scPDB - 4dyb entry

Protein Data Bank Entry:

PDB ID : 4dyb

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2012-02-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Nucleoprotein
ID:	B4URF1_9INFA
AC:	B4URF1
Organism:	Influenza A virus )
Reign:	Viruses
TaxID:	382835
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	38 %
B	62 %

Ligand binding site composition:

B-Factor:	49.369
Number of residues:	37
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.562	1005.750

% Hydrophobic	% Polar
37.92	62.08
According to VolSite

Ligand :

HET Code:	0MH
Formula:	C27H24ClN5O6S
Molecular weight:	582.027 g/mol
DrugBank ID:	-
Buried Surface Area:	64.21 %
Polar Surface area:	161.97 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	1
Rings:	5
Aromatic rings:	4
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
0.94175	-32.909	12.3209

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
C23	CZ	TYR- 52	4.36	0	Hydrophobic	false
C26	CB	TYR- 52	4.27	0	Hydrophobic	false
CL4	CZ	TYR- 52	3.36	0	Hydrophobic	false
C26	CD1	LEU- 56	3.75	0	Hydrophobic	false
C4	CG	ARG- 99	4.27	0	Hydrophobic	false
C27	CD	ARG- 99	4.41	0	Hydrophobic	false
C15	CD	ARG- 99	3.83	0	Hydrophobic	false
C26	CZ2	TRP- 104	4.02	0	Hydrophobic	false
C23	CD1	TYR- 289	3.82	0	Hydrophobic	false
CL4	CD1	TYR- 289	3.75	0	Hydrophobic	false
DuAr	DuAr	TYR- 289	3.73	0	Aromatic Face/Face	false
DuAr	DuAr	TYR- 289	3.73	0	Aromatic Face/Face	false
C7	CB	ARG- 305	4.4	0	Hydrophobic	false
CL4	CD1	LEU- 306	3.98	0	Hydrophobic	false
C8	CD1	LEU- 306	3.76	0	Hydrophobic	false
CL4	CB	ASN- 309	3.8	0	Hydrophobic	false
C26	CG	TYR- 313	3.39	0	Hydrophobic	false
O34	OG	SER- 376	2.81	162.49	H-Bond (Protein Donor)	false