scPDB - 5ifi entry

Protein Data Bank Entry:

PDB ID : 5ifi

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2016-02-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Acetyl-coenzyme A synthetase
ID:	J9VFT1_CRYNH
AC:	J9VFT1
Organism:	Cryptococcus neoformans var. grubii serotype A
Reign:	Eukaryota
TaxID:	235443
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	68.246
Number of residues:	33
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.345	2237.625

% Hydrophobic	% Polar
51.43	48.57
According to VolSite

Ligand :

HET Code:	PRX
Formula:	C13H19N5O7P
Molecular weight:	388.293 g/mol
DrugBank ID:	DB03230
Buried Surface Area:	70.35 %
Polar Surface area:	187.7 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
24.622	32.8562	19.7246

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
C2P	CG2	ILE- 335	4.17	0	Hydrophobic	false
C3P	CG2	VAL- 411	3.71	0	Hydrophobic	false
N7	N	GLY- 412	3.49	151.26	H-Bond (Protein Donor)	false
N6	OD1	ASP- 436	2.94	156.47	H-Bond (Ligand Donor)	false
N6	O	THR- 437	2.65	153.97	H-Bond (Ligand Donor)	false
C2'	CE1	TYR- 438	4.05	0	Hydrophobic	false
C3P	CE2	TRP- 439	3.42	0	Hydrophobic	false
C5'	CB	MET- 440	3.85	0	Hydrophobic	false
C3'	CG	MET- 440	3.8	0	Hydrophobic	false
O2P	N	THR- 441	2.78	144.93	H-Bond (Protein Donor)	false
O2P	OG1	THR- 441	2.83	170.22	H-Bond (Protein Donor)	false
O2'	OD1	ASP- 527	2.97	143.91	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 527	3	163.61	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 527	3.01	129.67	H-Bond (Ligand Donor)	false
O3'	NH1	ARG- 542	3.24	142.52	H-Bond (Protein Donor)	false
C3'	CD	ARG- 542	4.17	0	Hydrophobic	false
O2P	CZ	ARG- 553	3.69	0	Ionic (Protein Cationic)	false
C5'	CD	ARG- 553	3.78	0	Hydrophobic	false