scPDB - 4wh3 entry

Protein Data Bank Entry:

PDB ID : 4wh3

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2014-09-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	N-acetylhexosamine 1-kinase
ID:	NAHK_BIFL2
AC:	E8MF12
Organism:	Bifidobacterium longum subsp. longum
Reign:	Bacteria
TaxID:	565042
EC Number:	2.7.1.162

Chains:

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

Ligand binding site composition:

B-Factor:	23.606
Number of residues:	35
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.571	621.000

% Hydrophobic	% Polar
44.02	55.98
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	70.85 %
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
49.8897	44.4205	64.5437

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
C1'	CE2	TYR- 27	4	0	Hydrophobic	false
O3'	N	ASP- 29	3.48	152.92	H-Bond (Protein Donor)	false
O2G	N	HIS- 31	2.87	164.81	H-Bond (Protein Donor)	false
O3B	N	HIS- 31	3.24	129.09	H-Bond (Protein Donor)	false
O3B	N	ILE- 32	3.27	160.2	H-Bond (Protein Donor)	false
O1B	N	ASN- 33	2.71	152.91	H-Bond (Protein Donor)	false
O1B	ND2	ASN- 33	2.93	131.72	H-Bond (Protein Donor)	false
C5'	CB	THR- 35	4.33	0	Hydrophobic	false
C4'	CG2	THR- 35	4.2	0	Hydrophobic	false
O1A	NE2	GLN- 48	3.02	154.11	H-Bond (Protein Donor)	false
N6	O	LYS- 103	3.12	139.51	H-Bond (Ligand Donor)	false
N1	N	ILE- 105	2.83	172.23	H-Bond (Protein Donor)	false
C2'	CD1	ILE- 227	3.61	0	Hydrophobic	false
O3G	MG	MG- 402	2.01	0	Metal Acceptor	false
O2A	MG	MG- 402	1.89	0	Metal Acceptor	false
O1G	MG	MG- 403	2.09	0	Metal Acceptor	false
O2B	MG	MG- 403	1.95	0	Metal Acceptor	false