scPDB - 3hvi entry

Protein Data Bank Entry:

PDB ID : 3hvi

Resolution :1.200 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:	10.579
Number of residues:	39
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.548	286.875

% Hydrophobic	% Polar
65.88	34.12
According to VolSite

Ligand :

HET Code:	619
Formula:	C27H27FN6O6
Molecular weight:	550.538 g/mol
DrugBank ID:	-
Buried Surface Area:	67.92 %
Polar Surface area:	174.87 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	6
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-2.95408	17.256	13.9433

Binding mode :

What is Poseview ?

2D View
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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
O34	MG	MG- 1	2.07	0	Metal Acceptor	false
O32	MG	MG- 1	2.14	0	Metal Acceptor	false
C20	SD	MET- 83	3.75	0	Hydrophobic	false
C4	CE	MET- 83	4.02	0	Hydrophobic	false
C33	CB	MET- 83	3.79	0	Hydrophobic	false
C4	CD1	TYR- 111	4.43	0	Hydrophobic	false
O5	OE1	GLU- 133	2.69	154.06	H-Bond (Ligand Donor)	false
O3	OE2	GLU- 133	2.64	163.88	H-Bond (Ligand Donor)	false
C1	CG	MET- 134	4.43	0	Hydrophobic	false
C37	SD	MET- 134	4.06	0	Hydrophobic	false
N40	N	MET- 134	3.09	141.17	H-Bond (Protein Donor)	false
C4	CD2	TYR- 138	4.05	0	Hydrophobic	false
N38	N	SER- 162	2.97	159.07	H-Bond (Protein Donor)	false
N7	OG	SER- 162	2.83	150.52	H-Bond (Ligand Donor)	false
C2	CZ2	TRP- 186	4.26	0	Hydrophobic	false
O32	NZ	LYS- 187	2.86	169.25	H-Bond (Protein Donor)	false
C36	CG	ARG- 189	3.61	0	Hydrophobic	false
O34	ND2	ASN- 213	2.78	137.42	H-Bond (Protein Donor)	false
C28	CG1	VAL- 216	3.76	0	Hydrophobic	false
C24	CG	PRO- 217	3.78	0	Hydrophobic	false
C21	CG	PRO- 217	3.68	0	Hydrophobic	false
C28	CD2	LEU- 241	3.87	0	Hydrophobic	false
C27	CD1	LEU- 241	3.73	0	Hydrophobic	false
C23	CD1	LEU- 241	4.11	0	Hydrophobic	false
O34	OE1	GLU- 242	3.41	163.52	H-Bond (Ligand Donor)	false