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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:

3l3m

2.500 Å

X-ray

2009-12-17

Activity from ChEMBL: What is pChEMBL ?
MinMeanMedianStandard DeviationMaxCount
pChEMBL:8.2208.2208.2200.0008.2201

List of CHEMBLId :

CHEMBL1089125


Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Poly [ADP-ribose] polymerase 1
ID:PARP1_HUMAN
AC:P09874
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.4.2.30


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:27.796
Number of residues:33
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.769867.375

% Hydrophobic% Polar
40.0859.92
According to VolSite

Ligand :
3l3m_1 Structure
HET Code: A92
Formula: C19H20FN4O
Molecular weight: 339.387 g/mol
DrugBank ID: -
Buried Surface Area:66.22 %
Polar Surface area: 88.38 Å2
Number of
H-Bond Acceptors: 2
H-Bond Donors: 3
Rings: 4
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
26.365111.22227.0235


Binding mode :
What is Poseview ?
  • 2D View
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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
C16CBALA- 1013.830Hydrophobic
C16CBGLU- 1024.090Hydrophobic
N22OD2ASP- 1053.240Ionic
(Ligand Cationic)
N23OGLY- 2022.91157.36H-Bond
(Ligand Donor)
O24NGLY- 2022.74166.99H-Bond
(Protein Donor)
FCD2TYR- 2284.240Hydrophobic
FCZTYR- 2353.420Hydrophobic
C11CBTYR- 2353.410Hydrophobic
C1CBALA- 2374.050Hydrophobic
C1CGLYS- 2423.770Hydrophobic
O24OGSER- 2433.18156.84H-Bond
(Protein Donor)
C5CBGLU- 3274.110Hydrophobic