scPDB - 1bif entry

Protein Data Bank Entry:

PDB ID : 1bif

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 1996-11-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4
ID:	F264_RAT
AC:	P25114
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	2.7.1.105

Chains:

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

Ligand binding site composition:

B-Factor:	33.324
Number of residues:	42
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
1.514	421.875

% Hydrophobic	% Polar
64.80	35.20
According to VolSite

Ligand :

HET Code:	AGS
Formula:	C10H14N5O12P3S
Molecular weight:	521.231 g/mol
DrugBank ID:	DB02930
Buried Surface Area:	70.04 %
Polar Surface area:	329.24 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
53.7971	54.0035	61.569

Binding mode :

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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
O3B	N	ALA- 48	2.86	165.56	H-Bond (Protein Donor)	false
O2B	N	ARG- 49	2.79	149.88	H-Bond (Protein Donor)	false
O3A	N	GLY- 50	3.12	134.24	H-Bond (Protein Donor)	false
O2B	N	LYS- 51	3.18	163.17	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 51	3.06	162.94	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 51	3.06	0	Ionic (Protein Cationic)	false
O1B	N	THR- 52	3.01	163.67	H-Bond (Protein Donor)	false
O2A	N	TYR- 53	2.71	148.95	H-Bond (Protein Donor)	false
C5'	CB	TYR- 53	3.77	0	Hydrophobic	false
C2'	CD1	TYR- 53	4.18	0	Hydrophobic	false
C4'	CB	ASN- 167	4.37	0	Hydrophobic	false
N3	ND2	ASN- 167	3.34	135.06	H-Bond (Protein Donor)	false
C3'	CG1	VAL- 171	3.85	0	Hydrophobic	false
O2G	NZ	LYS- 172	3.82	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 172	2.51	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 172	3.15	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 172	2.51	127.23	H-Bond (Protein Donor)	false
O3B	NZ	LYS- 172	2.78	134.45	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 172	3.15	169.04	H-Bond (Protein Donor)	false
C2'	CG1	VAL- 246	4.48	0	Hydrophobic	false
C3'	CB	ALA- 426	4.03	0	Hydrophobic	false
O2A	OH	TYR- 427	3.46	163.98	H-Bond (Protein Donor)	false
C5'	CE1	TYR- 427	4.21	0	Hydrophobic	false
O2G	MG	MG- 501	2.25	0	Metal Acceptor	false
O2G	O	HOH- 907	3.5	126	H-Bond (Protein Donor)	false