scPDB - 4hn1 entry

Protein Data Bank Entry:

PDB ID : 4hn1

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2012-10-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	dTDP-4-dehydro-6-deoxyglucose 3-epimerase
ID:	CHMJ_STRBI
AC:	Q5SFD1
Organism:	Streptomyces bikiniensis
Reign:	Bacteria
TaxID:	1896
EC Number:	5.1.3.27

Chains:

Chain Name:	Percentage of Residues within binding site
A	7 %
C	22 %
D	70 %

Ligand binding site composition:

B-Factor:	28.380
Number of residues:	31
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.023	880.875

% Hydrophobic	% Polar
33.33	66.67
According to VolSite

Ligand :

HET Code:	TYD
Formula:	C10H13N2O11P2
Molecular weight:	399.165 g/mol
DrugBank ID:	DB03103
Buried Surface Area:	47.78 %
Polar Surface area:	220.27 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	2
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
38.3051	-12.5406	-21.2458

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
C4'	CB	HIS- 17	3.95	0	Hydrophobic	false
O2A	NH2	ARG- 21	2.96	160.59	H-Bond (Protein Donor)	false
O3B	NH1	ARG- 21	2.81	145.93	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 21	3.93	0	Ionic (Protein Cationic)	false
O3B	CZ	ARG- 21	3.67	0	Ionic (Protein Cationic)	false
N3	OE2	GLU- 26	2.73	177.8	H-Bond (Ligand Donor)	false
O4	NE2	GLN- 45	2.74	133.78	H-Bond (Protein Donor)	false
O2B	CZ	ARG- 57	3.42	0	Ionic (Protein Cationic)	false
O2B	NH1	ARG- 57	2.58	131.08	H-Bond (Protein Donor)	false
C5M	CE1	TYR- 136	3.7	0	Hydrophobic	false
C2'	CZ	TYR- 136	4.04	0	Hydrophobic	false
O4	O	HOH- 448	2.67	179.96	H-Bond (Protein Donor)	false