scPDB - 2hek entry

Protein Data Bank Entry:

PDB ID : 2hek

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2006-06-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uncharacterized protein
ID:	O67745_AQUAE
AC:	O67745
Organism:	Aquifex aeolicus
Reign:	Bacteria
TaxID:	224324
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	46 %
B	54 %

Ligand binding site composition:

B-Factor:	36.488
Number of residues:	24
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.381	2038.500

% Hydrophobic	% Polar
54.30	45.70
According to VolSite

Ligand :

HET Code:	GDP
Formula:	C10H12N5O11P2
Molecular weight:	440.177 g/mol
DrugBank ID:	DB04315
Buried Surface Area:	51.4 %
Polar Surface area:	276.39 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
19.0198	22.4883	22.1675

Binding mode :

What is Poseview ?

2D View
3D View

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	NZ	LYS- 3	3.78	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 3	2.98	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 3	2.98	137.2	H-Bond (Protein Donor)	false
C3'	CD	LYS- 3	4.08	0	Hydrophobic	false
C2'	CE1	PHE- 5	4.03	0	Hydrophobic	false
C1'	CD1	PHE- 5	4	0	Hydrophobic	false
N1	OD1	ASP- 24	2.92	157.74	H-Bond (Ligand Donor)	false
N2	OD1	ASP- 24	3.32	135.61	H-Bond (Ligand Donor)	false
O6	NE2	GLN- 29	2.92	153.82	H-Bond (Protein Donor)	false
N7	NH2	ARG- 32	3.15	176.85	H-Bond (Protein Donor)	false
O6	NH1	ARG- 32	2.97	148.99	H-Bond (Protein Donor)	false
C5'	CG1	VAL- 225	4.45	0	Hydrophobic	false
O2A	NE2	HIS- 282	3.06	145.73	H-Bond (Protein Donor)	false