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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:

3bqr

1.750 Å

X-ray

2007-12-20

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Death-associated protein kinase 3
ID:DAPK3_HUMAN
AC:O43293
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:26.360
Number of residues:30
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.238850.500

% Hydrophobic% Polar
51.5948.41
According to VolSite

Ligand :
3bqr_1 Structure
HET Code: 4RB
Formula: C17H18N4O3
Molecular weight: 326.350 g/mol
DrugBank ID: DB07125
Buried Surface Area:63.8 %
Polar Surface area: 103.83 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 3
Rings: 3
Aromatic rings: 3
Anionic atoms: 1
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 6

Mass center Coordinates

XYZ
3.8272543.74335.5442


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
C1LCBLEU- 194.380Hydrophobic
C1LCBVAL- 273.880Hydrophobic
C1ACG2VAL- 273.960Hydrophobic
C1HCG2VAL- 274.130Hydrophobic
C1SCBALA- 404.230Hydrophobic
O1DNZLYS- 422.8156.71H-Bond
(Protein Donor)
O1DNZLYS- 422.80Ionic
(Protein Cationic)
C1GCG1ILE- 774.020Hydrophobic
C1ECD1LEU- 933.850Hydrophobic
N1NNVAL- 962.94172.11H-Bond
(Protein Donor)
O1COE2GLU- 1002.89171.03H-Bond
(Ligand Donor)
C1MSDMET- 1464.310Hydrophobic
C1SSDMET- 1463.930Hydrophobic
C1GCG2ILE- 1603.80Hydrophobic
C1MCD1ILE- 1604.310Hydrophobic
C1ECBILE- 1603.620Hydrophobic
C1FCD1ILE- 1604.050Hydrophobic
O1BNASP- 1612.92149.28H-Bond
(Protein Donor)
O1BOHOH- 6372.69159.51H-Bond
(Protein Donor)