scPDB - 4hdh entry

Protein Data Bank Entry:

PDB ID : 4hdh

Resolution :2.280 Å

Experimental Method : X-ray

Deposition Date : 2012-10-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Genome polyprotein
ID:	POLG_JAEV1
AC:	P27395
Organism:	Japanese encephalitis virus
Reign:	Viruses
TaxID:	11073
EC Number:	2.7.7.48

Chains:

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

Ligand binding site composition:

B-Factor:	38.824
Number of residues:	35
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.763	1103.625

% Hydrophobic	% Polar
37.31	62.69
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	62.77 %
Polar Surface area:	319.88 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-34.6964	24.3741	-19.3587

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
O3A	NH2	ARG- 460	3.31	136.32	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 474	3.13	0	Ionic (Protein Cationic)	false
C2'	CB	CYS- 714	3.92	0	Hydrophobic	false
O3'	OG	SER- 715	2.8	173.52	H-Bond (Protein Donor)	false
O2G	CZ	ARG- 734	2.72	0	Ionic (Protein Cationic)	false
O1G	CZ	ARG- 742	3.73	0	Ionic (Protein Cationic)	false
O2B	CZ	ARG- 742	3.4	0	Ionic (Protein Cationic)	false
O2B	NH2	ARG- 742	2.7	165.62	H-Bond (Protein Donor)	false
O2B	NH1	ARG- 742	3.28	130.33	H-Bond (Protein Donor)	false
O3B	NH1	ARG- 742	2.57	136.38	H-Bond (Protein Donor)	false
O1G	OG	SER- 799	2.59	157.1	H-Bond (Protein Donor)	false
O2B	N	TRP- 800	2.75	155.71	H-Bond (Protein Donor)	false
C2'	CB	SER- 801	4.09	0	Hydrophobic	false