scPDB - 3fre entry

Protein Data Bank Entry:

PDB ID : 3fre

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2009-01-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	8.290	8.590	8.470	0.270	8.920	5

List of CHEMBLId :

CHEMBL22

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:	19.796
Number of residues:	28
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	NDP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.199	455.625

% Hydrophobic	% Polar
62.22	37.78
According to VolSite

Ligand :

HET Code:	TOP
Formula:	C14H18N4O3
Molecular weight:	290.318 g/mol
DrugBank ID:	DB00440
Buried Surface Area:	63.61 %
Polar Surface area:	105.51 Å2

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

Mass center Coordinates

X	Y	Z
30.0096	11.5503	42.1329

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	2.66	158.39	H-Bond (Ligand Donor)	false
C17	CD1	LEU- 20	4.01	0	Hydrophobic	false
C18	CG	LEU- 20	3.94	0	Hydrophobic	false
C20	CG	LEU- 20	4.11	0	Hydrophobic	false
C21	CD2	LEU- 20	4.16	0	Hydrophobic	false
C15	CD1	LEU- 20	4.03	0	Hydrophobic	false
N2	OD1	ASP- 27	2.91	153.98	H-Bond (Ligand Donor)	false
N4	OD2	ASP- 27	2.92	153.58	H-Bond (Ligand Donor)	false
N4	OD1	ASP- 27	3.08	140.88	H-Bond (Ligand Donor)	false
C14	CD2	LEU- 28	3.3	0	Hydrophobic	false
C17	CD1	LEU- 28	3.91	0	Hydrophobic	false
C12	CD2	LEU- 28	3.76	0	Hydrophobic	false
C8	CG2	VAL- 31	4.31	0	Hydrophobic	false
C14	CG1	VAL- 31	4.42	0	Hydrophobic	false
C20	CB	SER- 49	4.16	0	Hydrophobic	false
C15	CG1	ILE- 50	3.82	0	Hydrophobic	false
C10	CD1	ILE- 50	4.02	0	Hydrophobic	false
C14	CD2	LEU- 54	4.49	0	Hydrophobic	false
N7	O	PHE- 92	2.72	131.92	H-Bond (Ligand Donor)	false
C9	CZ	PHE- 92	3.58	0	Hydrophobic	false
C9	C4N	NDP- 301	3.4	0	Hydrophobic	false
C20	C2D	NDP- 301	3.58	0	Hydrophobic	false