scPDB - 4fda entry

Protein Data Bank Entry:

PDB ID : 4fda

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2012-05-27

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
ID:	FABG_YEAST
AC:	P35731
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	1.1.1.100

Chains:

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

Ligand binding site composition:

B-Factor:	18.116
Number of residues:	44
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.166	283.500

% Hydrophobic	% Polar
28.57	71.43
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	51.75 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-41.2558	21.9613	19.2431

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	OG1	THR- 13	2.78	172.54	H-Bond (Ligand Donor)	false
O1X	OG1	THR- 13	2.56	151.17	H-Bond (Protein Donor)	false
C3B	CG	ARG- 14	3.93	0	Hydrophobic	false
O1N	NH1	ARG- 14	3.27	156.7	H-Bond (Protein Donor)	false
O1X	NE	ARG- 14	3.2	142.86	H-Bond (Protein Donor)	false
O3X	NH2	ARG- 14	3.13	152.5	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 14	3.92	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 14	3.98	0	Ionic (Protein Cationic)	false
O2X	N	SER- 36	2.95	163.81	H-Bond (Protein Donor)	false
O2X	OG	SER- 36	2.59	151.94	H-Bond (Protein Donor)	false
O2X	OG	SER- 40	2.57	174.78	H-Bond (Protein Donor)	false
N6A	OD1	ASP- 66	2.86	146.02	H-Bond (Ligand Donor)	false
N1A	N	PHE- 67	2.88	160.22	H-Bond (Protein Donor)	false
C1B	CB	ALA- 121	3.87	0	Hydrophobic	false
O4B	N	GLY- 122	2.99	164.36	H-Bond (Protein Donor)	false
C3D	CG2	THR- 124	3.87	0	Hydrophobic	false
C3N	CG2	THR- 124	4.05	0	Hydrophobic	false
O7N	N	GLN- 125	3.47	132.55	H-Bond (Protein Donor)	false
O7N	N	GLU- 126	3.21	155.8	H-Bond (Protein Donor)	false
O2D	OG	SER- 183	3.37	153.02	H-Bond (Protein Donor)	false
C4N	CG2	THR- 195	3.79	0	Hydrophobic	false
O2D	OH	TYR- 198	2.87	146.71	H-Bond (Ligand Donor)	false
C2D	CZ	TYR- 198	3.53	0	Hydrophobic	false
O1A	O	HOH- 408	3.05	179.97	H-Bond (Protein Donor)	false