scPDB - 4ekg entry

Protein Data Bank Entry:

PDB ID : 4ekg

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2012-04-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	7.890	7.890	7.890	0.000	7.890	1

List of CHEMBLId :

CHEMBL3087500

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:	67.164
Number of residues:	39
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.509	1140.750

% Hydrophobic	% Polar
54.44	45.56
According to VolSite

Ligand :

HET Code:	0QJ
Formula:	C25H37N8O4
Molecular weight:	513.612 g/mol
DrugBank ID:	-
Buried Surface Area:	64.89 %
Polar Surface area:	164.88 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	6
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
45.1762	51.3847	8.09943

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
CAJ	CE1	TYR- 136	4.33	0	Hydrophobic	false
CBC	CD2	LEU- 143	3.96	0	Hydrophobic	false
CBB	CG	MET- 147	3.57	0	Hydrophobic	false
NAU	OD2	ASP- 161	3.27	142.82	H-Bond (Ligand Donor)	false
NAU	OD1	ASP- 161	3.08	149.54	H-Bond (Ligand Donor)	false
NAS	OD2	ASP- 161	2.94	165.03	H-Bond (Ligand Donor)	false
NAN	O	GLY- 163	2.6	154.97	H-Bond (Ligand Donor)	false
CBE	CG2	VAL- 169	4.14	0	Hydrophobic	false
OAK	OE2	GLU- 186	3.01	132.27	H-Bond (Ligand Donor)	false
OAK	OE1	GLU- 186	2.52	155.79	H-Bond (Ligand Donor)	false
OAI	OE2	GLU- 186	2.57	167.24	H-Bond (Ligand Donor)	false
N6	OD1	ASP- 222	3.36	154.2	H-Bond (Ligand Donor)	false
N1	N	PHE- 223	3.41	165.84	H-Bond (Protein Donor)	false
CBB	CD2	PHE- 239	4.02	0	Hydrophobic	false
CAW	CB	PHE- 239	3.79	0	Hydrophobic	false
OBF	ND2	ASN- 241	3.28	157.19	H-Bond (Protein Donor)	false
CBE	CB	ASN- 241	4.05	0	Hydrophobic	false
CAW	CB	ASN- 241	3.98	0	Hydrophobic	false
CBB	CG1	VAL- 267	4.35	0	Hydrophobic	false
CBA	CD1	TYR- 312	3.86	0	Hydrophobic	false
CBC	CE1	TYR- 312	3.86	0	Hydrophobic	false