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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:

4g1c

1.940 Å

X-ray

2012-07-10

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:NAD-dependent protein deacylase sirtuin-5, mitochondrial
ID:SIR5_HUMAN
AC:Q9NXA8
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A98 %
B2 %


Ligand binding site composition:

B-Factor:33.697
Number of residues:51
Including
Standard Amino Acids: 45
Non Standard Amino Acids: 0
Water Molecules: 6
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.1571107.000

% Hydrophobic% Polar
47.8752.13
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median4g1cHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
4g1c_1 Structure
HET Code: CNA
Formula: C22H28N7O13P2
Molecular weight: 660.444 g/mol
DrugBank ID: DB02498
Buried Surface Area:73.9 %
Polar Surface area: 334.31 Å2
Number of
H-Bond Acceptors: 17
H-Bond Donors: 6
Rings: 5
Aromatic rings: 3
Anionic atoms: 2
Cationic atoms: 1
Rule of Five Violation: 3
Rotatable Bonds: 11

Mass center Coordinates

XYZ
18.58555.6029520.8205
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median4g1cRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation801020Highcharts.com


Binding mode :
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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
O1ANALA- 592.72159.75H-Bond
(Protein Donor)
C5BCBALA- 594.160Hydrophobic
C2DCBALA- 594.140Hydrophobic
C4NCBALA- 593.910Hydrophobic
N6AOE1GLU- 643.04150.64H-Bond
(Ligand Donor)
C4NCG1VAL- 674.330Hydrophobic
C5BCG2THR- 694.190Hydrophobic
O2NNPHE- 702.76161.68H-Bond
(Protein Donor)
C4'CE1PHE- 703.430Hydrophobic
C5NCE2PHE- 703.30Hydrophobic
C5DCD1PHE- 703.720Hydrophobic
C5BCGARG- 713.960Hydrophobic
C3BCGARG- 714.010Hydrophobic
O2ANE2GLN- 1403.04164.6H-Bond
(Protein Donor)
O2DNE2GLN- 1403.39163.47H-Bond
(Protein Donor)
C3DCBGLN- 1404.360Hydrophobic
O2DOD1ASN- 1413.08138.87H-Bond
(Ligand Donor)
O7NNILE- 1423.05141.54H-Bond
(Protein Donor)
N7NOD2ASP- 1432.79164.38H-Bond
(Ligand Donor)
O3DND1HIS- 1583.48120.12H-Bond
(Protein Donor)
C4DCZPHE- 2234.270Hydrophobic
O2ANSER- 2512.9171.38H-Bond
(Protein Donor)
O2AOGSER- 2512.72174.21H-Bond
(Protein Donor)
C3BCBSER- 2514.10Hydrophobic
C3DCG2VAL- 2544.10Hydrophobic
O3BND2ASN- 2752.73156.67H-Bond
(Protein Donor)
O2BOD1ASN- 2752.93158.64H-Bond
(Ligand Donor)
O2BOG1THR- 2763.39122.2H-Bond
(Protein Donor)
N1ANCYS- 2932.84155.44H-Bond
(Protein Donor)