scPDB - 4hyv entry

Protein Data Bank Entry:

PDB ID : 4hyv

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2012-11-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pyruvate kinase 1
ID:	KPYK1_TRYBB
AC:	P30615
Organism:	Trypanosoma brucei brucei
Reign:	Eukaryota
TaxID:	5702
EC Number:	2.7.1.40

Chains:

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

Ligand binding site composition:

B-Factor:	30.168
Number of residues:	28
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:
Metals:	MG K

Cavity properties

Ligandability	Volume (Å3)
0.138	695.250

% Hydrophobic	% Polar
31.55	68.45
According to VolSite

Ligand :

HET Code:	PEP
Formula:	C3H2O6P
Molecular weight:	165.018 g/mol
DrugBank ID:	DB01819
Buried Surface Area:	65.06 %
Polar Surface area:	122.36 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	0
Rings:	0
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
-73.1716	-23.311	51.1531

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
O2	NZ	LYS- 239	3.04	150.76	H-Bond (Protein Donor)	false
O1P	NZ	LYS- 239	3.21	137.82	H-Bond (Protein Donor)	false
O1P	NZ	LYS- 239	3.21	0	Ionic (Protein Cationic)	false
C3	SD	MET- 260	3.6	0	Hydrophobic	false
C2	CB	ALA- 262	3.97	0	Hydrophobic	false
O2'	N	GLY- 264	2.72	144.61	H-Bond (Protein Donor)	false
O1	N	ASP- 265	2.83	175.46	H-Bond (Protein Donor)	false
C3	CB	ALA- 296	3.96	0	Hydrophobic	false
O2'	OG1	THR- 297	2.61	159.62	H-Bond (Protein Donor)	false
C3	CE	MET- 329	3.62	0	Hydrophobic	false
O1	MG	MG- 1001	2.16	0	Metal Acceptor	false
O2	MG	MG- 1001	2.56	0	Metal Acceptor	false
O2P	MG	MG- 1001	2.11	0	Metal Acceptor	false
O3P	O	HOH- 1261	2.58	129.29	H-Bond (Protein Donor)	false