scPDB - 2e82 entry

Protein Data Bank Entry:

PDB ID : 2e82

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2007-01-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	D-amino-acid oxidase
ID:	OXDA_HUMAN
AC:	P14920
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.4.3.3

Chains:

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

Ligand binding site composition:

B-Factor:	30.955
Number of residues:	29
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.392	475.875

% Hydrophobic	% Polar
65.96	34.04
According to VolSite

Ligand :

HET Code:	IM3
Formula:	C9H8NO4
Molecular weight:	194.164 g/mol
DrugBank ID:	DB07979
Buried Surface Area:	68.32 %
Polar Surface area:	104.44 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	1
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
68.609	-67.4225	-7.70979

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
CE2	CD1	LEU- 3215	4.09	0	Hydrophobic	false
CG	CD2	LEU- 3215	3.78	0	Hydrophobic	false
CE1	CD1	TYR- 3224	3.48	0	Hydrophobic	false
CB	CE1	TYR- 3228	4.12	0	Hydrophobic	false
CD1	CB	TYR- 3228	4.34	0	Hydrophobic	false
CD1	CD2	TYR- 3228	3.42	0	Hydrophobic	false
CB	CD1	ILE- 3230	4.13	0	Hydrophobic	false
OXT	CZ	ARG- 3283	3.62	0	Ionic (Protein Cationic)	false
O	CZ	ARG- 3283	3.97	0	Ionic (Protein Cationic)	false
OXT	NE	ARG- 3283	2.74	151.98	H-Bond (Protein Donor)	false
O	NH2	ARG- 3283	3.27	159.82	H-Bond (Protein Donor)	false