scPDB - 2fdy entry

Protein Data Bank Entry:

PDB ID : 2fdy

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2005-12-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cytochrome P450 2A6
ID:	CP2A6_HUMAN
AC:	P11509
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.14.13

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	20.157
Number of residues:	25
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.388	357.750

% Hydrophobic	% Polar
73.58	26.42
According to VolSite

Ligand :

HET Code:	D4G
Formula:	C10H8N2S2
Molecular weight:	220.314 g/mol
DrugBank ID:	DB07623
Buried Surface Area:	79 %
Polar Surface area:	76.38 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	0
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
55.4048	78.5459	59.7905

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
S2	CZ	PHE- 107	3.91	0	Hydrophobic	false
C10	CE2	PHE- 107	3.42	0	Hydrophobic	false
C7	CG2	VAL- 117	4.16	0	Hydrophobic	false
S1	CE1	PHE- 209	3.96	0	Hydrophobic	false
N2	ND2	ASN- 297	2.78	140.63	H-Bond (Protein Donor)	false
S1	CG2	ILE- 300	4.47	0	Hydrophobic	false
C10	CG2	ILE- 300	3.89	0	Hydrophobic	false
C5	CG2	THR- 305	3.36	0	Hydrophobic	false
C3	CD2	LEU- 370	3.76	0	Hydrophobic	false
S1	CE2	PHE- 480	4.03	0	Hydrophobic	false
S2	CZ	PHE- 480	3.63	0	Hydrophobic	false