scPDB - 4do0 entry

Protein Data Bank Entry:

PDB ID : 4do0

Resolution :2.550 Å

Experimental Method : X-ray

Deposition Date : 2012-02-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Histone lysine demethylase PHF8
ID:	PHF8_HUMAN
AC:	Q9UPP1
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.14.11.27

Chains:

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

Ligand binding site composition:

B-Factor:	42.195
Number of residues:	27
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
1.033	1444.500

% Hydrophobic	% Polar
43.22	56.78
According to VolSite

Ligand :

HET Code:	DZA
Formula:	C6H11N2O3
Molecular weight:	159.163 g/mol
DrugBank ID:	-
Buried Surface Area:	66.37 %
Polar Surface area:	72.47 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	0
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
-15.7213	-20.0275	25.1896

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
C08	CD1	ILE- 191	3.63	0	Hydrophobic	false
C06	CD1	ILE- 191	4.47	0	Hydrophobic	false
C07	CD2	LEU- 236	4.33	0	Hydrophobic	false
O11	OG1	THR- 244	2.59	149.83	H-Bond (Protein Donor)	false
C08	CB	THR- 244	3.8	0	Hydrophobic	false
C05	CB	ASP- 249	4.32	0	Hydrophobic	false
C05	CE2	PHE- 250	4	0	Hydrophobic	false
C07	CZ	TYR- 257	3.85	0	Hydrophobic	false
O10	NZ	LYS- 264	2.98	143.32	H-Bond (Protein Donor)	false
O10	NZ	LYS- 264	2.98	0	Ionic (Protein Cationic)	false
O11	NZ	LYS- 264	3.53	0	Ionic (Protein Cationic)	false
C07	CG2	VAL- 321	3.98	0	Hydrophobic	false
O01	ZN	ZN- 502	2.23	0	Metal Acceptor	false