scPDB - 4pne entry

Protein Data Bank Entry:

PDB ID : 4pne

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2014-05-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Methyltransferase-like protein
ID:	Q9ALM7_9PSEU
AC:	Q9ALM7
Organism:	Saccharopolyspora spinosa
Reign:	Bacteria
TaxID:	60894
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	14.253
Number of residues:	41
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.319	887.625

% Hydrophobic	% Polar
51.71	48.29
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	80.15 %
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
9.04892	8.32385	8.65115

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
SD	CZ	TYR- 23	3.94	0	Hydrophobic	false
C2'	CE2	TYR- 23	3.7	0	Hydrophobic	false
SD	CG2	ILE- 40	3.98	0	Hydrophobic	false
CB	CB	ILE- 40	4.14	0	Hydrophobic	false
O	N	ILE- 40	2.87	167.34	H-Bond (Protein Donor)	false
N	O	GLY- 80	2.69	157.21	H-Bond (Ligand Donor)	false
O3'	N	GLY- 82	2.96	130.97	H-Bond (Protein Donor)	false
O3'	OG1	THR- 102	3.4	126.42	H-Bond (Protein Donor)	false
O2'	OG1	THR- 102	2.83	151.48	H-Bond (Ligand Donor)	false
C2'	CG2	VAL- 103	4.34	0	Hydrophobic	false
O3'	OE1	GLN- 107	2.79	163.85	H-Bond (Ligand Donor)	false
N6	OD1	ASP- 130	3.06	166.9	H-Bond (Ligand Donor)	false
N1	N	ALA- 131	2.93	171.87	H-Bond (Protein Donor)	false
N	O	MET- 147	2.93	162.55	H-Bond (Ligand Donor)	false
C1'	CB	SER- 149	4.47	0	Hydrophobic	false
C4'	CB	SER- 149	4.23	0	Hydrophobic	false
O	O	HOH- 449	2.91	179.95	H-Bond (Protein Donor)	false