scPDB - 2yit entry

Protein Data Bank Entry:

PDB ID : 2yit

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2011-05-16

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:	45.196
Number of residues:	34
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.037	874.125

% Hydrophobic	% Polar
49.03	50.97
According to VolSite

Ligand :

HET Code:	YIT
Formula:	C21H25N6O2
Molecular weight:	393.462 g/mol
DrugBank ID:	-
Buried Surface Area:	58.4 %
Polar Surface area:	130.12 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	5
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
47.6892	-14.5007	-10.3665

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
CAO	CD2	LEU- 226	4.27	0	Hydrophobic	false
CAK	CD1	LEU- 226	4.04	0	Hydrophobic	false
CAG	CB	LEU- 226	3.86	0	Hydrophobic	false
CAV	CG2	VAL- 234	4.25	0	Hydrophobic	false
CAR	CB	LYS- 249	4.25	0	Hydrophobic	false
CAS	CG	LYS- 249	3.93	0	Hydrophobic	false
CAU	CD	LYS- 249	3.83	0	Hydrophobic	false
CBA	CG	GLU- 273	4.11	0	Hydrophobic	false
NAD	OE2	GLU- 273	2.89	150.55	H-Bond (Ligand Donor)	false
NAF	OE1	GLU- 273	2.79	176.12	H-Bond (Ligand Donor)	false
NAF	OE2	GLU- 273	3.46	127.29	H-Bond (Ligand Donor)	false
CBA	CD1	ILE- 274	4.11	0	Hydrophobic	false
CBA	CD1	LEU- 277	3.64	0	Hydrophobic	false
CAX	CD1	ILE- 286	3.87	0	Hydrophobic	false
CBA	CD1	ILE- 286	4.2	0	Hydrophobic	false
CBA	CD1	ILE- 288	3.74	0	Hydrophobic	false
CAZ	CD1	ILE- 299	4.17	0	Hydrophobic	false
CBA	CG2	ILE- 299	4.06	0	Hydrophobic	false
CAR	CD1	LEU- 301	4.02	0	Hydrophobic	false
CAS	CD2	LEU- 301	4.17	0	Hydrophobic	false
CAK	CD1	LEU- 303	4.33	0	Hydrophobic	false
CAR	CD1	LEU- 354	4.44	0	Hydrophobic	false
CAV	CG2	THR- 367	3.93	0	Hydrophobic	false
CAT	CB	THR- 367	4.39	0	Hydrophobic	false
CAU	CB	ASP- 368	4.32	0	Hydrophobic	false
OBC	O	HOH- 2035	3.09	164.52	H-Bond (Protein Donor)	false