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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:

4d9e

2.470 Å

X-ray

2012-01-11

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:D-cysteine desulfhydrase
ID:DCYD_SALTY
AC:Q8ZNT7
Organism:Salmonella typhimurium
Reign:Bacteria
TaxID:99287
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
C100 %


Ligand binding site composition:

B-Factor:16.364
Number of residues:42
Including
Standard Amino Acids: 39
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.611732.375

% Hydrophobic% Polar
41.4758.53
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median4d9eHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
4d9e_4 Structure
HET Code: LCS
Formula: C11H12N3O7P
Molecular weight: 329.203 g/mol
DrugBank ID: DB03787
Buried Surface Area:75.41 %
Polar Surface area: 166.04 Å2
Number of
H-Bond Acceptors: 9
H-Bond Donors: 2
Rings: 2
Aromatic rings: 1
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
24.367571.49078.70264
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median4d9eRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation80510Highcharts.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
O4PND2ASN- 503.29128.73H-Bond
(Protein Donor)
O1PNZLYS- 513.32161.9H-Bond
(Protein Donor)
O1PNZLYS- 513.320Ionic
(Protein Cationic)
O3PNZLYS- 512.890Ionic
(Protein Cationic)
OOGSER- 783.25150.09H-Bond
(Protein Donor)
O3ND2ASN- 792.69168.26H-Bond
(Protein Donor)
O2PNGLY- 1943165.24H-Bond
(Protein Donor)
O1POGSER- 1952.63164.06H-Bond
(Protein Donor)
O1PNSER- 1952.8140.19H-Bond
(Protein Donor)
CBCBSER- 1954.020Hydrophobic
O1PNALA- 1963.44133.18H-Bond
(Protein Donor)
O2PNALA- 1963.21148.8H-Bond
(Protein Donor)
O4POG1THR- 1983.46143.14H-Bond
(Protein Donor)
O3PNTHR- 1982.99155.3H-Bond
(Protein Donor)
O3POG1THR- 1982.57155.06H-Bond
(Protein Donor)
C2ACBTYR- 2873.690Hydrophobic
C3CBTYR- 2874.40Hydrophobic
C5ACD1TYR- 2874.110Hydrophobic
CBCE1TYR- 2873.780Hydrophobic
OGOHTYR- 2873.46161.83H-Bond
(Protein Donor)
DuArDuArTYR- 2873.610Aromatic Face/Face
C2ACG2THR- 2884.40Hydrophobic
N1OG1THR- 3152.76162.58H-Bond
(Protein Donor)
C2ACBTHR- 3154.020Hydrophobic
OOHOH- 5183.35159.68H-Bond
(Protein Donor)