scPDB - 2yhu entry

Protein Data Bank Entry:

PDB ID : 2yhu

Resolution :2.010 Å

Experimental Method : X-ray

Deposition Date : 2011-05-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

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

Chains:

Chain Name:	Percentage of Residues within binding site
B	4 %
C	96 %

Ligand binding site composition:

B-Factor:	23.214
Number of residues:	25
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:	NDP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.769	772.875

% Hydrophobic	% Polar
48.47	51.53
According to VolSite

Ligand :

HET Code:	WHF
Formula:	C9H9N3OS2
Molecular weight:	239.317 g/mol
DrugBank ID:	-
Buried Surface Area:	74.3 %
Polar Surface area:	125.35 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
0.5446	15.1676	30.3917

Binding mode :

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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	3.12	149.35	H-Bond (Ligand Donor)	false
CAF	CZ	PHE- 97	4.35	0	Hydrophobic	false
CAG	CE2	PHE- 97	3.95	0	Hydrophobic	false
SAK	CB	PHE- 97	4.01	0	Hydrophobic	false
DuAr	DuAr	PHE- 97	3.84	0	Aromatic Face/Face	false
SAJ	CG2	VAL- 206	3.57	0	Hydrophobic	false
CAG	CG	PRO- 210	4.18	0	Hydrophobic	false
SAJ	CE2	TRP- 221	3.43	0	Hydrophobic	false
CAF	C4N	NDP- 301	3.69	0	Hydrophobic	false
CAG	C3N	NDP- 301	4.1	0	Hydrophobic	false
NAA	O2D	NDP- 301	3.37	123.55	H-Bond (Ligand Donor)	false
NAA	O2A	NDP- 301	2.93	153.25	H-Bond (Ligand Donor)	false