scPDB - 4er7 entry

Protein Data Bank Entry:

PDB ID : 4er7

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2012-04-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

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:	41.788
Number of residues:	39
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.121	472.500

% Hydrophobic	% Polar
56.43	43.57
According to VolSite

Ligand :

HET Code:	AW3
Formula:	C25H35BrN7O4
Molecular weight:	577.494 g/mol
DrugBank ID:	-
Buried Surface Area:	60.61 %
Polar Surface area:	164.16 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:	9

Mass center Coordinates

X	Y	Z
20.4239	63.2371	-4.85178

Binding mode :

What is Poseview ?

2D View
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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
CAA	CB	LEU- 143	3.97	0	Hydrophobic	false
CAL	CG2	VAL- 144	4.14	0	Hydrophobic	false
CAC	CG	MET- 147	3.77	0	Hydrophobic	false
NAV	OD2	ASP- 161	3.22	156.49	H-Bond (Ligand Donor)	false
NAW	OD1	ASP- 161	3.2	164.81	H-Bond (Ligand Donor)	false
NAU	O	GLY- 163	2.59	131.14	H-Bond (Ligand Donor)	false
CAJ	CG2	VAL- 169	3.88	0	Hydrophobic	false
OAF	OE2	GLU- 186	3.22	124.75	H-Bond (Ligand Donor)	false
OAG	OE2	GLU- 186	2.66	159.24	H-Bond (Ligand Donor)	false
N3	N	LYS- 187	3.17	130.17	H-Bond (Protein Donor)	false
C5	CD	LYS- 187	3.97	0	Hydrophobic	false
NAD	OD1	ASP- 222	3.11	146.98	H-Bond (Ligand Donor)	false
N1	N	PHE- 223	3.28	165.12	H-Bond (Protein Donor)	false
BRH	CZ	PHE- 223	4.03	0	Hydrophobic	false
CAC	CD2	PHE- 239	4.06	0	Hydrophobic	false
CAK	CB	PHE- 239	3.71	0	Hydrophobic	false
OAE	ND2	ASN- 241	3.06	175.89	H-Bond (Protein Donor)	false
CAJ	CB	ASN- 241	4.2	0	Hydrophobic	false
CAK	CB	ASN- 241	3.94	0	Hydrophobic	false
BRH	CG1	VAL- 249	4.04	0	Hydrophobic	false
CAB	CG1	VAL- 267	4.08	0	Hydrophobic	false
CAC	CG1	VAL- 267	3.76	0	Hydrophobic	false
CAA	CD2	TYR- 312	4.4	0	Hydrophobic	false
CAB	CB	TYR- 312	4.12	0	Hydrophobic	false