scPDB - 4xf6 entry

Protein Data Bank Entry:

PDB ID : 4xf6

Resolution :2.080 Å

Experimental Method : X-ray

Deposition Date : 2014-12-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Carbohydrate/pyrimidine kinase, PfkB family
ID:	Q5JDA3_THEKO
AC:	Q5JDA3
Organism:	Thermococcus kodakarensis )
Reign:	Archaea
TaxID:	69014
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	40.603
Number of residues:	43
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	2
Water Molecules:	3
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.233	732.375

% Hydrophobic	% Polar
38.25	61.75
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	71.12 %
Polar Surface area:	260.7 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
6.25804	35.8093	-12.709

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
N7	ND2	ASN- 83	3.38	163.31	H-Bond (Protein Donor)	false
N6	OD1	ASN- 83	3.17	160.19	H-Bond (Ligand Donor)	false
O3B	OD2	ASP- 166	2.64	154.09	H-Bond (Protein Donor)	false
O1A	OG	SER- 187	2.57	153.85	H-Bond (Protein Donor)	false
C5'	CB	SER- 187	3.77	0	Hydrophobic	false
O1A	N	GLY- 189	2.84	171.72	H-Bond (Protein Donor)	false
C2'	CG	PRO- 206	3.66	0	Hydrophobic	false
C5'	CB	ALA- 217	4.38	0	Hydrophobic	false
O2B	N	GLY- 218	2.72	142.37	H-Bond (Protein Donor)	false
C4'	CG	PHE- 221	4.27	0	Hydrophobic	false
C4'	CG2	THR- 245	4.4	0	Hydrophobic	false
C1'	CG2	THR- 245	3.59	0	Hydrophobic	false
C1'	CD1	LEU- 249	4.25	0	Hydrophobic	false
O1B	MG	MG- 304	2.02	0	Metal Acceptor	false
O3'	O	HOH- 407	2.92	151.99	H-Bond (Ligand Donor)	false
O2'	O	HOH- 421	2.55	158.16	H-Bond (Protein Donor)	false