scPDB - 2ym3 entry

Protein Data Bank Entry:

PDB ID : 2ym3

Resolution :2.010 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:	44.610
Number of residues:	22
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.906	405.000

% Hydrophobic	% Polar
51.67	48.33
According to VolSite

Ligand :

HET Code:	YM3
Formula:	C14H21N5O3
Molecular weight:	307.348 g/mol
DrugBank ID:	-
Buried Surface Area:	56.04 %
Polar Surface area:	109.23 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	2
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
17.5837	-1.31945	10.1649

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
NAA	O	LEU- 15	3.11	139.34	H-Bond (Ligand Donor)	false
CAR	CD1	LEU- 15	3.82	0	Hydrophobic	false
CAK	CB	LEU- 15	3.85	0	Hydrophobic	false
CAT	CG1	VAL- 23	4.43	0	Hydrophobic	false
CAK	CB	VAL- 23	3.72	0	Hydrophobic	false
CAT	CB	ALA- 36	4.33	0	Hydrophobic	false
NAO	O	GLU- 85	2.94	159.06	H-Bond (Ligand Donor)	false
NAN	N	CYS- 87	2.96	177.98	H-Bond (Protein Donor)	false
CAL	CG	GLU- 91	4.45	0	Hydrophobic	false
NAA	OE2	GLU- 91	3.69	0	Ionic (Ligand Cationic)	false
CAL	CD2	LEU- 137	4.15	0	Hydrophobic	false
CAT	CD1	LEU- 137	3.47	0	Hydrophobic	false