scPDB - 3nwe entry

Protein Data Bank Entry:

PDB ID : 3nwe

Resolution :1.500 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:	16.456
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)
0.845	472.500

% Hydrophobic	% Polar
67.14	32.86
According to VolSite

Ligand :

HET Code:	662
Formula:	C29H31FN6O5
Molecular weight:	562.592 g/mol
DrugBank ID:	-
Buried Surface Area:	62.43 %
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:	9

Mass center Coordinates

X	Y	Z
-3.36195	10.0522	25.7562

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
C14	CE	MET- 40	3.58	0	Hydrophobic	false
C7	SD	MET- 40	3.63	0	Hydrophobic	false
C12	CB	MET- 40	3.81	0	Hydrophobic	false
C14	CD1	TYR- 68	3.91	0	Hydrophobic	false
O11	OE2	GLU- 90	2.57	169.5	H-Bond (Ligand Donor)	false
N19	N	ILE- 91	3.08	148.71	H-Bond (Protein Donor)	false
C40	CD1	ILE- 91	4.01	0	Hydrophobic	false
C2	CG2	ILE- 91	4.1	0	Hydrophobic	false
N22	N	SER- 119	2.94	159.66	H-Bond (Protein Donor)	false
N32	OG	SER- 119	2.95	130.02	H-Bond (Ligand Donor)	false
N32	OE1	GLN- 120	3.3	132.7	H-Bond (Ligand Donor)	false
C2	CB	HIS- 142	4.3	0	Hydrophobic	false
C3	CZ2	TRP- 143	4.29	0	Hydrophobic	false
C14	CH2	TRP- 143	4.42	0	Hydrophobic	false
O33	NZ	LYS- 144	2.95	166.04	H-Bond (Protein Donor)	false
C41	CD	ARG- 146	3.85	0	Hydrophobic	false
C39	CG	ARG- 146	3.67	0	Hydrophobic	false
O20	ND2	ASN- 170	2.81	138.71	H-Bond (Protein Donor)	false
C36	CG1	VAL- 173	3.92	0	Hydrophobic	false
C16	CG	PRO- 174	3.73	0	Hydrophobic	false
C30	CG	PRO- 174	3.82	0	Hydrophobic	false
C23	CD1	LEU- 198	4.05	0	Hydrophobic	false
C30	CD1	LEU- 198	3.65	0	Hydrophobic	false
C36	CD2	LEU- 198	3.88	0	Hydrophobic	false
O20	OE1	GLU- 199	3.37	163.4	H-Bond (Ligand Donor)	false
O20	MG	MG- 222	2.08	0	Metal Acceptor	false
O33	MG	MG- 222	2.15	0	Metal Acceptor	false