scPDB - 5f8f entry

Protein Data Bank Entry:

PDB ID : 5f8f

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2015-12-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Possible transcriptional regulatory protein
ID:	O53532_MYCTU
AC:	O53532
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	35.804
Number of residues:	35
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.363	2170.125

% Hydrophobic	% Polar
55.37	44.63
According to VolSite

Ligand :

HET Code:	SFG
Formula:	C15H24N7O5
Molecular weight:	382.395 g/mol
DrugBank ID:	DB01910
Buried Surface Area:	61.46 %
Polar Surface area:	214.71 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
105.525	-32.1056	74.9217

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
C2'	CZ	TYR- 132	4.15	0	Hydrophobic	false
O	OG	SER- 146	2.53	164.88	H-Bond (Protein Donor)	false
N	O	GLY- 179	2.66	168.49	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 202	2.66	157.1	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 202	3.41	133.96	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 202	2.82	146.85	H-Bond (Ligand Donor)	false
N3	N	PHE- 203	3.3	142.17	H-Bond (Protein Donor)	false
DuAr	DuAr	PHE- 203	3.71	0	Aromatic Face/Face	false
C2'	CE1	PHE- 203	3.67	0	Hydrophobic	false
N6	OD1	ASP- 229	3	170.06	H-Bond (Ligand Donor)	false
N1	N	LEU- 230	2.76	163.1	H-Bond (Protein Donor)	false
N	O	PHE- 245	3.09	168.72	H-Bond (Ligand Donor)	false
NE	OD2	ASP- 246	3.2	0	Ionic (Ligand Cationic)	false
NE	O	ASP- 246	2.85	163.19	H-Bond (Ligand Donor)	false
C5'	CB	ALA- 247	4.2	0	Hydrophobic	false
N7	NE2	GLN- 251	3.1	128.37	H-Bond (Protein Donor)	false