scPDB - 4nvq entry

Protein Data Bank Entry:

PDB ID : 4nvq

Resolution :2.030 Å

Experimental Method : X-ray

Deposition Date : 2013-12-05

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 EHMT2
ID:	EHMT2_HUMAN
AC:	Q96KQ7
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	54.770
Number of residues:	31
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.914	955.125

% Hydrophobic	% Polar
41.34	58.66
According to VolSite

Ligand :

HET Code:	2OD
Formula:	C19H29N3O2
Molecular weight:	331.452 g/mol
DrugBank ID:	-
Buried Surface Area:	73.74 %
Polar Surface area:	62.89 Å2

Number of
H-Bond Acceptors:	2
H-Bond Donors:	3
Rings:	4
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	2
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
22.0774	11.3564	-27.7016

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
C12	CE1	TYR- 1067	3.49	0	Hydrophobic	false
N3	OD2	ASP- 1074	3.22	171.9	H-Bond (Ligand Donor)	false
N3	OD1	ASP- 1074	3.35	123.86	H-Bond (Ligand Donor)	false
C17	CB	ALA- 1077	4.24	0	Hydrophobic	false
N3	OD1	ASP- 1078	3.2	173.22	H-Bond (Ligand Donor)	false
C3	CB	ASP- 1083	4.27	0	Hydrophobic	false
C1	CB	ASP- 1083	4.17	0	Hydrophobic	false
N1	O	LEU- 1086	2.84	156.41	H-Bond (Ligand Donor)	false
C17	CD1	LEU- 1086	3.57	0	Hydrophobic	false
C6	CB	LEU- 1086	3.87	0	Hydrophobic	false
C4	CD1	LEU- 1086	3.69	0	Hydrophobic	false
C12	CD1	PHE- 1087	3.89	0	Hydrophobic	false
C15	OD2	ASP- 1088	3.95	0	Ionic (Ligand Cationic)	false
N2	OD1	ASP- 1088	3.5	126.16	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 1088	2.78	151.16	H-Bond (Ligand Donor)	false
C12	CZ	PHE- 1152	3.78	0	Hydrophobic	false
C13	CZ	TYR- 1154	4.2	0	Hydrophobic	false
C5	CD	ARG- 1157	4.11	0	Hydrophobic	false
C1	CD1	PHE- 1158	3.55	0	Hydrophobic	false
C2	CB	PHE- 1158	4.43	0	Hydrophobic	false
C8	CB	PHE- 1158	3.63	0	Hydrophobic	false
C1	CD1	ILE- 1161	4.15	0	Hydrophobic	false
C19	CD1	ILE- 1161	3.71	0	Hydrophobic	false
C3	CD1	ILE- 1161	3.66	0	Hydrophobic	false
C1	CG	LYS- 1162	3.78	0	Hydrophobic	false
O2	O	HOH- 1359	2.61	179.99	H-Bond (Protein Donor)	false