scPDB - 3fra entry

Protein Data Bank Entry:

PDB ID : 3fra

Resolution :2.350 Å

Experimental Method : X-ray

Deposition Date : 2009-01-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Dihydrofolate reductase
ID:	DYR_STAAU
AC:	P0A017
Organism:	Staphylococcus aureus
Reign:	Bacteria
TaxID:	1280
EC Number:	1.5.1.3

Chains:

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

Ligand binding site composition:

B-Factor:	35.189
Number of residues:	33
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:	NAP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.139	391.500

% Hydrophobic	% Polar
63.79	36.21
According to VolSite

Ligand :

HET Code:	I2H
Formula:	C19H22N4O3
Molecular weight:	354.403 g/mol
DrugBank ID:	DB07938
Buried Surface Area:	62.65 %
Polar Surface area:	105.51 Å2

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

Mass center Coordinates

X	Y	Z
30.4114	11.3967	42.0782

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
N7	O	LEU- 5	2.63	141.4	H-Bond (Ligand Donor)	false
C21	CD2	LEU- 20	4.24	0	Hydrophobic	false
C18	CG	LEU- 20	3.99	0	Hydrophobic	false
C20	CG	LEU- 20	3.9	0	Hydrophobic	false
C15	CD1	LEU- 20	3.85	0	Hydrophobic	false
N4	OD2	ASP- 27	2.53	154.04	H-Bond (Ligand Donor)	false
N4	OD1	ASP- 27	3.13	135.72	H-Bond (Ligand Donor)	false
N2	OD1	ASP- 27	2.87	153.49	H-Bond (Ligand Donor)	false
C12	CD2	LEU- 28	4.16	0	Hydrophobic	false
C26	CB	LEU- 28	3.28	0	Hydrophobic	false
C28	CD2	LEU- 28	3.48	0	Hydrophobic	false
C8	CG2	VAL- 31	4.49	0	Hydrophobic	false
C28	CG1	VAL- 31	3.55	0	Hydrophobic	false
C20	CB	SER- 49	4.39	0	Hydrophobic	false
C12	CD1	ILE- 50	4.38	0	Hydrophobic	false
C15	CG1	ILE- 50	4.34	0	Hydrophobic	false
N7	O	PHE- 92	2.59	149.28	H-Bond (Ligand Donor)	false
C9	CZ	PHE- 92	3.69	0	Hydrophobic	false
C27	CE2	PHE- 92	3.49	0	Hydrophobic	false
C28	CZ	PHE- 92	3.73	0	Hydrophobic	false
N4	O	HOH- 160	3.08	161.92	H-Bond (Ligand Donor)	false
C9	C5N	NAP- 301	3.36	0	Hydrophobic	false
C20	C5N	NAP- 301	4.41	0	Hydrophobic	false