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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:

2a5y

2.600 Å

X-ray

2005-07-01

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Cell death protein 4
ID:CED4_CAEEL
AC:P30429
Organism:Caenorhabditis elegans
Reign:Eukaryota
TaxID:6239
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:75.693
Number of residues:40
Including
Standard Amino Acids: 39
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.5371971.000

% Hydrophobic% Polar
50.6849.32
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median2a5yHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy80204060Highcharts.com
Ligand :
2a5y_1 Structure
HET Code: ATP
Formula: C10H12N5O13P3
Molecular weight: 503.149 g/mol
DrugBank ID: DB00171
Buried Surface Area:74.05 %
Polar Surface area: 319.88 Å2
Number of
H-Bond Acceptors: 17
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
96.014548.621575.4147
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median2a5yRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation801020Highcharts.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
N6OTYR- 1312.91160.61H-Bond
(Ligand Donor)
O1GNGLY- 1623.28160.37H-Bond
(Protein Donor)
O2BNGLY- 1623.27137.15H-Bond
(Protein Donor)
O3BNGLY- 1623.26125.79H-Bond
(Protein Donor)
O2BNGLY- 1643.19158.78H-Bond
(Protein Donor)
O2BNLYS- 1653.21163.68H-Bond
(Protein Donor)
O1BNSER- 1663.1165.46H-Bond
(Protein Donor)
O1ANVAL- 1673.01161.77H-Bond
(Protein Donor)
C5'CG2VAL- 1673.380Hydrophobic
O3GNH2ARG- 2732.71172.37H-Bond
(Protein Donor)
O3GNEARG- 2733.42130.51H-Bond
(Protein Donor)
O3GCZARG- 2733.490Ionic
(Protein Cationic)
C1'CBPRO- 3304.130Hydrophobic
C4'CBALA- 3314.180Hydrophobic
C1'CBMET- 3344.50Hydrophobic
C2'CGPRO- 3684.350Hydrophobic
O3GOHTYR- 3692.62139.91H-Bond
(Protein Donor)
C3'CBTYR- 3693.50Hydrophobic
C4'CD1TYR- 3693.530Hydrophobic
O2GMG MG- 5502.30Metal Acceptor
O1BMG MG- 5502.370Metal Acceptor