scPDB - 1ffy entry

Protein Data Bank Entry:

PDB ID : 1ffy

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2000-07-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Isoleucine--tRNA ligase
ID:	SYI1_STAAU
AC:	P41972
Organism:	Staphylococcus aureus
Reign:	Bacteria
TaxID:	1280
EC Number:	6.1.1.5

Chains:

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

Ligand binding site composition:

B-Factor:	19.930
Number of residues:	37
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.722	533.250

% Hydrophobic	% Polar
42.41	57.59
According to VolSite

Ligand :

HET Code:	MRC
Formula:	C26H43O9
Molecular weight:	499.614 g/mol
DrugBank ID:	DB00410
Buried Surface Area:	58.7 %
Polar Surface area:	148.88 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	3
Rings:	2
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	17

Mass center Coordinates

X	Y	Z
28.6684	79.8849	80.986

Binding mode :

What is Poseview ?

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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
C14	CG	PRO- 56	3.83	0	Hydrophobic	false
C10	CB	PRO- 57	3.97	0	Hydrophobic	false
C9'	CB	HIS- 64	4.3	0	Hydrophobic	false
C6'	CB	HIS- 64	3.95	0	Hydrophobic	false
C16	CB	ASN- 70	4.13	0	Hydrophobic	false
C13	CZ3	TRP- 528	3.94	0	Hydrophobic	false
C14	CB	SER- 531	3.72	0	Hydrophobic	false
C7	CB	GLU- 554	4.33	0	Hydrophobic	false
C17	CG	GLU- 554	3.97	0	Hydrophobic	false
O7	OE1	GLU- 554	2.59	169.99	H-Bond (Ligand Donor)	false
O7	N	GLY- 555	3.07	152.22	H-Bond (Protein Donor)	false
O6	N	GLY- 555	2.96	124.16	H-Bond (Protein Donor)	false
O6	OD1	ASP- 557	2.72	148.67	H-Bond (Ligand Donor)	false
C6	CG	GLN- 558	4.34	0	Hydrophobic	false
C17	CG	GLN- 558	3.76	0	Hydrophobic	false
O6	NE2	GLN- 558	3.19	152.29	H-Bond (Protein Donor)	false
C17	CB	TRP- 562	4.18	0	Hydrophobic	false
C14	CB	TRP- 562	3.98	0	Hydrophobic	false
C4	CE1	PHE- 587	3.69	0	Hydrophobic	false
C15	CD1	PHE- 587	3.75	0	Hydrophobic	false
O1B	N	VAL- 588	2.75	166.4	H-Bond (Protein Donor)	false
C5'	CB	MET- 596	4.34	0	Hydrophobic	false
C8'	CE	MET- 596	3.53	0	Hydrophobic	false
C3'	CD	LYS- 598	4.42	0	Hydrophobic	false
O13	O	HOH- 2085	2.65	161.23	H-Bond (Ligand Donor)	false