scPDB - 3r6t entry

Protein Data Bank Entry:

PDB ID : 3r6t

Resolution :1.200 Å

Experimental Method : X-ray

Deposition Date : 2011-03-22

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:	7.583
Number of residues:	37
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	CL MG

Cavity properties

Ligandability	Volume (Å3)
0.790	384.750

% Hydrophobic	% Polar
63.16	36.84
According to VolSite

Ligand :

HET Code:	LU1
Formula:	C26H24FN5O5
Molecular weight:	505.498 g/mol
DrugBank ID:	-
Buried Surface Area:	65.98 %
Polar Surface area:	142.62 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	4
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-2.71003	10.8063	25.0926

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
C2	SD	MET- 83	3.68	0	Hydrophobic	false
C12	CE	MET- 83	4.23	0	Hydrophobic	false
C9	CB	MET- 83	3.84	0	Hydrophobic	false
C12	CB	TYR- 111	4.39	0	Hydrophobic	false
C11	CD1	TYR- 111	4.24	0	Hydrophobic	false
O22	OE2	GLU- 133	2.54	166.65	H-Bond (Ligand Donor)	false
N33	N	ILE- 134	3.04	141.85	H-Bond (Protein Donor)	false
C8	CG2	ILE- 134	4.18	0	Hydrophobic	false
N35	N	SER- 162	2.93	156.58	H-Bond (Protein Donor)	false
C37	CB	SER- 162	4.3	0	Hydrophobic	false
C1	CB	HIS- 185	4.41	0	Hydrophobic	false
N31	N	TRP- 186	3.47	161.53	H-Bond (Protein Donor)	false
C37	CE3	TRP- 186	4.21	0	Hydrophobic	false
O20	NZ	LYS- 187	2.88	169.18	H-Bond (Protein Donor)	false
C37	CG	ARG- 189	4.27	0	Hydrophobic	false
O21	ND2	ASN- 213	2.81	138.4	H-Bond (Protein Donor)	false
C24	CG2	VAL- 216	3.79	0	Hydrophobic	false
C13	CG	PRO- 217	3.76	0	Hydrophobic	false
C10	CD1	LEU- 241	4.06	0	Hydrophobic	false
C17	CD1	LEU- 241	3.65	0	Hydrophobic	false
C24	CD2	LEU- 241	3.84	0	Hydrophobic	false
O21	OE1	GLU- 242	3.4	164.49	H-Bond (Ligand Donor)	false
O20	MG	MG- 301	2.14	0	Metal Acceptor	false
O21	MG	MG- 301	2.08	0	Metal Acceptor	false