scPDB - 4r57 entry

Protein Data Bank Entry:

PDB ID : 4r57

Resolution :2.080 Å

Experimental Method : X-ray

Deposition Date : 2014-08-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Spermidine N(1)-acetyltransferase
ID:	ATDA_VIBCH
AC:	Q9KL03
Organism:	Vibrio cholerae serotype O1
Reign:	Bacteria
TaxID:	243277
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	5 %
J	95 %

Ligand binding site composition:

B-Factor:	42.449
Number of residues:	38
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.800	715.500

% Hydrophobic	% Polar
49.06	50.94
According to VolSite

Ligand :

HET Code:	ACO
Formula:	C23H34N7O17P3S
Molecular weight:	805.539 g/mol
DrugBank ID:	-
Buried Surface Area:	50.2 %
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
116.394	118.979	-17.6565

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
C2P	CB	TYR- 30	4.43	0	Hydrophobic	false
C2P	CE2	PHE- 32	4.17	0	Hydrophobic	false
CH3	CE2	PHE- 32	4.12	0	Hydrophobic	false
CH3	CB	GLN- 86	3.86	0	Hydrophobic	false
O	N	ILE- 87	3.18	152.56	H-Bond (Protein Donor)	false
CDP	CD1	ILE- 89	3.6	0	Hydrophobic	false
O9P	N	ILE- 89	3.05	148.57	H-Bond (Protein Donor)	false
CAP	CG	GLN- 94	3.91	0	Hydrophobic	false
O1A	N	GLY- 97	2.94	154.55	H-Bond (Protein Donor)	false
O2A	N	ALA- 99	3.42	128.33	H-Bond (Protein Donor)	false
CCP	CB	ALA- 99	4.24	0	Hydrophobic	false
CDP	CB	ALA- 99	4.2	0	Hydrophobic	false
O7A	CZ	ARG- 100	3.29	0	Ionic (Protein Cationic)	false
O9A	CZ	ARG- 100	3.79	0	Ionic (Protein Cationic)	false
O7A	NH2	ARG- 100	3.26	124.46	H-Bond (Protein Donor)	false
O9A	NH2	ARG- 100	2.94	150.9	H-Bond (Protein Donor)	false
C2P	CG1	VAL- 123	3.25	0	Hydrophobic	false
C1B	CG	LYS- 129	4.19	0	Hydrophobic	false
OAP	NZ	LYS- 129	3.21	167.11	H-Bond (Protein Donor)	false
CEP	CB	ALA- 130	4.33	0	Hydrophobic	false
S1P	CE2	TYR- 134	4.15	0	Hydrophobic	false