scPDB - 4pgh entry

Protein Data Bank Entry:

PDB ID : 4pgh

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2014-05-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Caffeic acid O-methyltransferase
ID:	C5YH12_SORBI
AC:	C5YH12
Organism:	Sorghum bicolor
Reign:	Eukaryota
TaxID:	4558
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	51.870
Number of residues:	27
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.007	600.750

% Hydrophobic	% Polar
44.38	55.62
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	52.38 %
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
82.4931	64.5332	89.1723

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	GLY- 206	2.94	138.78	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 229	3.09	170.18	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 229	3.18	144.34	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 229	2.53	145.69	H-Bond (Ligand Donor)	false
N6	OD1	ASP- 249	2.73	172.39	H-Bond (Ligand Donor)	false
N1	N	MET- 250	3.01	172.51	H-Bond (Protein Donor)	false
N	O	LYS- 263	3.08	164.32	H-Bond (Ligand Donor)	false
OXT	NZ	LYS- 263	3.73	0	Ionic (Protein Cationic)	false
CB	CD1	ILE- 265	4.17	0	Hydrophobic	false
C5'	CD1	ILE- 265	3.62	0	Hydrophobic	false