scPDB - 2ym8 entry

Protein Data Bank Entry:

PDB ID : 2ym8

Resolution :2.070 Å

Experimental Method : X-ray

Deposition Date : 2011-06-06

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:	34.363
Number of residues:	29
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.862	344.250

% Hydrophobic	% Polar
55.88	44.12
According to VolSite

Ligand :

HET Code:	YM8
Formula:	C19H20ClN6O
Molecular weight:	383.855 g/mol
DrugBank ID:	-
Buried Surface Area:	64.41 %
Polar Surface area:	88.16 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
15.5114	-0.92863	11.1106

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
CAA	CB	LEU- 15	4.22	0	Hydrophobic	false
CAL	CD1	LEU- 15	4.27	0	Hydrophobic	false
CAS	CD2	LEU- 15	4.34	0	Hydrophobic	false
CAY	CD1	LEU- 15	4.28	0	Hydrophobic	false
CAI	CB	LEU- 15	4.01	0	Hydrophobic	false
CAA	CG1	VAL- 23	3.96	0	Hydrophobic	false
NAD	NZ	LYS- 38	3.14	172.47	H-Bond (Protein Donor)	false
NAQ	O	GLU- 85	3.24	165.84	H-Bond (Ligand Donor)	false
CL	CE1	TYR- 86	3.67	0	Hydrophobic	false
NAO	N	CYS- 87	2.97	168.01	H-Bond (Protein Donor)	false
CAL	CD1	LEU- 137	3.6	0	Hydrophobic	false