scPDB - 2nx3 entry

Protein Data Bank Entry:

PDB ID : 2nx3

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2006-11-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	2-dehydro-3-deoxyphosphooctonate aldolase
ID:	KDSA_AQUAE
AC:	O66496
Organism:	Aquifex aeolicus
Reign:	Bacteria
TaxID:	224324
EC Number:	2.5.1.55

Chains:

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

Ligand binding site composition:

B-Factor:	27.798
Number of residues:	24
Including
Standard Amino Acids:	23
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.303	681.750

% Hydrophobic	% Polar
40.59	59.41
According to VolSite

Ligand :

HET Code:	PEP
Formula:	C3H2O6P
Molecular weight:	165.018 g/mol
DrugBank ID:	DB01819
Buried Surface Area:	70.22 %
Polar Surface area:	122.36 Å2

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

Mass center Coordinates

X	Y	Z
55.5954	-83.2821	69.1889

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
O1	NZ	LYS- 41	3.45	0	Ionic (Protein Cationic)	false
O2'	NZ	LYS- 41	3	0	Ionic (Protein Cationic)	false
O2'	NZ	LYS- 41	3	145.35	H-Bond (Protein Donor)	false
O2'	NZ	LYS- 46	2.87	0	Ionic (Protein Cationic)	false
O1P	N	ALA- 102	2.95	167.54	H-Bond (Protein Donor)	false
O1	NZ	LYS- 124	3.15	175.11	H-Bond (Protein Donor)	false
O3P	NZ	LYS- 124	3.37	154.46	H-Bond (Protein Donor)	false
O1	NZ	LYS- 124	3.15	0	Ionic (Protein Cationic)	false
O3P	NZ	LYS- 124	3.37	0	Ionic (Protein Cationic)	false
O2P	CZ	ARG- 154	3.97	0	Ionic (Protein Cationic)	false
O3P	CZ	ARG- 154	3.43	0	Ionic (Protein Cationic)	false
O3P	NH1	ARG- 154	2.56	174.74	H-Bond (Protein Donor)	false