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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:

1hsk

2.300 Å

X-ray

2000-12-27

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:UDP-N-acetylenolpyruvoylglucosamine reductase
ID:MURB_STAAU
AC:P61431
Organism:Staphylococcus aureus
Reign:Bacteria
TaxID:1280
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:26.375
Number of residues:59
Including
Standard Amino Acids: 54
Non Standard Amino Acids: 0
Water Molecules: 5
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.1021302.750

% Hydrophobic% Polar
41.4558.55
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median1hskHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
1hsk_1 Structure
HET Code: FAD
Formula: C27H31N9O15P2
Molecular weight: 783.534 g/mol
DrugBank ID: DB03147
Buried Surface Area:78.27 %
Polar Surface area: 381.7 Å2
Number of
H-Bond Acceptors: 22
H-Bond Donors: 7
Rings: 6
Aromatic rings: 3
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 3
Rotatable Bonds: 13

Mass center Coordinates

XYZ
179.772149.015163.653
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median1hskRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation80102030Highcharts.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
C8MCE2TYR- 423.30Hydrophobic
O2BOTYR- 772.68154.76H-Bond
(Ligand Donor)
O1ANGLY- 792.86142.53H-Bond
(Protein Donor)
O1PNASN- 802.98169.42H-Bond
(Protein Donor)
O1ANGLY- 812.72144.17H-Bond
(Protein Donor)
C2'CBSER- 824.290Hydrophobic
O2'OGSER- 822.93151.05H-Bond
(Ligand Donor)
O2PNSER- 822.83156.71H-Bond
(Protein Donor)
O2ANASN- 832.73153.71H-Bond
(Protein Donor)
C5BCBASN- 834.190Hydrophobic
C5'CBASN- 834.060Hydrophobic
C2'CBASN- 833.910Hydrophobic
C5BCD1ILE- 844.080Hydrophobic
C3BCG2ILE- 843.920Hydrophobic
C7CGPRO- 1413.730Hydrophobic
C8CGPRO- 1413.790Hydrophobic
C8CGPRO- 1413.790Hydrophobic
O1PNSER- 1432.92168.72H-Bond
(Protein Donor)
O1POGSER- 1432.69165.27H-Bond
(Protein Donor)
C4BCE2TYR- 1493.790Hydrophobic
C3BCZTYR- 1494.310Hydrophobic
C1BCD1TYR- 1493.720Hydrophobic
O3BOHTYR- 1493.26120.74H-Bond
(Ligand Donor)
O2NGLY- 1532.88150.86H-Bond
(Protein Donor)
N3OGLY- 1532.65169.08H-Bond
(Ligand Donor)
N6AOVAL- 1993.05161.69H-Bond
(Ligand Donor)
N1ANVAL- 1992.79170.95H-Bond
(Protein Donor)
O4NH1ARG- 2253.07166.53H-Bond
(Protein Donor)
N5NH2ARG- 2253.23141.98H-Bond
(Protein Donor)
C7MCD2LEU- 2313.920Hydrophobic
C7MCE2PHE- 2743.330Hydrophobic
O4'OHOH- 5542.88163.34H-Bond
(Ligand Donor)