scPDB - 2ym5 entry

Protein Data Bank Entry:

PDB ID : 2ym5

Resolution :2.030 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:	36.450
Number of residues:	26
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.909	462.375

% Hydrophobic	% Polar
48.18	51.82
According to VolSite

Ligand :

HET Code:	YM5
Formula:	C18H22N5O2
Molecular weight:	340.400 g/mol
DrugBank ID:	-
Buried Surface Area:	56.52 %
Polar Surface area:	101.91 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
15.7941	-1.51492	11.4765

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
C04	CB	LEU- 15	4.2	0	Hydrophobic	false
C23	CB	LEU- 15	4.2	0	Hydrophobic	false
C23	CB	VAL- 23	3.87	0	Hydrophobic	false
C24	CG2	VAL- 23	4.12	0	Hydrophobic	false
C16	CG2	VAL- 23	3.63	0	Hydrophobic	false
C22	CB	ALA- 36	4.44	0	Hydrophobic	false
C15	CD1	LEU- 84	3.65	0	Hydrophobic	false
N11	O	GLU- 85	2.76	160.83	H-Bond (Ligand Donor)	false
N09	N	CYS- 87	3.08	166.79	H-Bond (Protein Donor)	false
N01	OE1	GLU- 91	3	142.09	H-Bond (Ligand Donor)	false
N01	OE1	GLU- 91	3	0	Ionic (Ligand Cationic)	false
O20	OD1	ASN- 135	2.78	142.13	H-Bond (Ligand Donor)	false
C22	CD1	LEU- 137	3.42	0	Hydrophobic	false
C21	CD1	LEU- 137	3.9	0	Hydrophobic	false
O20	OG	SER- 147	3.28	162.02	H-Bond (Protein Donor)	false
C21	CB	SER- 147	4.4	0	Hydrophobic	false
C19	CB	ASP- 148	4.31	0	Hydrophobic	false
C17	CB	ASP- 148	4.14	0	Hydrophobic	false