scPDB - 2rd5 entry

Protein Data Bank Entry:

PDB ID : 2rd5

Resolution :2.510 Å

Experimental Method : X-ray

Deposition Date : 2007-09-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Acetylglutamate kinase, chloroplastic
ID:	NAGK_ARATH
AC:	Q9SCL7
Organism:	Arabidopsis thaliana
Reign:	Eukaryota
TaxID:	3702
EC Number:	2.7.2.8

Chains:

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

Ligand binding site composition:

B-Factor:	65.397
Number of residues:	27
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	ADP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.791	880.875

% Hydrophobic	% Polar
41.76	58.24
According to VolSite

Ligand :

HET Code:	NLG
Formula:	C7H9NO5
Molecular weight:	187.150 g/mol
DrugBank ID:	DB04075
Buried Surface Area:	69.6 %
Polar Surface area:	109.36 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	1
Rings:	0
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
91.3871	38.1261	48.8312

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
C8	CD2	LEU- 97	3.98	0	Hydrophobic	false
OXT	CZ	ARG- 98	3.8	0	Ionic (Protein Cationic)	false
O	CZ	ARG- 98	3.65	0	Ionic (Protein Cationic)	false
OXT	NH2	ARG- 98	3.16	141.06	H-Bond (Protein Donor)	false
O	NE	ARG- 98	2.76	159.4	H-Bond (Protein Donor)	false
O7	N	ARG- 98	3.35	157.42	H-Bond (Protein Donor)	false
C8	CB	ARG- 98	4.43	0	Hydrophobic	false
CB	CD1	LEU- 112	4.14	0	Hydrophobic	false
C8	CG1	VAL- 156	4.13	0	Hydrophobic	false
O	ND2	ASN- 192	2.75	173.12	H-Bond (Protein Donor)	false
N2	OD1	ASN- 192	2.85	134.38	H-Bond (Ligand Donor)	false
OE1	N	ALA- 195	3.07	169.2	H-Bond (Protein Donor)	false