scPDB - 3p9k entry

Protein Data Bank Entry:

PDB ID : 3p9k

Resolution :2.250 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
C	88 %
D	12 %

Ligand binding site composition:

B-Factor:	24.259
Number of residues:	27
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.405	384.750

% Hydrophobic	% Polar
65.79	34.21
According to VolSite

Ligand :

HET Code:	CIY
Formula:	C10H10O3
Molecular weight:	178.185 g/mol
DrugBank ID:	-
Buried Surface Area:	75.95 %
Polar Surface area:	46.53 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	1
Rings:	1
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
57.9228	44.7412	8.90592

Binding mode :

What is Poseview ?

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3D View

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
C6	CE	MET- 127	3.55	0	Hydrophobic	false
O9	ND2	ASN- 128	2.78	146.96	H-Bond (Protein Donor)	false
C3	SD	MET- 177	4.37	0	Hydrophobic	false
C3M	SD	MET- 177	3.71	0	Hydrophobic	false
C1	CE	MET- 177	4	0	Hydrophobic	false
C3M	CB	TRP- 263	3.74	0	Hydrophobic	false
O3	NE2	HIS- 266	2.73	135.97	H-Bond (Protein Donor)	false
O3	OD1	ASP- 267	2.68	164.94	H-Bond (Protein Donor)	false
C6	CG2	ILE- 316	3.96	0	Hydrophobic	false
C3	CE	MET- 317	3.64	0	Hydrophobic	false
O4	ND2	ASN- 321	3.49	155.17	H-Bond (Protein Donor)	false