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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:

1pax

2.400 Å

X-ray

1996-05-06

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Poly [ADP-ribose] polymerase 1
ID:PARP1_CHICK
AC:P26446
Organism:Gallus gallus
Reign:Eukaryota
TaxID:9031
EC Number:2.4.2.30


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:23.261
Number of residues:16
Including
Standard Amino Acids: 15
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.737810.000

% Hydrophobic% Polar
45.8354.17
According to VolSite

Ligand :
1pax_1 Structure
HET Code: DHQ
Formula: C10H11NO
Molecular weight: 161.200 g/mol
DrugBank ID: DB03722
Buried Surface Area:71.26 %
Polar Surface area: 29.1 Å2
Number of
H-Bond Acceptors: 1
H-Bond Donors: 1
Rings: 2
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 0

Mass center Coordinates

XYZ
41.414222.990821.6615


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
ONGLY- 8632.74171.95H-Bond
(Protein Donor)
N2OGLY- 8632.99152.98H-Bond
(Ligand Donor)
C9CD2TYR- 8963.490Hydrophobic
C5CBTYR- 8963.540Hydrophobic
C7CBALA- 8983.950Hydrophobic
C7CDLYS- 9034.110Hydrophobic
OOGSER- 9043.04151.81H-Bond
(Protein Donor)
C4CZTYR- 9073.710Hydrophobic
C9CZTYR- 9073.960Hydrophobic
C6CGGLU- 9883.860Hydrophobic