scPDB - 3a7d entry

Protein Data Bank Entry:

PDB ID : 3a7d

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2009-09-26

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:	30.407
Number of residues:	36
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.931	526.500

% Hydrophobic	% Polar
65.38	34.62
According to VolSite

Ligand :

HET Code:	FBN
Formula:	C20H19N10O8
Molecular weight:	527.427 g/mol
DrugBank ID:	-
Buried Surface Area:	69.55 %
Polar Surface area:	268.22 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	5
Rings:	5
Aromatic rings:	4
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
28.1226	-6.06503	-12.0469

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
C27	CE	MET- 40	3.33	0	Hydrophobic	false
C42	SD	MET- 40	3.67	0	Hydrophobic	false
C46	CB	MET- 40	3.89	0	Hydrophobic	false
C17	CB	TYR- 68	3.96	0	Hydrophobic	false
C18	CD1	TYR- 68	4.15	0	Hydrophobic	false
C27	CD1	TYR- 68	3.7	0	Hydrophobic	false
O21	OE1	GLU- 90	2.58	156.15	H-Bond (Ligand Donor)	false
N2	N	MET- 91	3.44	145.38	H-Bond (Protein Donor)	false
C18	CD2	TYR- 95	3.55	0	Hydrophobic	false
N4	N	SER- 119	3.02	156.08	H-Bond (Protein Donor)	false
N11	OG	SER- 119	3.34	123.11	H-Bond (Ligand Donor)	false
N11	OE1	GLN- 120	3.14	151.75	H-Bond (Ligand Donor)	false
N8	N	TRP- 143	3.36	146.79	H-Bond (Protein Donor)	false
O52	NZ	LYS- 144	2.91	154.52	H-Bond (Protein Donor)	false
O53	ND2	ASN- 170	2.84	132.43	H-Bond (Protein Donor)	false
C47	CG	PRO- 174	4.46	0	Hydrophobic	false
C49	CG	PRO- 174	3.67	0	Hydrophobic	false
C47	CD1	LEU- 198	4.07	0	Hydrophobic	false
O53	OE1	GLU- 199	3.4	168.93	H-Bond (Ligand Donor)	false
O52	MG	MG- 300	2.38	0	Metal Acceptor	false
O53	MG	MG- 300	2.19	0	Metal Acceptor	false