scPDB - 3znq entry

Protein Data Bank Entry:

PDB ID : 3znq

Resolution :2.750 Å

Experimental Method : X-ray

Deposition Date : 2013-02-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	5.220	5.640	5.430	0.550	6.720	5

List of CHEMBLId :

CHEMBL2375519

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
A	100 %

Ligand binding site composition:

B-Factor:	49.547
Number of residues:	30
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.378	486.000

% Hydrophobic	% Polar
54.86	45.14
According to VolSite

Ligand :

HET Code:	SS8
Formula:	C15H10NO3
Molecular weight:	252.245 g/mol
DrugBank ID:	-
Buried Surface Area:	77.32 %
Polar Surface area:	69.06 Å2

Number of
H-Bond Acceptors:	2
H-Bond Donors:	1
Rings:	3
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
-9.63574	-0.973263	16.3037

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
C19	CG	GLN- 53	4.48	0	Hydrophobic	false
C12	CB	GLN- 53	4.26	0	Hydrophobic	false
C18	CD1	LEU- 56	3.61	0	Hydrophobic	false
C17	CD1	LEU- 215	4.09	0	Hydrophobic	false
C18	CD1	ILE- 223	4.1	0	Hydrophobic	false
C13	CE1	TYR- 224	4.43	0	Hydrophobic	false
O2	CZ	ARG- 283	3.15	0	Ionic (Protein Cationic)	false
O3	CZ	ARG- 283	3.09	0	Ionic (Protein Cationic)	false
O3	NE	ARG- 283	2.96	127.59	H-Bond (Protein Donor)	false
C12	CB	TYR- 314	4.37	0	Hydrophobic	false