scPDB - 2bfa entry

Protein Data Bank Entry:

PDB ID : 2bfa

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2004-12-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pteridine reductase 1
ID:	PTR1_LEIMA
AC:	Q01782
Organism:	Leishmania major
Reign:	Eukaryota
TaxID:	5664
EC Number:	1.5.1.33

Chains:

Chain Name:	Percentage of Residues within binding site
A	91 %
D	9 %

Ligand binding site composition:

B-Factor:	25.022
Number of residues:	35
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:	NDP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.620	523.125

% Hydrophobic	% Polar
55.48	44.52
According to VolSite

Ligand :

HET Code:	CB3
Formula:	C24H21N5O6
Molecular weight:	475.453 g/mol
DrugBank ID:	DB03541
Buried Surface Area:	49.26 %
Polar Surface area:	180.08 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
-6.71651	35.4202	68.4207

Binding mode :

What is Poseview ?

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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
O4	NH2	ARG- 17	3.44	125.75	H-Bond (Protein Donor)	false
NA2	O	SER- 111	3.27	134.3	H-Bond (Ligand Donor)	false
NA2	OG	SER- 111	2.63	136.22	H-Bond (Ligand Donor)	false
DuAr	DuAr	PHE- 113	3.89	0	Aromatic Face/Face	false
CP1	CE2	PHE- 113	3.54	0	Hydrophobic	false
C13	CD2	LEU- 188	4.07	0	Hydrophobic	false
C12	CD1	LEU- 188	3.66	0	Hydrophobic	false
CP3	CD2	LEU- 188	4.17	0	Hydrophobic	false
C9	CD2	LEU- 226	3.76	0	Hydrophobic	false
C13	CD2	LEU- 226	3.56	0	Hydrophobic	false
C9	CD1	LEU- 229	4.27	0	Hydrophobic	false
CP1	CD1	LEU- 229	4.35	0	Hydrophobic	false
C15	CD1	LEU- 229	3.95	0	Hydrophobic	false
N3	O1A	NDP- 1289	2.72	165.74	H-Bond (Ligand Donor)	false