scPDB - 2ydk entry

Protein Data Bank Entry:

PDB ID : 2ydk

Resolution :1.900 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:	27.606
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.747	361.125

% Hydrophobic	% Polar
54.21	45.79
According to VolSite

Ligand :

HET Code:	YDK
Formula:	C17H21N4O2S
Molecular weight:	345.439 g/mol
DrugBank ID:	-
Buried Surface Area:	62.72 %
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
2.75929	73.7498	11.356

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
S01	CD1	LEU- 15	4	0	Hydrophobic	false
C19	CD2	LEU- 15	4	0	Hydrophobic	false
C18	CG2	VAL- 23	4.42	0	Hydrophobic	false
N08	O	GLU- 85	2.77	159.56	H-Bond (Ligand Donor)	false
O09	N	CYS- 87	2.84	168.19	H-Bond (Protein Donor)	false
N15	O	GLU- 134	2.83	133.34	H-Bond (Ligand Donor)	false
S01	CD1	LEU- 137	4.18	0	Hydrophobic	false
N15	OD2	ASP- 148	2.73	137.42	H-Bond (Ligand Donor)	false
N15	OD2	ASP- 148	2.73	0	Ionic (Ligand Cationic)	false