scPDB - 4fr8 entry

Protein Data Bank Entry:

PDB ID : 4fr8

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2012-06-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Aldehyde dehydrogenase, mitochondrial
ID:	ALDH2_HUMAN
AC:	P05091
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.2.1.3

Chains:

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

Ligand binding site composition:

B-Factor:	19.985
Number of residues:	31
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.330	340.875

% Hydrophobic	% Polar
75.25	24.75
According to VolSite

Ligand :

HET Code:	TNG
Formula:	C3H5N3O9
Molecular weight:	227.087 g/mol
DrugBank ID:	DB00727
Buried Surface Area:	76.03 %
Polar Surface area:	165.14 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	0
Rings:	0
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	3
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
1.42233	49.9923	49.4008

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
C1	CD2	PHE- 170	3.75	0	Hydrophobic	false
C2	CE2	PHE- 170	4.15	0	Hydrophobic	false
C1	CE	MET- 174	3.55	0	Hydrophobic	false
C1	CH2	TRP- 177	3.6	0	Hydrophobic	false
O2	NE2	GLN- 268	2.94	164.2	H-Bond (Protein Donor)	false
O9	OG	SER- 301	2.52	135.18	H-Bond (Protein Donor)	false
N3	OG	SER- 301	3.1	162.02	H-Bond (Protein Donor)	false
O7	OG	SER- 301	2.93	152.18	H-Bond (Protein Donor)	false
O1	N	CYS- 302	3.13	154.68	H-Bond (Protein Donor)	false
C3	CE1	PHE- 459	3.26	0	Hydrophobic	false
C2	CZ	PHE- 459	3.64	0	Hydrophobic	false
O9	O	HOH- 1000	3.05	124.9	H-Bond (Protein Donor)	false