scPDB - 2ydj entry

Protein Data Bank Entry:

PDB ID : 2ydj

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2011-03-22

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 Chk1
ID:	CHK1_HUMAN
AC:	O14757
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:	29.941
Number of residues:	29
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.741	600.750

% Hydrophobic	% Polar
50.56	49.44
According to VolSite

Ligand :

HET Code:	YDJ
Formula:	C17H20FN4O2S
Molecular weight:	363.430 g/mol
DrugBank ID:	DB12242
Buried Surface Area:	58.26 %
Polar Surface area:	129.07 Å2

Number of
H-Bond Acceptors:	2
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
4.11456	-3.32404	45.0858

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
C4	CB	LEU- 15	3.93	0	Hydrophobic	false
S1	CB	LEU- 15	4.12	0	Hydrophobic	false
C3	CD2	LEU- 15	3.96	0	Hydrophobic	false
C13	CZ	TYR- 20	3.69	0	Hydrophobic	false
C14	CE2	TYR- 20	3.73	0	Hydrophobic	false
C13	CG2	VAL- 23	4.12	0	Hydrophobic	false
N4	O	GLU- 85	2.95	165.4	H-Bond (Ligand Donor)	false
O2	N	CYS- 87	2.78	174.83	H-Bond (Protein Donor)	false
N2	O	GLU- 134	2.82	140.79	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 148	2.78	151.28	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 148	2.78	0	Ionic (Ligand Cationic)	false