scPDB - 3f5m entry

Protein Data Bank Entry:

PDB ID : 3f5m

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2008-11-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	ATP-dependent 6-phosphofructokinase
ID:	PFKA_TRYBB
AC:	O15648
Organism:	Trypanosoma brucei brucei
Reign:	Eukaryota
TaxID:	5702
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	31.527
Number of residues:	37
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.780	1535.625

% Hydrophobic	% Polar
36.48	63.52
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	58.98 %
Polar Surface area:	319.88 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
5.05377	-20.5034	8.98984

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
C5'	CB	CYS- 105	3.84	0	Hydrophobic	false
O3G	N	GLY- 107	2.72	159.81	H-Bond (Protein Donor)	false
C4'	CD2	TYR- 139	3.85	0	Hydrophobic	false
C1'	CD2	TYR- 139	4.25	0	Hydrophobic	false
O1G	CZ	ARG- 173	4	0	Ionic (Protein Cationic)	false
O3G	CZ	ARG- 173	3.94	0	Ionic (Protein Cationic)	false
O1A	CZ	ARG- 173	3.74	0	Ionic (Protein Cationic)	false
O1A	NE	ARG- 173	2.93	155.57	H-Bond (Protein Donor)	false
O1B	N	GLY- 200	3.25	146.77	H-Bond (Protein Donor)	false
O2B	N	THR- 201	2.98	163.32	H-Bond (Protein Donor)	false
O2B	OG1	THR- 201	2.72	168	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 226	3.98	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 226	3.27	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 226	3.27	151.03	H-Bond (Protein Donor)	false
O1A	OG	SER- 341	2.85	164.14	H-Bond (Protein Donor)	false
C2'	CB	SER- 341	3.84	0	Hydrophobic	false
O2A	ND2	ASN- 343	2.87	169.09	H-Bond (Protein Donor)	false
O1B	MG	MG- 1002	2.56	0	Metal Acceptor	false
O2A	MG	MG- 1002	2.79	0	Metal Acceptor	false