scPDB - 2hk9 entry

Protein Data Bank Entry:

PDB ID : 2hk9

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2006-07-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Shikimate dehydrogenase (NADP(+))
ID:	AROE_AQUAE
AC:	O67049
Organism:	Aquifex aeolicus
Reign:	Bacteria
TaxID:	224324
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	48.850
Number of residues:	27
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.273	469.125

% Hydrophobic	% Polar
51.08	48.92
According to VolSite

Ligand :

HET Code:	ATR
Formula:	C10H11N5O13P3
Molecular weight:	502.141 g/mol
DrugBank ID:	DB02363
Buried Surface Area:	48.44 %
Polar Surface area:	322.71 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	5
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
49.3824	64.3284	76.9224

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
O3'	N	ALA- 131	3.11	170.12	H-Bond (Protein Donor)	false
O2A	N	GLY- 133	2.77	140.05	H-Bond (Protein Donor)	false
O1B	N	ALA- 134	3.12	132.28	H-Bond (Protein Donor)	false
O2B	N	ALA- 134	3.06	145.48	H-Bond (Protein Donor)	false
O2P	ND2	ASN- 153	2.74	165.96	H-Bond (Protein Donor)	false
O2'	NH2	ARG- 154	3.35	140.24	H-Bond (Protein Donor)	false
O1P	NE	ARG- 154	2.96	169.5	H-Bond (Protein Donor)	false
O3P	NH2	ARG- 154	2.73	148.71	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 154	3.72	0	Ionic (Protein Cationic)	false
O3P	CZ	ARG- 154	3.72	0	Ionic (Protein Cationic)	false
DuAr	CZ	ARG- 154	3.43	165.2	Pi/Cation	false
O1P	OG1	THR- 155	2.64	158.2	H-Bond (Protein Donor)	false
O1P	N	THR- 155	2.9	124	H-Bond (Protein Donor)	false
O2P	NZ	LYS- 158	3.62	0	Ionic (Protein Cationic)	false
C4'	CB	THR- 188	4.4	0	Hydrophobic	false
C1'	CB	THR- 188	3.67	0	Hydrophobic	false
C5'	CB	SER- 189	4.36	0	Hydrophobic	false
O4'	N	SER- 189	3.26	162.71	H-Bond (Protein Donor)	false