scPDB - 3sj7 entry

Protein Data Bank Entry:

PDB ID : 3sj7

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2011-06-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	3-oxoacyl-(Acyl-carrier-protein) reductase, putative
ID:	Q2FZ53_STAA8
AC:	Q2FZ53
Organism:	Staphylococcus aureus
Reign:	Bacteria
TaxID:	93061
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	45.456
Number of residues:	46
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.964	833.625

% Hydrophobic	% Polar
40.49	59.51
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	65.48 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-4.25444	39.4741	22.4234

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
O3B	OG	SER- 11	2.98	154.22	H-Bond (Ligand Donor)	false
O3X	OG	SER- 11	2.93	130.66	H-Bond (Protein Donor)	false
C3B	CD	ARG- 12	4.36	0	Hydrophobic	false
O1X	NH1	ARG- 12	3.1	130.11	H-Bond (Protein Donor)	false
O3X	CZ	ARG- 12	3.46	0	Ionic (Protein Cationic)	false
O1N	N	ILE- 14	2.91	157.61	H-Bond (Protein Donor)	false
C5D	CB	ILE- 14	3.9	0	Hydrophobic	false
C3N	CD1	ILE- 14	4.42	0	Hydrophobic	false
O2X	N	ALA- 34	2.72	122.36	H-Bond (Protein Donor)	false
O2X	N	GLY- 35	2.6	163.77	H-Bond (Protein Donor)	false
O2X	N	SER- 36	2.93	176.79	H-Bond (Protein Donor)	false
O3X	OG	SER- 36	2.87	152.88	H-Bond (Protein Donor)	false
N6A	OD1	ASN- 60	2.72	160.2	H-Bond (Ligand Donor)	false
N1A	N	VAL- 61	2.93	168.09	H-Bond (Protein Donor)	false
O3D	O	ASN- 87	2.81	142.24	H-Bond (Ligand Donor)	false
C1B	CB	ALA- 88	3.99	0	Hydrophobic	false
N6A	OG1	THR- 110	3.47	126.17	H-Bond (Ligand Donor)	false
C4D	CB	LEU- 137	4.02	0	Hydrophobic	false
C4N	CB	SER- 139	4.3	0	Hydrophobic	false
C2D	CZ	TYR- 152	4.44	0	Hydrophobic	false
O3D	NZ	LYS- 156	2.96	147.54	H-Bond (Protein Donor)	false
C5N	CG	PRO- 182	3.42	0	Hydrophobic	false
O7N	N	ILE- 185	3.27	169.88	H-Bond (Protein Donor)	false
O1N	O	HOH- 298	2.5	157.11	H-Bond (Protein Donor)	false