Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

4h6p

2.560 Å

X-ray

2012-09-19

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Chromate reductase
ID:D5QFC5_KOMHA
AC:D5QFC5
Organism:Komagataeibacter hansenii ATCC 23769
Reign:Bacteria
TaxID:714995
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
H19 %
I81 %


Ligand binding site composition:

B-Factor:89.522
Number of residues:41
Including
Standard Amino Acids: 39
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.772867.375

% Hydrophobic% Polar
38.9161.09
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median4h6pHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
4h6p_6 Structure
HET Code: FMN
Formula: C17H19N4O9P
Molecular weight: 454.328 g/mol
DrugBank ID: DB03247
Buried Surface Area:60.54 %
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
-62.49238.845823.5141
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median4h6pRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation8051015Highcharts.com


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
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
O2POGSER- 152.73168.76H-Bond
(Protein Donor)
O4'NH2ARG- 173.38135.68H-Bond
(Protein Donor)
O1PNH2ARG- 172.63140.83H-Bond
(Protein Donor)
O2PNEARG- 173.15153.39H-Bond
(Protein Donor)
O1PCZARG- 173.490Ionic
(Protein Cationic)
O2PCZARG- 173.950Ionic
(Protein Cationic)
O3POGSER- 202.7174.92H-Bond
(Protein Donor)
O1PNPHE- 213.09158.73H-Bond
(Protein Donor)
O3PNASN- 223163.94H-Bond
(Protein Donor)
O3PND2ASN- 222.77171.15H-Bond
(Protein Donor)
C8MCE2TYR- 513.570Hydrophobic
C5'CBPRO- 823.920Hydrophobic
N3OE2GLU- 832.81129.54H-Bond
(Ligand Donor)
C7MCGTYR- 844.320Hydrophobic
C8MCE1TYR- 844.420Hydrophobic
C5'CE1TYR- 844.470Hydrophobic
C6CBTYR- 843.780Hydrophobic
N5NASN- 852.76159.51H-Bond
(Protein Donor)
O4NTYR- 862.69161.43H-Bond
(Protein Donor)
C7MCBASP- 974.460Hydrophobic
O2OGSER- 1183.1153.88H-Bond
(Protein Donor)
C3'CGPRO- 1193.980Hydrophobic
C1'CG1VAL- 1673.790Hydrophobic
C3'CG1VAL- 1674.460Hydrophobic
O2OHOH- 3082.84179.96H-Bond
(Protein Donor)