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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:

4dsg

2.250 Å

X-ray

2012-02-18

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Uncharacterized protein
ID:Q4E1W2_TRYCC
AC:Q4E1W2
Organism:Trypanosoma cruzi
Reign:Eukaryota
TaxID:353153
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:24.489
Number of residues:65
Including
Standard Amino Acids: 59
Non Standard Amino Acids: 1
Water Molecules: 5
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.2001211.625

% Hydrophobic% Polar
41.5058.50
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median4dsgHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
4dsg_1 Structure
HET Code: FAD
Formula: C27H31N9O15P2
Molecular weight: 783.534 g/mol
DrugBank ID: DB03147
Buried Surface Area:68.83 %
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
70.009-15.7632-28.8423
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median4dsgRingsAromatic 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
C4'CGPRO- 163.790Hydrophobic
O1POG1THR- 172.59166.18H-Bond
(Protein Donor)
O2PNTHR- 173.17150.73H-Bond
(Protein Donor)
O3BOE1GLU- 372.66161.97H-Bond
(Ligand Donor)
O3BOE2GLU- 373.23128.5H-Bond
(Ligand Donor)
O2BOE2GLU- 372.65158.21H-Bond
(Ligand Donor)
O2ANLEU- 453.02166.47H-Bond
(Protein Donor)
C2'CBLEU- 454.480Hydrophobic
O4'OGSER- 463.1152.8H-Bond
(Protein Donor)
DuArDuArHIS- 623.920Aromatic Face/Face
N3OVAL- 632.78150.85H-Bond
(Ligand Donor)
O4NVAL- 632.86163.67H-Bond
(Protein Donor)
N6AOALA- 2362.99162.19H-Bond
(Ligand Donor)
N1ANALA- 2362.9157.74H-Bond
(Protein Donor)
C7MCG2THR- 2953.930Hydrophobic
C7MCE2TYR- 3954.380Hydrophobic
C1'CDARG- 4234.270Hydrophobic
C3'CDARG- 4233.930Hydrophobic
C5'CBARG- 4233.780Hydrophobic
O1PNARG- 4232.91150.69H-Bond
(Protein Donor)
O3'OGLY- 4322.63163.23H-Bond
(Ligand Donor)
N1NGLN- 4343.36130.33H-Bond
(Protein Donor)
O2NGLN- 4342.76164.96H-Bond
(Protein Donor)
C2'CGGLN- 43440Hydrophobic
O3'OGSER- 4373.22156.26H-Bond
(Protein Donor)
C5'CBSER- 4373.880Hydrophobic
O3BOHOH- 6032.94135.87H-Bond
(Protein Donor)
O2POHOH- 6202.75179.98H-Bond
(Protein Donor)
O1POHOH- 6222.84179.96H-Bond
(Protein Donor)