scPDB - 2hnk entry

Protein Data Bank Entry:

PDB ID : 2hnk

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2006-07-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	SAM-dependent O-methyltransferase
ID:	Q8F8Y3_LEPIN
AC:	Q8F8Y3
Organism:	Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai
Reign:	Bacteria
TaxID:	189518
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	29.985
Number of residues:	36
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.537	546.750

% Hydrophobic	% Polar
38.27	61.73
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	73.54 %
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
67.6602	-35.62	25.3137

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
C3'	CE	MET- 42	3.7	0	Hydrophobic	false
SD	SD	MET- 42	3.7	0	Hydrophobic	false
N	O	GLY- 68	3.03	162.89	H-Bond (Ligand Donor)	false
SD	CB	PHE- 70	3.67	0	Hydrophobic	false
CB	CB	PHE- 70	3.64	0	Hydrophobic	false
C3'	CB	PHE- 70	4.11	0	Hydrophobic	false
N	OG	SER- 74	2.96	162.45	H-Bond (Ligand Donor)	false
OXT	N	SER- 74	3.23	145.71	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 92	3.08	159.09	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 92	3.09	158.64	H-Bond (Ligand Donor)	false
N3	N	VAL- 93	3.46	125.62	H-Bond (Protein Donor)	false
C1'	CG2	VAL- 93	4.08	0	Hydrophobic	false
C3'	CZ3	TRP- 97	4.04	0	Hydrophobic	false
N1	N	ALA- 121	3.15	145.97	H-Bond (Protein Donor)	false
N	OD2	ASP- 154	3.03	157.69	H-Bond (Ligand Donor)	false
N	OD2	ASP- 154	3.03	0	Ionic (Ligand Cationic)	false
CG	CB	ASP- 154	4.3	0	Hydrophobic	false
N6	O	HOH- 3114	2.95	164.58	H-Bond (Ligand Donor)	false