scPDB - 4bdb entry

Protein Data Bank Entry:

PDB ID : 4bdb

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2012-10-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Serine/threonine-protein kinase Chk2
ID:	CHK2_HUMAN
AC:	O96017
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.11.1

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	68.779
Number of residues:	19
Including
Standard Amino Acids:	19
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.112	573.750

% Hydrophobic	% Polar
61.18	38.82
According to VolSite

Ligand :

HET Code:	ODO
Formula:	C8H9NO3
Molecular weight:	167.162 g/mol
DrugBank ID:	-
Buried Surface Area:	59.45 %
Polar Surface area:	73.05 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	1
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	1

Mass center Coordinates

X	Y	Z
-37.5218	33.7085	7.46458

Binding mode :

What is Poseview ?

2D View
3D View

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

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
C1	CG1	VAL- 234	3.59	0	Hydrophobic	false
C8	CB	ALA- 247	3.72	0	Hydrophobic	false
C3	CB	ALA- 247	4.29	0	Hydrophobic	false
C8	CD1	ILE- 286	4.44	0	Hydrophobic	false
C8	CB	LEU- 301	3.72	0	Hydrophobic	false
O10	N	MET- 304	2.88	140.91	H-Bond (Protein Donor)	false
C3	CB	MET- 304	4.02	0	Hydrophobic	false
C8	CD1	LEU- 354	4.05	0	Hydrophobic	false
C2	CD1	LEU- 354	3.93	0	Hydrophobic	false
C1	CD2	LEU- 354	4.23	0	Hydrophobic	false