scPDB - 1snf entry

Protein Data Bank Entry:

PDB ID : 1snf

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2004-03-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Deoxyuridine 5'-triphosphate nucleotidohydrolase
ID:	DUT_MYCTU
AC:	P9WNS5
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	3.6.1.23

Chains:

Chain Name:	Percentage of Residues within binding site
B	33 %
C	67 %

Ligand binding site composition:

B-Factor:	18.901
Number of residues:	32
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.139	286.875

% Hydrophobic	% Polar
34.12	65.88
According to VolSite

Ligand :

HET Code:	UMP
Formula:	C9H11N2O8P
Molecular weight:	306.166 g/mol
DrugBank ID:	DB03800
Buried Surface Area:	57.93 %
Polar Surface area:	161.1 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	2
Rings:	2
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
15.5831	6.05735	10.3231

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
C5'	CB	SER- 65	4.33	0	Hydrophobic	false
OP2	N	SER- 65	3.38	164.7	H-Bond (Protein Donor)	false
OP1	N	GLY- 66	3.36	164.63	H-Bond (Protein Donor)	false
C2'	CD1	ILE- 82	3.72	0	Hydrophobic	false
O3'	N	ASP- 83	3.16	173.07	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 83	2.82	148.01	H-Bond (Ligand Donor)	false
C1'	CZ	TYR- 86	3.88	0	Hydrophobic	false
C2'	CD2	TYR- 86	3.48	0	Hydrophobic	false
C3'	CG	TYR- 86	4.16	0	Hydrophobic	false
C4'	CD1	TYR- 86	4.37	0	Hydrophobic	false
N3	O	LYS- 91	2.73	136.81	H-Bond (Ligand Donor)	false
O2	N	LYS- 91	3.22	177.84	H-Bond (Protein Donor)	false
OP3	MG	MG- 3171	2.4	0	Metal Acceptor	false
OP2	O	HOH- 3212	2.98	167.95	H-Bond (Protein Donor)	false