scPDB - 1p33 entry

Protein Data Bank Entry:

PDB ID : 1p33

Resolution :2.860 Å

Experimental Method : X-ray

Deposition Date : 2003-04-16

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_LEITA
AC:	P42556
Organism:	Leishmania tarentolae
Reign:	Eukaryota
TaxID:	5689
EC Number:	1.5.1.33

Chains:

Chain Name:	Percentage of Residues within binding site
A	97 %
B	3 %

Ligand binding site composition:

B-Factor:	41.175
Number of residues:	30
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:	NDP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.718	675.000

% Hydrophobic	% Polar
44.00	56.00
According to VolSite

Ligand :

HET Code:	MTX
Formula:	C20H20N8O5
Molecular weight:	452.423 g/mol
DrugBank ID:	DB00563
Buried Surface Area:	51.84 %
Polar Surface area:	216.2 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	3
Rings:	3
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
17.4333	15.8969	43.1955

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
NA2	OG	SER- 111	2.86	159.7	H-Bond (Ligand Donor)	false
NA2	O	SER- 111	2.78	124.18	H-Bond (Ligand Donor)	false
C9	CE2	PHE- 113	4.18	0	Hydrophobic	false
DuAr	DuAr	PHE- 113	3.88	0	Aromatic Face/Face	false
C16	CD2	LEU- 188	3.37	0	Hydrophobic	false
NA4	OH	TYR- 194	2.63	166.61	H-Bond (Ligand Donor)	false
CM	CD2	LEU- 229	3.66	0	Hydrophobic	false
C9	CG	PRO- 230	3.75	0	Hydrophobic	false
C13	CG	PRO- 230	3.51	0	Hydrophobic	false
C13	CE	MET- 233	3.83	0	Hydrophobic	false
N3	O2D	NDP- 300	2.84	145.62	H-Bond (Protein Donor)	false