scPDB - 3irh entry

Protein Data Bank Entry:

PDB ID : 3irh

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2009-08-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	HD domain protein
ID:	Q836G9_ENTFA
AC:	Q836G9
Organism:	Enterococcus faecalis
Reign:	Bacteria
TaxID:	226185
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	41.799
Number of residues:	35
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:	CA

Cavity properties

Ligandability	Volume (Å3)
0.197	732.375

% Hydrophobic	% Polar
26.73	73.27
According to VolSite

Ligand :

HET Code:	DTP
Formula:	C10H12N5O12P3
Molecular weight:	487.150 g/mol
DrugBank ID:	DB03222
Buried Surface Area:	56.67 %
Polar Surface area:	299.64 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-51.1821	28.9884	6.19007

Binding mode :

What is Poseview ?

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3D View

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
C1'	CD2	LEU- 49	4.21	0	Hydrophobic	false
O2A	CZ	ARG- 63	3.89	0	Ionic (Protein Cationic)	false
O2A	NH1	ARG- 63	2.86	157.95	H-Bond (Protein Donor)	false
O3B	NE2	HIS- 119	3.21	142.3	H-Bond (Protein Donor)	false
C5'	CE2	TYR- 187	3.7	0	Hydrophobic	false
C4'	CE1	TYR- 187	3.69	0	Hydrophobic	false
C3'	CZ	TYR- 187	4.42	0	Hydrophobic	false
C3'	CZ	TYR- 239	4.48	0	Hydrophobic	false
C2'	CE1	TYR- 239	4.47	0	Hydrophobic	false
C2'	CG	TYR- 243	4.38	0	Hydrophobic	false
C1'	CD2	TYR- 243	3.5	0	Hydrophobic	false
O1G	OH	TYR- 368	2.68	159.09	H-Bond (Protein Donor)	false
C2'	CE2	TYR- 368	3.27	0	Hydrophobic	false
O4'	O	HOH- 519	2.94	179.96	H-Bond (Protein Donor)	false