scPDB - 4kdr entry

Protein Data Bank Entry:

PDB ID : 4kdr

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2013-04-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ubiquinone biosynthesis O-methyltransferase
ID:	UBIG_ECOLI
AC:	P17993
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	21.529
Number of residues:	42
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.933	796.500

% Hydrophobic	% Polar
53.39	46.61
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	70.14 %
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
-14.5723	7.791	-12.6516

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
N6	O	ASN- 11	3.29	132.05	H-Bond (Ligand Donor)	false
C2'	CD1	ILE- 17	4.31	0	Hydrophobic	false
SD	CE1	PHE- 20	3.48	0	Hydrophobic	false
C3'	CG	PHE- 20	3.51	0	Hydrophobic	false
C2'	CD2	PHE- 20	3.61	0	Hydrophobic	false
C5'	CZ	PHE- 20	3.66	0	Hydrophobic	false
CB	CZ2	TRP- 27	4.02	0	Hydrophobic	false
SD	CZ2	TRP- 27	4.12	0	Hydrophobic	false
C3'	CH2	TRP- 27	4.11	0	Hydrophobic	false
CB	CD1	LEU- 37	4.36	0	Hydrophobic	false
O	CZ	ARG- 44	3.5	0	Ionic (Protein Cationic)	false
OXT	CZ	ARG- 44	3.66	0	Ionic (Protein Cationic)	false
O	NH2	ARG- 44	2.8	149.45	H-Bond (Protein Donor)	false
O	NH1	ARG- 44	3.39	127.09	H-Bond (Protein Donor)	false
OXT	NH1	ARG- 44	2.78	156.1	H-Bond (Protein Donor)	false
N	O	GLY- 64	2.6	162.94	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 85	2.97	178.86	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 85	2.63	170.77	H-Bond (Ligand Donor)	false
N3	N	MET- 86	3.44	141.8	H-Bond (Protein Donor)	false
N	O	MET- 129	2.97	146.26	H-Bond (Ligand Donor)	false
CG	CB	GLU- 130	4.06	0	Hydrophobic	false
OXT	O	HOH- 401	2.84	167.18	H-Bond (Protein Donor)	false