scPDB - 4bis entry

Protein Data Bank Entry:

PDB ID : 4bis

Resolution :2.490 Å

Experimental Method : X-ray

Deposition Date : 2013-04-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Lysine-specific demethylase 4A
ID:	KDM4A_HUMAN
AC:	O75164
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.14.11

Chains:

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

Ligand binding site composition:

B-Factor:	31.358
Number of residues:	22
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.530	894.375

% Hydrophobic	% Polar
31.70	68.30
According to VolSite

Ligand :

HET Code:	8HQ
Formula:	C10H6NO3
Molecular weight:	188.160 g/mol
DrugBank ID:	-
Buried Surface Area:	61.09 %
Polar Surface area:	73.25 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	1

Mass center Coordinates

X	Y	Z
26.0261	-21.3235	-5.76007

Binding mode :

What is Poseview ?

2D View
3D View

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
OAB	OH	TYR- 132	3.07	121.95	H-Bond (Protein Donor)	false
OAA	OH	TYR- 132	2.69	170.61	H-Bond (Protein Donor)	false
CAD	CD2	PHE- 185	3.39	0	Hydrophobic	false
CAH	CB	PHE- 185	3.86	0	Hydrophobic	false
CAM	CB	PHE- 185	4.05	0	Hydrophobic	false
OAB	NZ	LYS- 206	2.53	172.23	H-Bond (Protein Donor)	false
OAB	NZ	LYS- 206	2.53	0	Ionic (Protein Cationic)	false
CAF	CD	LYS- 241	4.25	0	Hydrophobic	false