scPDB - 5jhn entry

Protein Data Bank Entry:

PDB ID : 5jhn

Resolution :1.670 Å

Experimental Method : X-ray

Deposition Date : 2016-04-21

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:	32.851
Number of residues:	32
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
1.254	1225.125

% Hydrophobic	% Polar
39.39	60.61
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	68.61 %
Polar Surface area:	189.77 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
28.168	0.898148	64.5312

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
N	O	TRP- 1050	2.82	166.99	H-Bond (Ligand Donor)	false
OXT	N	TRP- 1050	2.9	155.9	H-Bond (Protein Donor)	false
O3'	OG	SER- 1084	3.26	127.05	H-Bond (Ligand Donor)	false
C4'	CB	SER- 1084	4.27	0	Hydrophobic	false
O	OH	TYR- 1085	2.7	148.7	H-Bond (Protein Donor)	false
SD	CE2	TYR- 1085	3.45	0	Hydrophobic	false
CE	CD2	TYR- 1085	3.53	0	Hydrophobic	false
CB	CE2	TYR- 1085	4.33	0	Hydrophobic	false
CB	CD1	PHE- 1110	4.36	0	Hydrophobic	false
N	OD1	ASN- 1112	2.9	143.42	H-Bond (Ligand Donor)	false
N7	N	HIS- 1113	3.09	159.39	H-Bond (Protein Donor)	false
N6	O	HIS- 1113	2.87	140.31	H-Bond (Ligand Donor)	false
CE	CZ	TYR- 1154	4.19	0	Hydrophobic	false
C5'	CE2	TYR- 1154	4.07	0	Hydrophobic	false
C3'	CZ	PHE- 1158	4.23	0	Hydrophobic	false
C2'	CZ	PHE- 1166	3.63	0	Hydrophobic	false
N1	N	GLN- 1169	2.97	161.89	H-Bond (Protein Donor)	false