scPDB - 4yfy entry

Protein Data Bank Entry:

PDB ID : 4yfy

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2015-02-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	VioF
ID:	M9P0Q2_9ENTR
AC:	M9P0Q2
Organism:	Providencia alcalifaciens
Reign:	Bacteria
TaxID:	126385
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	15.457
Number of residues:	36
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.036	752.625

% Hydrophobic	% Polar
51.57	48.43
According to VolSite

Ligand :

HET Code:	0FX
Formula:	C16H26N3O14P2
Molecular weight:	546.337 g/mol
DrugBank ID:	-
Buried Surface Area:	53.49 %
Polar Surface area:	283.77 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	5
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
39.9127	41.3011	86.4815

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
O3P	ND2	ASN- 10	2.93	167.56	H-Bond (Protein Donor)	false
C1G	CB	HIS- 75	3.91	0	Hydrophobic	false
C5G	CB	HIS- 75	4.5	0	Hydrophobic	false
O2G	NZ	LYS- 77	2.71	159.02	H-Bond (Protein Donor)	false
C2G	CG	LYS- 77	3.49	0	Hydrophobic	false
C3G	CZ3	TRP- 104	3.92	0	Hydrophobic	false
C5A	CZ	PHE- 105	3.71	0	Hydrophobic	false
C3	CD1	PHE- 105	3.22	0	Hydrophobic	false
O3	NE2	GLN- 107	3.01	173.46	H-Bond (Protein Donor)	false
O4P	OH	TYR- 151	2.77	131.21	H-Bond (Protein Donor)	false
C5	CZ	TYR- 151	3.83	0	Hydrophobic	false
C4	CE1	TYR- 151	4.26	0	Hydrophobic	false
C1	CB	HIS- 217	4.14	0	Hydrophobic	false
C1	CE1	PHE- 220	3.83	0	Hydrophobic	false
C5A	CE2	PHE- 220	3.69	0	Hydrophobic	false
O21	ND2	ASN- 222	2.77	148.12	H-Bond (Protein Donor)	false
N31	OD1	ASN- 222	2.88	169.31	H-Bond (Ligand Donor)	false