scPDB - 5fmm entry

Protein Data Bank Entry:

PDB ID : 5fmm

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2015-11-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Polymerase basic protein 2
ID:	Q6DNN3_9INFA
AC:	Q6DNN3
Organism:	Influenza A virus )
Reign:	Viruses
TaxID:	284218
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	40.692
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.124	850.500

% Hydrophobic	% Polar
38.89	61.11
According to VolSite

Ligand :

HET Code:	MGT
Formula:	C11H16N5O14P3
Molecular weight:	535.191 g/mol
DrugBank ID:	DB03358
Buried Surface Area:	65.35 %
Polar Surface area:	324.22 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	4
Rings:	3
Aromatic rings:	0
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
52.8114	-34.0285	10.5364

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'	CD2	PHE- 323	3.95	0	Hydrophobic	false
C1'	CE2	PHE- 323	3.85	0	Hydrophobic	false
C5'	CD1	PHE- 325	4.29	0	Hydrophobic	false
O3G	NZ	LYS- 339	2.72	157.69	H-Bond (Protein Donor)	false
O3G	NZ	LYS- 339	2.72	0	Ionic (Protein Cationic)	false
O1G	NH2	ARG- 355	3.43	134.75	H-Bond (Protein Donor)	false
O1G	NE	ARG- 355	2.88	172.39	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 355	2.92	129.15	H-Bond (Protein Donor)	false
O1G	CZ	ARG- 355	3.6	0	Ionic (Protein Cationic)	false
O2B	CZ	ARG- 355	3.91	0	Ionic (Protein Cationic)	false
O2G	NE2	HIS- 357	2.85	157.73	H-Bond (Protein Donor)	false
N1	OE1	GLU- 361	2.76	166.53	H-Bond (Ligand Donor)	false
N2	OE2	GLU- 361	2.87	156.84	H-Bond (Ligand Donor)	false
N2	OE1	GLU- 361	3.36	130.63	H-Bond (Ligand Donor)	false
O6	NZ	LYS- 376	3.11	125.66	H-Bond (Protein Donor)	false
C8	CE1	PHE- 404	3.65	0	Hydrophobic	false
CM7	CE1	PHE- 404	4	0	Hydrophobic	false
CM7	CG	GLN- 406	4.06	0	Hydrophobic	false
O1A	ND2	ASN- 429	2.89	155.27	H-Bond (Protein Donor)	false
CM7	CE	MET- 431	4.3	0	Hydrophobic	false