIS- 962.81168.62H-Bond
(Protein Donor)
O1ANE2HIS- 982.91164.62H-Bond
(Protein Donor)