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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:

2i14

2.900 Å

X-ray

2006-08-12

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Nicotinate-nucleotide pyrophosphorylase
ID:Q8TZS9_PYRFU
AC:Q8TZS9
Organism:Pyrococcus furiosus
Reign:Archaea
TaxID:186497
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
C73 %
D27 %


Ligand binding site composition:

B-Factor:57.615
Number of residues:33
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals: ZN

Cavity properties

LigandabilityVolume (Å3)
0.004644.625

% Hydrophobic% Polar
40.3159.69
According to VolSite

Ligand :
2i14_3 Structure
HET Code: PCP
Formula: C6H10O13P3
Molecular weight: 383.057 g/mol
DrugBank ID: DB03942
Buried Surface Area:56.38 %
Polar Surface area: 264.08 Å2
Number of
H-Bond Acceptors: 13
H-Bond Donors: 2
Rings: 1
Aromatic rings: 0
Anionic atoms: 5
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 7

Mass center Coordinates

XYZ
120.037145.657-117.072


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
C3CBPHE- 11343.50Hydrophobic
C4CD2PHE- 11343.820Hydrophobic
CPCBPHE- 11344.090Hydrophobic
C2CDARG- 11373.990Hydrophobic
O1BNHIS- 11782.78128.55H-Bond
(Protein Donor)
C4CBSER- 12684.210Hydrophobic
O3PNGLY- 12703.06151.14H-Bond
(Protein Donor)
O2PNGLY- 12893.17133.05H-Bond
(Protein Donor)
O1PNGLY- 12902.68175.5H-Bond
(Protein Donor)
O2BOHTYR- 14212.67168.82H-Bond
(Protein Donor)