scPDB - 4ek9 entry

Protein Data Bank Entry:

PDB ID : 4ek9

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2012-04-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	4.420	4.420	4.420	0.000	4.420	1

List of CHEMBLId :

CHEMBL472733

Binding Site :

Uniprot Annotation

Name:	Histone-lysine N-methyltransferase, H3 lysine-79 specific
ID:	DOT1L_HUMAN
AC:	Q8TEK3
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.1.1.43

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	56.191
Number of residues:	30
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.532	415.125

% Hydrophobic	% Polar
49.59	50.41
According to VolSite

Ligand :

HET Code:	EP4
Formula:	C12H19N6O3
Molecular weight:	295.318 g/mol
DrugBank ID:	-
Buried Surface Area:	69.66 %
Polar Surface area:	123.75 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
44.4165	48.3515	12.4104

Binding mode :

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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
O2'	OE1	GLU- 186	3.46	132.71	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 186	2.61	160.28	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 186	2.67	158.49	H-Bond (Ligand Donor)	false
O3'	OE2	GLU- 186	3.36	142.51	H-Bond (Ligand Donor)	false
N6	OD1	ASP- 222	3.02	161.09	H-Bond (Ligand Donor)	false
N1	N	PHE- 223	3.14	167.85	H-Bond (Protein Donor)	false
DuAr	DuAr	PHE- 223	3.86	0	Aromatic Face/Face	false