scPDB - 3dzv entry

Protein Data Bank Entry:

PDB ID : 3dzv

Resolution :2.570 Å

Experimental Method : X-ray

Deposition Date : 2008-07-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Hydroxyethylthiazole kinase
ID:	THIM_ENTFA
AC:	Q830K4
Organism:	Enterococcus faecalis
Reign:	Bacteria
TaxID:	226185
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	36.361
Number of residues:	34
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.495	675.000

% Hydrophobic	% Polar
40.00	60.00
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	64.47 %
Polar Surface area:	260.7 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
121.496	124.519	146.99

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
O2B	ND2	ASN- 121	3.12	166.38	H-Bond (Protein Donor)	false
O1A	OG1	THR- 172	2.59	164.03	H-Bond (Protein Donor)	false
C3'	CB	THR- 172	3.92	0	Hydrophobic	false
O2'	OD1	ASP- 176	2.57	168.28	H-Bond (Ligand Donor)	false
C1'	CD1	LEU- 194	3.89	0	Hydrophobic	false
C5'	CB	THR- 200	3.77	0	Hydrophobic	false
O1B	N	GLY- 201	3.48	132.85	H-Bond (Protein Donor)	false
C4'	CG2	VAL- 204	4.29	0	Hydrophobic	false
C4'	CE2	PHE- 229	4.39	0	Hydrophobic	false
O3'	ND2	ASN- 230	3.29	123.82	H-Bond (Protein Donor)	false
O2'	ND2	ASN- 230	2.7	154.01	H-Bond (Protein Donor)	false
O3'	OD1	ASN- 230	2.9	175.84	H-Bond (Ligand Donor)	false