scPDB - 4qvt entry

Protein Data Bank Entry:

PDB ID : 4qvt

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2014-07-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Acetyltransferase YpeA
ID:	YPEA_ECOLI
AC:	P76539
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	2.3.1

Chains:

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

Ligand binding site composition:

B-Factor:	53.006
Number of residues:	37
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.109	867.375

% Hydrophobic	% Polar
47.86	52.14
According to VolSite

Ligand :

HET Code:	ACO
Formula:	C23H34N7O17P3S
Molecular weight:	805.539 g/mol
DrugBank ID:	-
Buried Surface Area:	47.99 %
Polar Surface area:	429.68 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	20

Mass center Coordinates

X	Y	Z
-51.9013	-7.47545	82.8945

Binding mode :

What is Poseview ?

2D View
3D View

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
S1P	CD2	LEU- 23	4.04	0	Hydrophobic	false
CH3	CB	ALA- 69	4.48	0	Hydrophobic	false
CDP	CG	LEU- 72	3.93	0	Hydrophobic	false
S1P	CB	LEU- 72	3.77	0	Hydrophobic	false
CH3	CB	LEU- 72	3.83	0	Hydrophobic	false
CDP	CG2	VAL- 74	3.94	0	Hydrophobic	false
CAP	CB	VAL- 74	4.37	0	Hydrophobic	false
O9P	N	VAL- 74	2.9	162.7	H-Bond (Protein Donor)	false
CAP	CD	ARG- 79	3.95	0	Hydrophobic	false
O5A	N	GLY- 80	2.85	160.13	H-Bond (Protein Donor)	false
O1A	N	GLY- 82	2.87	148.51	H-Bond (Protein Donor)	false
O4A	N	ALA- 84	3.09	158.48	H-Bond (Protein Donor)	false
CCP	CB	ALA- 84	3.61	0	Hydrophobic	false
C5B	CB	ASN- 85	4.49	0	Hydrophobic	false
O2A	N	ASN- 85	2.77	158.34	H-Bond (Protein Donor)	false
CH3	CG2	ILE- 105	4.33	0	Hydrophobic	false
CCP	SD	MET- 117	4.07	0	Hydrophobic	false
CEP	SD	MET- 117	3.91	0	Hydrophobic	false
C5B	CG	MET- 117	3.89	0	Hydrophobic	false
O	OH	TYR- 118	2.75	171.26	H-Bond (Protein Donor)	false
C1B	CD	ARG- 120	4.42	0	Hydrophobic	false
O8A	CZ	ARG- 120	2.72	0	Ionic (Protein Cationic)	false
O4A	O	HOH- 343	2.51	154.13	H-Bond (Protein Donor)	false