scPDB - 4dkb entry

Protein Data Bank Entry:

PDB ID : 4dkb

Resolution :1.830 Å

Experimental Method : X-ray

Deposition Date : 2012-02-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Deoxyuridine triphosphatase, putative
ID:	Q57ZH3_TRYB2
AC:	Q57ZH3
Organism:	Trypanosoma brucei brucei
Reign:	Eukaryota
TaxID:	185431
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	13.103
Number of residues:	32
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	CA CA

Cavity properties

Ligandability	Volume (Å3)
0.462	573.750

% Hydrophobic	% Polar
51.76	48.24
According to VolSite

Ligand :

HET Code:	DUN
Formula:	C9H12N3O10P2
Molecular weight:	384.153 g/mol
DrugBank ID:	DB03641
Buried Surface Area:	66.31 %
Polar Surface area:	223.07 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	3
Rings:	2
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-4.40487	18.8449	21.8489

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
O2	NE2	GLN- 21	2.85	154.29	H-Bond (Protein Donor)	false
N3	OD1	ASN- 25	2.83	170.24	H-Bond (Ligand Donor)	false
C3'	CB	ASP- 79	4.05	0	Hydrophobic	false
O3'	OD1	ASP- 79	2.67	167.26	H-Bond (Ligand Donor)	false
C2'	CB	HIS- 82	3.45	0	Hydrophobic	false
C2'	CZ	PHE- 83	3.63	0	Hydrophobic	false
O2B	NZ	LYS- 208	2.56	167.55	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 208	2.56	0	Ionic (Protein Cationic)	false
O3'	ND2	ASN- 212	3.02	160.21	H-Bond (Protein Donor)	false
O2B	NH1	ARG- 215	2.81	161.52	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 215	3.33	133.26	H-Bond (Protein Donor)	false
O2B	CZ	ARG- 215	3.52	0	Ionic (Protein Cationic)	false
O1A	OH	TYR- 220	2.57	169.43	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 227	2.89	172.05	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 227	2.89	0	Ionic (Protein Cationic)	false
O1B	ND2	ASN- 235	3.42	141.67	H-Bond (Protein Donor)	false
O2A	CA	CA- 301	2.2	0	Metal Acceptor	false
O3B	CA	CA- 301	2.43	0	Metal Acceptor	false
O3B	CA	CA- 302	2.31	0	Metal Acceptor	false