scPDB - 1kf0 entry

Protein Data Bank Entry:

PDB ID : 1kf0

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2001-11-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Phosphoglycerate kinase 1
ID:	PGK1_PIG
AC:	Q7SIB7
Organism:	Sus scrofa
Reign:	Eukaryota
TaxID:	9823
EC Number:	2.7.2.3

Chains:

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

Ligand binding site composition:

B-Factor:	19.239
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.567	324.000

% Hydrophobic	% Polar
60.42	39.58
According to VolSite

Ligand :

HET Code:	ACP
Formula:	C11H14N5O12P3
Molecular weight:	501.176 g/mol
DrugBank ID:	DB03909
Buried Surface Area:	47.88 %
Polar Surface area:	310.64 Å2

Number of
H-Bond Acceptors:	16
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
6.88877	3.28168	24.5569

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
O1A	N	ALA- 214	3.23	160.24	H-Bond (Protein Donor)	false
C1'	CB	ALA- 214	4.25	0	Hydrophobic	false
C4'	CB	ALA- 214	4.19	0	Hydrophobic	false
O1A	NZ	LYS- 219	3.11	146.86	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 219	3.11	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 219	3.75	0	Ionic (Protein Cationic)	false
N7	N	GLY- 238	3.39	123.97	H-Bond (Protein Donor)	false
N6	O	GLY- 312	3.2	147.28	H-Bond (Ligand Donor)	false
C2'	CG	PRO- 338	4.21	0	Hydrophobic	false
O3'	OE2	GLU- 343	2.99	167.22	H-Bond (Ligand Donor)	false
O2B	MG	MG- 518	2.23	0	Metal Acceptor	false