scPDB - 4rvn entry

Protein Data Bank Entry:

PDB ID : 4rvn

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2014-11-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Phenylacetate-coenzyme A ligase
ID:	Q8AAN6_BACTN
AC:	Q8AAN6
Organism:	Bacteroides thetaiotaomicron
Reign:	Bacteria
TaxID:	226186
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	51.781
Number of residues:	30
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.062	648.000

% Hydrophobic	% Polar
43.75	56.25
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	46.89 %
Polar Surface area:	426.11 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	18

Mass center Coordinates

X	Y	Z
27.7258	7.87197	70.2093

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
N3A	N	GLY- 164	2.9	149.59	H-Bond (Protein Donor)	false
O7A	OG	SER- 166	2.71	167.15	H-Bond (Protein Donor)	false
O9A	N	SER- 166	2.81	171.31	H-Bond (Protein Donor)	false
C1B	CE1	TYR- 187	4	0	Hydrophobic	false
O7A	NE	ARG- 190	2.88	169.22	H-Bond (Protein Donor)	false
O7A	NH2	ARG- 190	3.41	134.3	H-Bond (Protein Donor)	false
O7A	CZ	ARG- 190	3.59	0	Ionic (Protein Cationic)	false
N6A	O	LYS- 336	3.06	143.51	H-Bond (Ligand Donor)	false
O1A	NZ	LYS- 336	2.89	131.72	H-Bond (Protein Donor)	false
O4A	NZ	LYS- 336	2.97	133.39	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 336	2.89	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 336	3.85	0	Ionic (Protein Cationic)	false
O4A	NZ	LYS- 336	2.97	0	Ionic (Protein Cationic)	false
O4A	N	THR- 407	2.8	166.61	H-Bond (Protein Donor)	false
O5A	OG1	THR- 407	3.34	159.38	H-Bond (Protein Donor)	false
N1A	O	HOH- 627	2.87	179.95	H-Bond (Protein Donor)	false