scPDB - 4er6 entry

Protein Data Bank Entry:

PDB ID : 4er6

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2012-04-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	10.220	10.220	10.220	0.000	10.220	1

List of CHEMBLId :

CHEMBL3087498

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:	53.600
Number of residues:	45
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	BR

Cavity properties

Ligandability	Volume (Å3)
1.245	877.500

% Hydrophobic	% Polar
46.15	53.85
According to VolSite

Ligand :

HET Code:	AW2
Formula:	C28H41BrN7O4
Molecular weight:	619.574 g/mol
DrugBank ID:	-
Buried Surface Area:	59.97 %
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
20.4957	63.1441	-5.1667

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
C30	CB	LEU- 143	4.2	0	Hydrophobic	false
C29	CG	MET- 147	3.86	0	Hydrophobic	false
N20	OD2	ASP- 161	3.43	138.17	H-Bond (Ligand Donor)	false
N22	OD2	ASP- 161	3.11	147.8	H-Bond (Ligand Donor)	false
N22	OD1	ASP- 161	3.26	153.51	H-Bond (Ligand Donor)	false
N16	O	GLY- 163	2.83	163.09	H-Bond (Ligand Donor)	false
C32	CG1	VAL- 169	4.21	0	Hydrophobic	false
C24	CG2	VAL- 169	3.55	0	Hydrophobic	false
O38	OE2	GLU- 186	3.17	130.61	H-Bond (Ligand Donor)	false
O38	OE1	GLU- 186	2.6	165.98	H-Bond (Ligand Donor)	false
O40	OE1	GLU- 186	3.47	143.22	H-Bond (Ligand Donor)	false
N05	N	LYS- 187	3.31	141.25	H-Bond (Protein Donor)	false
C07	CD	LYS- 187	3.81	0	Hydrophobic	false
N01	OD1	ASP- 222	2.99	153.25	H-Bond (Ligand Donor)	false
BR9	CZ	PHE- 223	4.33	0	Hydrophobic	false
N03	N	PHE- 223	3.2	164.63	H-Bond (Protein Donor)	false
DuAr	DuAr	PHE- 223	3.78	0	Aromatic Face/Face	false
C29	CD2	PHE- 239	3.68	0	Hydrophobic	false
C31	CB	PHE- 239	3.44	0	Hydrophobic	false
C32	CB	ASN- 241	4.33	0	Hydrophobic	false
C35	CB	ASN- 241	3.91	0	Hydrophobic	false
C36	CB	ASN- 241	3.83	0	Hydrophobic	false
C24	CB	ASN- 241	3.96	0	Hydrophobic	false
BR9	CE1	PHE- 245	4.49	0	Hydrophobic	false
C35	CZ	PHE- 245	3.33	0	Hydrophobic	false
C36	CE1	PHE- 245	4.46	0	Hydrophobic	false
BR9	CG2	VAL- 249	4.13	0	Hydrophobic	false
C29	CG1	VAL- 267	3.55	0	Hydrophobic	false
C30	CG	TYR- 312	3.7	0	Hydrophobic	false
C28	CD2	TYR- 312	3.48	0	Hydrophobic	false