scPDB - 3p9c entry

Protein Data Bank Entry:

PDB ID : 3p9c

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2010-10-17

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:	Q9ZTU2_LOLPR
AC:	Q9ZTU2
Organism:	Lolium perenne
Reign:	Eukaryota
TaxID:	4522
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	21.486
Number of residues:	25
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.614	482.625

% Hydrophobic	% Polar
42.66	57.34
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	52.56 %
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
4.02238	25.9191	100.051

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- 205	3.06	136.66	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 228	3.49	130.77	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 228	2.74	167.97	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 228	2.67	167.61	H-Bond (Ligand Donor)	false
N6	OD1	ASP- 248	2.9	166.28	H-Bond (Ligand Donor)	false
N1	N	MET- 249	2.86	175.92	H-Bond (Protein Donor)	false
N	O	LYS- 262	2.92	160.95	H-Bond (Ligand Donor)	false
O	NZ	LYS- 262	3.76	0	Ionic (Protein Cationic)	false
OXT	NZ	LYS- 262	2.66	0	Ionic (Protein Cationic)	false
OXT	NZ	LYS- 262	2.66	141.36	H-Bond (Protein Donor)	false
CB	CD1	ILE- 264	4.02	0	Hydrophobic	false
C5'	CD1	ILE- 264	4.06	0	Hydrophobic	false