scPDB - 3nwb entry

Protein Data Bank Entry:

PDB ID : 3nwb

Resolution :1.300 Å

Experimental Method : X-ray

Deposition Date : 2010-07-09

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:	14.700
Number of residues:	36
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.914	351.000

% Hydrophobic	% Polar
71.15	28.85
According to VolSite

Ligand :

HET Code:	659
Formula:	C26H24F2N6O5
Molecular weight:	538.503 g/mol
DrugBank ID:	-
Buried Surface Area:	67.9 %
Polar Surface area:	154.64 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	5
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-2.89356	17.2855	13.9553

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
F6	CE	MET- 40	3.29	0	Hydrophobic	false
C13	SD	MET- 40	3.71	0	Hydrophobic	false
C9	CB	MET- 40	3.85	0	Hydrophobic	false
F6	CD1	TYR- 68	3.9	0	Hydrophobic	false
O7	OE2	GLU- 90	2.54	171.85	H-Bond (Ligand Donor)	false
C4	CG	MET- 91	4.37	0	Hydrophobic	false
N34	N	MET- 91	3.1	147.09	H-Bond (Protein Donor)	false
F6	CE2	TYR- 95	3.31	0	Hydrophobic	false
C2	CD2	TYR- 95	3.9	0	Hydrophobic	false
N36	N	SER- 119	2.94	162.77	H-Bond (Protein Donor)	false
N38	OG	SER- 119	2.93	131.52	H-Bond (Ligand Donor)	false
N38	OE1	GLN- 120	3.25	129.38	H-Bond (Ligand Donor)	false
C4	CB	HIS- 142	4.46	0	Hydrophobic	false
C3	CZ2	TRP- 143	4.32	0	Hydrophobic	false
F6	CH2	TRP- 143	4.39	0	Hydrophobic	false
O21	NZ	LYS- 144	2.94	164.59	H-Bond (Protein Donor)	false
C39	CG	ARG- 146	3.64	0	Hydrophobic	false
O22	ND2	ASN- 170	2.82	137.01	H-Bond (Protein Donor)	false
C19	CG1	VAL- 173	3.84	0	Hydrophobic	false
C12	CG	PRO- 174	3.77	0	Hydrophobic	false
C20	CG	PRO- 174	3.85	0	Hydrophobic	false
C10	CD1	LEU- 198	4.12	0	Hydrophobic	false
C19	CD2	LEU- 198	3.85	0	Hydrophobic	false
C20	CD1	LEU- 198	3.78	0	Hydrophobic	false
O22	OE1	GLU- 199	3.38	164.59	H-Bond (Ligand Donor)	false
O21	MG	MG- 222	2.1	0	Metal Acceptor	false
O22	MG	MG- 222	2.08	0	Metal Acceptor	false