scPDB - 3hvk entry

Protein Data Bank Entry:

PDB ID : 3hvk

Resolution :1.300 Å

Experimental Method : X-ray

Deposition Date : 2009-06-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Catechol O-methyltransferase
ID:	COMT_RAT
AC:	P22734
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	2.1.1.6

Chains:

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

Ligand binding site composition:

B-Factor:	12.736
Number of residues:	37
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.339	320.625

% Hydrophobic	% Polar
61.05	38.95
According to VolSite

Ligand :

HET Code:	719
Formula:	C27H27FN6O7
Molecular weight:	566.538 g/mol
DrugBank ID:	-
Buried Surface Area:	67.3 %
Polar Surface area:	195.1 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	7
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-3.1922	17.2973	13.711

Binding mode :

What is Poseview ?

2D View
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
O31	MG	MG- 1	2.13	0	Metal Acceptor	false
O32	MG	MG- 1	2.09	0	Metal Acceptor	false
DuAr	MG	MG- 1	3.99	82.52	Pi/Cation	false
C7	SD	MET- 83	3.72	0	Hydrophobic	false
C10	CE	MET- 83	4.18	0	Hydrophobic	false
C17	CB	MET- 83	3.89	0	Hydrophobic	false
C18	CB	MET- 83	4.08	0	Hydrophobic	false
C10	CD1	TYR- 111	4.47	0	Hydrophobic	false
O25	OE2	GLU- 133	2.59	160.55	H-Bond (Ligand Donor)	false
O30	OE2	GLU- 133	3.17	132.8	H-Bond (Ligand Donor)	false
O30	OE1	GLU- 133	2.66	151.65	H-Bond (Ligand Donor)	false
N15	N	MET- 134	3.1	142.56	H-Bond (Protein Donor)	false
CA	SD	MET- 134	3.58	0	Hydrophobic	false
C10	CD2	TYR- 138	4.09	0	Hydrophobic	false
N20	N	SER- 162	3	161.31	H-Bond (Protein Donor)	false
N38	OG	SER- 162	2.87	139.23	H-Bond (Ligand Donor)	false
N38	OE1	GLN- 163	3.3	120.02	H-Bond (Ligand Donor)	false
OB	OE1	GLN- 163	2.79	144.39	H-Bond (Ligand Donor)	false
OB	NE2	GLN- 163	2.86	139.19	H-Bond (Protein Donor)	false
C2	CB	HIS- 185	4.45	0	Hydrophobic	false
CA	CE3	TRP- 186	3.23	0	Hydrophobic	false
O31	NZ	LYS- 187	2.91	165.59	H-Bond (Protein Donor)	false
C39	CG	ARG- 189	3.69	0	Hydrophobic	false
O32	ND2	ASN- 213	2.82	137.07	H-Bond (Protein Donor)	false
C34	CG2	VAL- 216	3.7	0	Hydrophobic	false
C12	CG	PRO- 217	3.77	0	Hydrophobic	false
C28	CG	PRO- 217	3.84	0	Hydrophobic	false
C18	CD1	LEU- 241	4.05	0	Hydrophobic	false
C28	CD1	LEU- 241	3.69	0	Hydrophobic	false
C34	CD2	LEU- 241	3.81	0	Hydrophobic	false
O32	OE1	GLU- 242	3.41	166.41	H-Bond (Ligand Donor)	false