scPDB - 3kmt entry

Protein Data Bank Entry:

PDB ID : 3kmt

Resolution :1.780 Å

Experimental Method : X-ray

Deposition Date : 2009-11-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Histone H3K27 methylase
ID:	O41094_PBCV1
AC:	O41094
Organism:	Paramecium bursaria Chlorella virus 1
Reign:	Viruses
TaxID:	10506
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	4 %
B	96 %
H	0 %

Ligand binding site composition:

B-Factor:	42.471
Number of residues:	25
Including
Standard Amino Acids:	23
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.846	614.250

% Hydrophobic	% Polar
38.46	61.54
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	63.07 %
Polar Surface area:	212.38 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
45.8786	13.1799	19.8382

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	TYR- 16	2.92	132.53	H-Bond (Ligand Donor)	false
OXT	N	TYR- 16	2.74	167.82	H-Bond (Protein Donor)	false
C5'	CB	ASP- 49	4.32	0	Hydrophobic	false
SD	CE1	TYR- 50	3.31	0	Hydrophobic	false
CB	CE1	TYR- 50	4.19	0	Hydrophobic	false
O	OH	TYR- 50	2.83	157.03	H-Bond (Protein Donor)	false
N	OD1	ASN- 69	2.93	167.04	H-Bond (Ligand Donor)	false
N7	N	HIS- 70	2.99	169.08	H-Bond (Protein Donor)	false
N6	O	HIS- 70	2.94	154.73	H-Bond (Ligand Donor)	false
C5'	CE2	TYR- 105	4.2	0	Hydrophobic	false
C3'	CZ	TYR- 109	4.42	0	Hydrophobic	false
O3'	OH	TYR- 109	2.79	171.34	H-Bond (Ligand Donor)	false
C2'	CH2	TRP- 110	4.46	0	Hydrophobic	false
C2'	CD2	LEU- 116	4	0	Hydrophobic	false
N6	O	ASN- 119	2.87	171.24	H-Bond (Ligand Donor)	false
N1	N	ASN- 119	2.89	169.96	H-Bond (Protein Donor)	false