scPDB - 2wd7 entry

Protein Data Bank Entry:

PDB ID : 2wd7

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2009-03-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pteridine reductase
ID:	O76290_TRYBB
AC:	O76290
Organism:	Trypanosoma brucei brucei
Reign:	Eukaryota
TaxID:	5702
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	27.069
Number of residues:	20
Including
Standard Amino Acids:	19
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	NAP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.786	793.125

% Hydrophobic	% Polar
50.21	49.79
According to VolSite

Ligand :

HET Code:	VGD
Formula:	C7H6ClN3
Molecular weight:	167.596 g/mol
DrugBank ID:	-
Buried Surface Area:	72.12 %
Polar Surface area:	54.7 Å2

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

Mass center Coordinates

X	Y	Z
1.852	16.4827	32.0673

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
NAA	OG	SER- 95	2.71	164.9	H-Bond (Ligand Donor)	false
CAJ	CB	PHE- 97	4.17	0	Hydrophobic	false
DuAr	DuAr	PHE- 97	3.63	0	Aromatic Face/Face	false
CLA	CD2	LEU- 209	4.15	0	Hydrophobic	false
CAE	CG	PRO- 210	4.02	0	Hydrophobic	false
CLA	CG	PRO- 210	4.16	0	Hydrophobic	false
CLA	C4N	NAP- 269	4.35	0	Hydrophobic	false
CAJ	C2D	NAP- 269	4.46	0	Hydrophobic	false
NAF	O2A	NAP- 269	3.31	137.93	H-Bond (Ligand Donor)	false
NAA	O2A	NAP- 269	3.3	149.02	H-Bond (Ligand Donor)	false