scPDB - 4xpd entry

Protein Data Bank Entry:

PDB ID : 4xpd

Resolution :2.810 Å

Experimental Method : X-ray

Deposition Date : 2015-01-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	N-terminal acetyltransferase A complex subunit NAT5
ID:	NAT5_YEAST
AC:	Q08689
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	2.3.1

Chains:

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

Ligand binding site composition:

B-Factor:	42.768
Number of residues:	34
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.069	712.125

% Hydrophobic	% Polar
48.82	51.18
According to VolSite

Ligand :

HET Code:	ACO
Formula:	C23H34N7O17P3S
Molecular weight:	805.539 g/mol
DrugBank ID:	-
Buried Surface Area:	52.42 %
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
54.8002	-12.783	15.8207

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
C6P	CG2	VAL- 27	4.43	0	Hydrophobic	false
CH3	CD2	LEU- 30	3.76	0	Hydrophobic	false
CEP	CD2	LEU- 96	3.39	0	Hydrophobic	false
CEP	CG2	VAL- 98	4.12	0	Hydrophobic	false
CAP	CB	VAL- 98	4.45	0	Hydrophobic	false
CAP	CD	ARG- 103	3.97	0	Hydrophobic	false
O5A	N	HIS- 104	3.08	167.44	H-Bond (Protein Donor)	false
O1A	N	LYS- 105	3.15	124.35	H-Bond (Protein Donor)	false
O1A	N	SER- 106	3.06	125.95	H-Bond (Protein Donor)	false
O3A	N	GLY- 108	3.26	122.77	H-Bond (Protein Donor)	false
O4A	N	GLY- 108	3.15	147.35	H-Bond (Protein Donor)	false
O2A	N	SER- 109	2.83	133.91	H-Bond (Protein Donor)	false
C2P	CD2	LEU- 131	3.64	0	Hydrophobic	false
CH3	CD2	LEU- 131	4.46	0	Hydrophobic	false
O5B	NE1	TRP- 141	2.94	153.31	H-Bond (Protein Donor)	false
CCP	CE2	TRP- 141	3.75	0	Hydrophobic	false
CDP	CD2	TRP- 141	3.93	0	Hydrophobic	false