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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:

5iw5

2.700 Å

X-ray

2016-03-22

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:NADH pyrophosphatase
ID:D6JHV3_ECOLX
AC:D6JHV3
Organism:Escherichia coli B354
Reign:Bacteria
TaxID:550677
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:56.703
Number of residues:29
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.0011269.000

% Hydrophobic% Polar
46.0153.99
According to VolSite

Ligand :
5iw5_2 Structure
HET Code: NMN
Formula: C11H14N2O8P
Molecular weight: 333.211 g/mol
DrugBank ID: DB03227
Buried Surface Area:52.41 %
Polar Surface area: 178.89 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 3
Rings: 2
Aromatic rings: 1
Anionic atoms: 2
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
140.0728.8874536.5649


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
O2RNH1ARG- 692.54128.97H-Bond
(Protein Donor)
C5RCD2TRP- 1944.220Hydrophobic
C4RCE2TRP- 1943.680Hydrophobic
C3RCZ2TRP- 1944.350Hydrophobic
C5RCEMET- 2013.290Hydrophobic
C4CBPRO- 2354.430Hydrophobic
C5CBTHR- 2393.680Hydrophobic
C4CBTHR- 2393.830Hydrophobic
C5CBVAL- 2404.080Hydrophobic
C4CBALA- 2413.40Hydrophobic