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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:

4wf0

1.950 Å

X-ray

2014-09-11

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:NPH1-1
ID:O49003_AVESA
AC:O49003
Organism:Avena sativa
Reign:Eukaryota
TaxID:4498
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A91 %
B9 %


Ligand binding site composition:

B-Factor:23.318
Number of residues:36
Including
Standard Amino Acids: 34
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors: FMN
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.5421971.000

% Hydrophobic% Polar
36.3063.70
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median4wf0HydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
4wf0_1 Structure
HET Code: FMN
Formula: C17H19N4O9P
Molecular weight: 454.328 g/mol
DrugBank ID: DB03247
Buried Surface Area:76.53 %
Polar Surface area: 217.05 Å2
Number of
H-Bond Acceptors: 12
H-Bond Donors: 4
Rings: 3
Aromatic rings: 1
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 7

Mass center Coordinates

XYZ
-2.984588.46855-0.775258
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median4wf0RingsAromatic 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
C6CG2VAL- 4163.490Hydrophobic
C7MCG2THR- 4183.360Hydrophobic
O2'OD1ASN- 4492.89155.79H-Bond
(Ligand Donor)
C9ACBCYS- 4503.820Hydrophobic
C2'CBCYS- 4504.360Hydrophobic
C6SGCYS- 4503.630Hydrophobic
C2'CBARG- 4514.290Hydrophobic
O3PNH1ARG- 4513.49166.29H-Bond
(Protein Donor)
O2NE2GLN- 4543.29153.82H-Bond
(Protein Donor)
O4'NE2GLN- 4542.65170.57H-Bond
(Protein Donor)
C5'CG1VAL- 4633.820Hydrophobic
C1'CG2ILE- 4663.840Hydrophobic
C4'CG2ILE- 4664.430Hydrophobic
C5'CBARG- 4673.80Hydrophobic
O5'NH1ARG- 4672.85147.19H-Bond
(Protein Donor)
C3'CD1ILE- 4704.460Hydrophobic
C8MCD1ILE- 4703.860Hydrophobic
O2ND2ASN- 4823146.87H-Bond
(Protein Donor)
N3OD1ASN- 4822.84177.26H-Bond
(Ligand Donor)
O4ND2ASN- 4923.34132.65H-Bond
(Protein Donor)
C8CD1LEU- 4963.780Hydrophobic
C7MCBPHE- 5093.80Hydrophobic
C8MCBPHE- 50940Hydrophobic
O4NE2GLN- 5133.12149.37H-Bond
(Protein Donor)