scPDB - 4eki entry

Protein Data Bank Entry:

PDB ID : 4eki

Resolution :2.850 Å

Experimental Method : X-ray

Deposition Date : 2012-04-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	6.520	9.030	9.520	1.120	9.600	6

List of CHEMBLId :

CHEMBL2169919

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:	86.753
Number of residues:	41
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.384	988.875

% Hydrophobic	% Polar
56.66	43.34
According to VolSite

Ligand :

HET Code:	0QK
Formula:	C28H42N7O4
Molecular weight:	540.678 g/mol
DrugBank ID:	-
Buried Surface Area:	67.65 %
Polar Surface area:	151.99 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	6
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
44.5967	50.7143	8.33244

Binding mode :

What is Poseview ?

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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
CAM	CE1	TYR- 136	4.47	0	Hydrophobic	false
CBI	CG	LEU- 143	3.78	0	Hydrophobic	false
CBC	CG2	VAL- 144	4.38	0	Hydrophobic	false
CBI	CG	MET- 147	4.09	0	Hydrophobic	false
CBK	CG	MET- 147	4.43	0	Hydrophobic	false
NAZ	OD1	ASP- 161	2.94	136.03	H-Bond (Ligand Donor)	false
NAZ	OD2	ASP- 161	3.24	138.14	H-Bond (Ligand Donor)	false
NAX	OD2	ASP- 161	2.8	158.22	H-Bond (Ligand Donor)	false
NAS	O	GLY- 163	2.81	162.24	H-Bond (Ligand Donor)	false
CBC	CG2	VAL- 169	3.93	0	Hydrophobic	false
OAQ	OE2	GLU- 186	2.58	153.53	H-Bond (Ligand Donor)	false
OAQ	OE1	GLU- 186	2.72	129.5	H-Bond (Ligand Donor)	false
OAP	OE1	GLU- 186	2.53	176.07	H-Bond (Ligand Donor)	false
C5	CD	LYS- 187	3.64	0	Hydrophobic	false
N3	N	LYS- 187	3.1	130.55	H-Bond (Protein Donor)	false
NAJ	OD1	ASP- 222	3.21	150.54	H-Bond (Ligand Donor)	false
N1	N	PHE- 223	3.14	153.56	H-Bond (Protein Donor)	false
C5	CE2	PHE- 223	3.22	0	Hydrophobic	false
CBG	CB	PHE- 239	3.79	0	Hydrophobic	false
CBJ	CB	ASN- 241	4.45	0	Hydrophobic	false
CBM	CB	ASN- 241	4.47	0	Hydrophobic	false
CBL	CB	ASN- 241	4.36	0	Hydrophobic	false
CBG	CB	ASN- 241	3.85	0	Hydrophobic	false
CBM	CZ	PHE- 245	3.84	0	Hydrophobic	false
CBK	CG1	VAL- 267	3.79	0	Hydrophobic	false
CBJ	CB	SER- 269	4.16	0	Hydrophobic	false
CBJ	CD1	TYR- 312	3.86	0	Hydrophobic	false